Proposed Changes to the Enzyme List

References:

1.	Bate, N. and Cundliffe, E. The mycinose-biosynthetic genes of Streptomyces fradiae, producer of tylosin. J Ind Microbiol Biotechnol 23 (1999) 118–122. [PMID: 10510490]
2.	Anzai, Y., Saito, N., Tanaka, M., Kinoshita, K., Koyama, Y. and Kato, F. Organization of the biosynthetic gene cluster for the polyketide macrolide mycinamicin in Micromonospora griseorubida. FEMS Microbiol. Lett. 218 (2003) 135–141. [DOI] [PMID: 12583909]
3.	Thuy, T.T., Liou, K., Oh, T.J., Kim, D.H., Nam, D.H., Yoo, J.C. and Sohng, J.K. Biosynthesis of dTDP-6-deoxy-β-D-allose, biochemical characterization of dTDP-4-keto-6-deoxyglucose reductase (GerKI) from Streptomyces sp. KCTC 0041BP. Glycobiology 17 (2007) 119–126. [DOI] [PMID: 17053005]
4.	Kubiak, R.L., Phillips, R.K., Zmudka, M.W., Ahn, M.R., Maka, E.M., Pyeatt, G.L., Roggensack, S.J. and Holden, H.M. Structural and functional studies on a 3′-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 51 (2012) 9375–9383. [DOI] [PMID: 23116432]

[EC 1.1.1.364 created 2013]

1.1.1.365

Accepted name:

D-galacturonate reductase

Reaction:

L-galactonate + NADP⁺ = D-galacturonate + NADPH + H⁺

Other name(s):

GalUR; gar1 (gene name)

Systematic name:

L-galactonate:NADP⁺ oxidoreductase

Comments:

The enzyme from plants is involved in ascorbic acid (vitamin C) biosynthesis [1,2]. The enzyme from the fungus Trichoderma reesei (Hypocrea jecorina) is involved in a eukaryotic degradation pathway of D-galacturonate. It is also active with D-glucuronate and glyceraldehyde [3]. Neither enzyme shows any activity with NADH.

Links to other databases:

References:

1.	Isherwood, F.A. and Mapson, L.W. Biological synthesis of ascorbic acid: the conversion of derivatives of D-galacturonic acid into L-ascorbic acid by plant extracts. Biochem. J. 64 (1956) 13–22. [PMID: 13363799]
2.	Agius, F., Gonzalez-Lamothe, R., Caballero, J.L., Munoz-Blanco, J., Botella, M.A. and Valpuesta, V. Engineering increased vitamin C levels in plants by overexpression of a D-galacturonic acid reductase. Nat. Biotechnol. 21 (2003) 177–181. [DOI] [PMID: 12524550]
3.	Kuorelahti, S., Kalkkinen, N., Penttila, M., Londesborough, J. and Richard, P. Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase. Biochemistry 44 (2005) 11234–11240. [DOI] [PMID: 16101307]
4.	Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449–1457. [DOI] [PMID: 18768163]

[EC 1.1.1.365 created 2013]

1.1.1.366

Accepted name:

L-idonate 5-dehydrogenase (NAD⁺)

Reaction:

L-idonate + NAD⁺ = 5-dehydro-D-gluconate + NADH + H⁺

Systematic name:

L-idonate:NAD⁺ oxidoreductase

Comments:

Involved in the catabolism of ascorbate (vitamin C) to tartrate. No activity is observed with NADP⁺ (cf. EC 1.1.1.264, L-idonate 5-dehydrogenase).

Links to other databases:

References:

1.	DeBolt, S., Cook, D.R. and Ford, C.M. L-Tartaric acid synthesis from vitamin C in higher plants. Proc. Natl. Acad. Sci. USA 103 (2006) 5608–5613. [DOI] [PMID: 16567629]

[EC 1.1.1.366 created 2013]

1.1.1.367

Accepted name:

UDP-2-acetamido-2,6-β-L-arabino-hexul-4-ose reductase

Reaction:

UDP-2-acetamido-2,6-dideoxy-β-L-talose + NAD(P)⁺ = UDP-2-acetamido-2,6-β-L-arabino-hexul-4-ose + NAD(P)H + H⁺

For diagram of UDP-N-acetyl-β-L-fucosamine biosynthesis, click here

Glossary:

UDP-2-acetamido-2,6-dideoxy-β-L-talose = UDP-N-acetyl-β-L-pneumosamine

Other name(s):

WbjC; Cap5F

Systematic name:

UDP-2-acetamido-2,6-dideoxy-L-talose:NADP⁺ oxidoreductase

Comments:

Part of the biosynthesis of UDP-N-acetyl-L-fucosamine. Isolated from the bacteria Pseudomonas aeruginosa and Staphylococcus aureus.

Links to other databases:

References:

1.	Kneidinger, B., O'Riordan, K., Li, J., Brisson, J.R., Lee, J.C. and Lam, J.S. Three highly conserved proteins catalyze the conversion of UDP-N-acetyl-D-glucosamine to precursors for the biosynthesis of O antigen in Pseudomonas aeruginosa O11 and capsule in Staphylococcus aureus type 5. Implications for the UDP-N-acetyl-L-fucosamine biosynthetic pathway. J. Biol. Chem. 278 (2003) 3615–3627. [DOI] [PMID: 12464616]
2.	Mulrooney, E.F., Poon, K.K., McNally, D.J., Brisson, J.R. and Lam, J.S. Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11. J. Biol. Chem. 280 (2005) 19535–19542. [DOI] [PMID: 15778500]
3.	Miyafusa, T., Tanaka, Y., Kuroda, M., Ohta, T. and Tsumoto, K. Expression, purification, crystallization and preliminary diffraction analysis of CapF, a capsular polysaccharide-synthesis enzyme from Staphylococcus aureus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 512–515. [DOI] [PMID: 18540063]

[EC 1.1.1.367 created 2014]

1.1.1.368

Accepted name:

6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase

Reaction:

6-hydroxycyclohex-1-ene-1-carbonyl-CoA + NAD⁺ = 6-oxocyclohex-1-ene-1-carbonyl-CoA + NADH + H⁺

For diagram of benzoyl-CoA catabolism, click here

Systematic name:

6-hydroxycyclohex-1-ene-1-carbonyl-CoA:NAD⁺ 6-oxidoreductase

Comments:

The enzyme participates in the central benzoyl-CoA degradation pathway of some anaerobic bacteria such as Thauera aromatica.

Links to other databases:

References:

Laempe, D., Jahn, M. and Fuchs, G. 6-Hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, enzymes of the benzoyl-CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 263 (1999) 420–429. [DOI] [PMID: 10406950]

[EC 1.1.1.368 created 2014]

1.1.1.369

Accepted name:

D-chiro-inositol 1-dehydrogenase

Reaction:

1D-chiro-inositol + NAD⁺ = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH + H⁺

For diagram of inositol catabolism, click here

Glossary:

1D-chiro-inositol = 1,2,4/3,5,6-cyclohexane-1,2,3,4,5,6-hexol

Other name(s):

DCI 1-dehydrogenase; IolG

Systematic name:

1D-chiro-inositol:NAD⁺ 1-oxidoreductase

Comments:

The enzyme, found in the bacterium Bacillus subtilis, also catalyses the reaction of EC 1.1.1.18, inositol 2-dehydrogenase, and can also use D-glucose and D-xylose. It shows trace activity with D-ribose and D-fructose [1]. It is part of a myo-inositol/D-chiro-inositol degradation pathway leading to acetyl-CoA.

Links to other databases:

References:

1.	Ramaley, R., Fujita, Y. and Freese, E. Purification and properties of Bacillus subtilis inositol dehydrogenase. J. Biol. Chem. 254 (1979) 7684–7690. [PMID: 112095]
2.	Yoshida, K., Yamaguchi, M., Morinaga, T., Ikeuchi, M., Kinehara, M. and Ashida, H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl. Environ. Microbiol. 72 (2006) 1310–1315. [DOI] [PMID: 16461681]

[EC 1.1.1.369 created 2014]

1.1.1.370

Accepted name:

scyllo-inositol 2-dehydrogenase (NAD⁺)

Reaction:

scyllo-inositol + NAD⁺ = 2,4,6/3,5-pentahydroxycyclohexanone + NADH + H⁺

For diagram of inositol catabolism, click here

Glossary:

2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s):

iolX (gene name)

Systematic name:

scyllo-inositol:NAD⁺ 2-oxidoreductase

Comments:

The enzyme, found in the bacterium Bacillus subtilis, has no activity with NADP⁺ [cf. EC 1.1.1.371, scyllo-inositol 2-dehydrogenase (NADP⁺)]. It is part of a scyllo-inositol degradation pathway leading to acetyl-CoA.

Links to other databases:

References:

1.	Morinaga, T., Ashida, H. and Yoshida, K. Identification of two scyllo-inositol dehydrogenases in Bacillus subtilis. Microbiology 156 (2010) 1538–1546. [DOI] [PMID: 20133360]

[EC 1.1.1.370 created 2014]

1.1.1.371

Accepted name:

scyllo-inositol 2-dehydrogenase (NADP⁺)

Reaction:

scyllo-inositol + NADP⁺ = 2,4,6/3,5-pentahydroxycyclohexanone + NADPH + H⁺

For diagram of inositol catabolism, click here

Glossary:

2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s):

iolW (gene name)

Systematic name:

scyllo-inositol:NADP⁺ 2-oxidoreductase

Comments:

The enzyme, found in the bacterium Bacillus subtilis, has no activity with NAD⁺ [cf. EC 1.1.1.370, scyllo-inositol 2-dehydrogenase (NAD⁺)].

Links to other databases:

References:

1.	Morinaga, T., Ashida, H. and Yoshida, K. Identification of two scyllo-inositol dehydrogenases in Bacillus subtilis. Microbiology 156 (2010) 1538–1546. [DOI] [PMID: 20133360]

[EC 1.1.1.371 created 2014]

1.1.5.10

Accepted name:

D-2-hydroxyacid dehydrogenase (quinone)

Reaction:

(R)-2-hydroxyacid + a quinone = 2-oxoacid + a quinol

Other name(s):

(R)-2-hydroxy acid dehydrogenase; (R)-2-hydroxy-acid:(acceptor) 2-oxidoreductase; D-lactate dehydrogenase (ambiguous)

Systematic name:

(R)-2-hydroxyacid:quinone oxidoreductase

Comments:

The enzyme from mammalian kidney contains one mole of FAD per mole of enzyme.(R)-lactate, (R)-malate and meso-tartrate are good substrates. Ubiquinone-1 and the dye 2,6-dichloroindophenol can act as acceptors; NAD⁺ and NADP⁺ are not acceptors.

Links to other databases:

References:

1.	Tubbs, P.K. and Greville, G.D. Dehydrogenation of D-lactate by a soluble enzyme from kidney mitochondria. Biochim. Biophys. Acta 34 (1959) 290–291. [DOI] [PMID: 13839714]
2.	Tubbs, P.K. and Greville, G.D. The oxidation of D-α-hydroxy acids in animal tissues. Biochem. J. 81 (1961) 104–114. [PMID: 13922962]
3.	Cammack, R. Assay, purification and properties of mammalian D-2-hydroxy acid dehydrogenase. Biochem. J. 115 (1969) 55–64. [PMID: 5359443]
4.	Cammack, R. D-2-hydroxy acid dehydrogenase from animal tissue. Methods Enzymol. 41 (1975) 323–329. [DOI] [PMID: 236454]

[EC 1.1.5.10 created 2014]

1.1.98.4

Accepted name:

F₄₂₀H₂:quinone oxidoreductase

Reaction:

a quinol + oxidized coenzyme F₄₂₀ = a quinone + reduced coenzyme F₄₂₀

Glossary:

oxidized coenzyme F₄₂₀ = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate

Other name(s):

FqoF protein

Systematic name:

quinol:coenzyme-F₄₂₀ oxidoreductase

Comments:

An enzyme complex that contains FAD and iron-sulfur clusters. The enzyme has been described in the archaea Methanosarcina mazei and Archaeoglobus fulgidus.

Links to other databases:

References:

1.	Bruggemann, H., Falinski, F. and Deppenmeier, U. Structure of the F₄₂₀H₂:quinone oxidoreductase of Archaeoglobus fulgidus identification and overproduction of the F₄₂₀H₂-oxidizing subunit. Eur. J. Biochem. 267 (2000) 5810–5814. [DOI] [PMID: 10971593]
2.	Kunow, J., Linder, D., Stetter, K.O. and Thauer, R.K. F₄₂₀H₂: quinone oxidoreductase from Archaeoglobus fulgidus. Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters. Eur. J. Biochem. 223 (1994) 503–511. [DOI] [PMID: 8055920]
3.	Abken, H.-J. and Deppenmeier, U. Purification and properties of an F₄₂₀H₂ dehydrogenase from Methanosarcina mazei Gö1. FEMS Microbiol. Lett. 154 (1997) 231–237.

[EC 1.1.98.4 created 2013]

1.1.98.5

Accepted name:

secondary-alcohol dehydrogenase (coenzyme-F₄₂₀)

Reaction:

R-CHOH-R′ + oxidized coenzyme F₄₂₀ = R-CO-R′ + reduced coenzyme F₄₂₀

Glossary:

oxidized coenzyme F₄₂₀ = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate

Other name(s):

F₄₂₀-dependent alcohol dehydrogenase; secondary alcohol:F420 oxidoreductase; F₄₂₀-dependent secondary alcohol dehydrogenase

Systematic name:

secondary-alcohol:coenzyme F₄₂₀ oxidoreductase

Comments:

The enzyme isolated from the methanogenic archaea Methanogenium liminatans catalyses the reversible oxidation of various secondary and cyclic alcohols to the corresponding ketones.

Links to other databases:

References:

1.	Bleicher, K. and Winter, J. Purification and properties of F₄₂₀- and NADP⁺-dependent alcohol dehydrogenases of Methanogenium liminatans and Methanobacterium palustre, specific for secondary alcohols. Eur. J. Biochem. 200 (1991) 43–51. [DOI] [PMID: 1879431]
2.	Aufhammer, S.W., Warkentin, E., Berk, H., Shima, S., Thauer, R.K. and Ermler, U. Coenzyme binding in F₄₂₀-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family. Structure 12 (2004) 361–370. [DOI] [PMID: 15016352]

[EC 1.1.98.5 created 2013]

*EC

1.1.99.2

Accepted name:

L-2-hydroxyglutarate dehydrogenase

Reaction:

(S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor

Other name(s):

α-ketoglutarate reductase; α-hydroxyglutarate dehydrogenase; L-α-hydroxyglutarate dehydrogenase; hydroxyglutaric dehydrogenase; α-hydroxyglutarate oxidoreductase; L-α-hydroxyglutarate:NAD⁺ 2-oxidoreductase; α-hydroxyglutarate dehydrogenase (NAD⁺ specific); (S)-2-hydroxyglutarate:(acceptor) 2-oxidoreductase

Systematic name:

(S)-2-hydroxyglutarate:acceptor 2-oxidoreductase

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9028-80-2

References:

1.	Weil-Malherbe, H. The oxidation of l(–)α-hydroxyglutaric acid in animal tissues. Biochem. J. 31 (1937) 2080–2094. [PMID: 16746551]

[EC 1.1.99.2 created 1961, modified 2013]

*EC

1.1.99.6

Accepted name:

D-lactate dehydrogenase (acceptor)

Reaction:

(R)-lactate + acceptor = pyruvate + reduced acceptor

Other name(s):

D-2-hydroxy acid dehydrogenase; D-2-hydroxy-acid dehydrogenase; (R)-2-hydroxy-acid:acceptor 2-oxidoreductase

Systematic name:

(R)-lactate:acceptor 2-oxidoreductase

Comments:

The zinc flavoprotein (FAD) from the archaeon Archaeoglobus fulgidus cannot utilize NAD⁺, cytochrome c, methylene blue or dimethylnaphthoquinone as acceptors. In vitro it is active with artificial electron acceptors such as 2,6-dichlorophenolindophenol, but the physiological acceptor is not yet known.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 9028-83-5

References:

1.	Reed, D.W. and Hartzell, P.L. The Archaeoglobus fulgidus D-lactate dehydrogenase is a Zn²⁺ flavoprotein. J. Bacteriol. 181 (1999) 7580–7587. [PMID: 10601217]

[EC 1.1.99.6 created 1965, modified 2013]

1.1.99.39

Accepted name:

D-2-hydroxyglutarate dehydrogenase

Reaction:

(R)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor

Other name(s):

D2HGDH (gene name)

Systematic name:

(R)-2-hydroxyglutarate:acceptor 2-oxidoreductase

Comments:

Contains FAD. The enzyme has no activity with NAD⁺ or NADP⁺, and was assayed in vitro using artificial electron acceptors. It has lower activity with (R)-lactate, (R)-2-hydroxybutyrate and meso-tartrate, and no activity with the (S) isomers. The mammalian enzyme is stimulated by Zn²⁺, Co²⁺ and Mn²⁺.

Links to other databases:

References:

1.	Engqvist, M., Drincovich, M.F., Flugge, U.I. and Maurino, V.G. Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and β-oxidation pathways. J. Biol. Chem. 284 (2009) 25026–25037. [DOI] [PMID: 19586914]
2.	Achouri, Y., Noel, G., Vertommen, D., Rider, M.H., Veiga-Da-Cunha, M. and Van Schaftingen, E. Identification of a dehydrogenase acting on D-2-hydroxyglutarate. Biochem. J. 381 (2004) 35–42. [DOI] [PMID: 15070399]

[EC 1.1.99.39 created 2013]

1.2.1.89

Accepted name:

D-glyceraldehyde dehydrogenase (NADP⁺)

Reaction:

D-glyceraldehyde + NADP⁺ + H₂O = D-glycerate + NADPH + H⁺

Other name(s):

glyceraldehyde dehydrogenase; GADH

Systematic name:

D-glyceraldehyde:NADP⁺ oxidoreductase

Comments:

The enzyme from the archaea Thermoplasma acidophilum and Picrophilus torridus is involved in the non-phosphorylative Entner-Doudoroff pathway. cf. EC 1.2.99.8, glyceraldehyde dehydrogenase (FAD-containing).

Links to other databases:

References:

1.	Jung, J.H. and Lee, S.B. Identification and characterization of Thermoplasma acidophilum glyceraldehyde dehydrogenase: a new class of NADP⁺-specific aldehyde dehydrogenase. Biochem. J. 397 (2006) 131–138. [DOI] [PMID: 16566751]
2.	Reher, M. and Schonheit, P. Glyceraldehyde dehydrogenases from the thermoacidophilic euryarchaeota Picrophilus torridus and Thermoplasma acidophilum, key enzymes of the non-phosphorylative Entner-Doudoroff pathway, constitute a novel enzyme family within the aldehyde dehydrogenase superfamily. FEBS Lett. 580 (2006) 1198–1204. [DOI] [PMID: 16458304]

[EC 1.2.1.89 created 2014]

*EC

1.3.1.74

Accepted name:

2-alkenal reductase [NAD(P)⁺]

Reaction:

a n-alkanal + NAD(P)⁺ = an alk-2-enal + NAD(P)H + H⁺

Other name(s):

NAD(P)H-dependent alkenal/one oxidoreductase; NADPH:2-alkenal α,β-hydrogenase; 2-alkenal reductase

Systematic name:

n-alkanal:NAD(P)⁺ 2-oxidoreductase

Comments:

Highly specific for 4-hydroxynon-2-enal and non-2-enal. Alk-2-enals of shorter chain have lower affinities. Exhibits high activities also for alk-2-enones such as but-3-en-2-one and pent-3-en-2-one. Inactive with cyclohex-2-en-1-one and 12-oxophytodienoic acid. Involved in the detoxication of α,β-unsaturated aldehydes and ketones [cf. EC 1.3.1.102, 2-alkenal reductase (NADP⁺)].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 52227-95-9

References:

1.	Mano, J., Torii, Y., Hayashi, S., Takimoto, K., Matsui, K., Nakamura, K., Inzé, D., Babiychuk, E., Kushnir, S. and Asada, K. The NADPH:quinone oxidoreductase P1-ζ-crystallin in Arabidopsis catalyzes the α,β-hydrogenation of 2-alkenals: detoxication of the lipid peroxide-derived reactive aldehydes. Plant Cell Physiol. 43 (2002) 1445–1455. [PMID: 12514241]
2.	Dick, R.A., Kwak, M.K., Sutter, T.R. and Kensler, T.W. Antioxidative function and substrate specificity of NAD(P)H-dependent alkenal/one oxidoreductase. A new role for leukotriene B₄ 12-hydroxydehydrogenase/15-oxoprostaglandin 13-reductase. J. Biol. Chem. 276 (2001) 40803–40810. [DOI] [PMID: 11524419]

[EC 1.3.1.74 created 2003, modified 2014]

1.3.1.105

Accepted name:

2-methylene-furan-3-one reductase

Reaction:

4-hydroxy-2,5-dimethylfuran-3(2H)-one + NADP⁺ = 4-hydroxy-5-methyl-2-methylenefuran-3(2H)-one + NADPH + H⁺

Glossary:

furaneol = 4-hydroxy-2,5-dimethylfuran-3(2H)-one
homofuraneol = 2-ethyl-4-hydroxy-5-methylfuran-3(2H)-one

Other name(s):

FaEO; SIEO; enone oxidoreductase; 4-hydroxy-2,5-dimethylfuran-3(2H)-one:NAD(P)⁺ oxidoreductase

Systematic name:

4-hydroxy-2,5-dimethylfuran-3(2H)-one:NADP⁺ oxidoreductase

Comments:

The enzyme was dicovered in strawberry (Fragaria x ananassa), where it produces furaneol, one of the major aroma compounds in the fruits. It has also been detected in tomato (Solanum lycopersicum) and pineapple (Ananas comosus). The enzyme can also act on derivatives substituted at the methylene functional group. The enzyme from the yeast Saccharomyces cerevisiae acts on (2E)-2-ethylidene-4-hydroxy-5-methylfuran-3(2H)-one and produces homofuraneol, an important aroma compound in soy sauce and miso. NADPH is the preferred cofactor.

Links to other databases:

References:

1.	Raab, T., Lopez-Raez, J.A., Klein, D., Caballero, J.L., Moyano, E., Schwab, W. and Munoz-Blanco, J. FaQR, required for the biosynthesis of the strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone, encodes an enone oxidoreductase. Plant Cell 18 (2006) 1023–1037. [DOI] [PMID: 16517758]
2.	Klein, D., Fink, B., Arold, B., Eisenreich, W. and Schwab, W. Functional characterization of enone oxidoreductases from strawberry and tomato fruit. J. Agric. Food Chem. 55 (2007) 6705–6711. [DOI] [PMID: 17636940]
3.	Schiefner, A., Sinz, Q., Neumaier, I., Schwab, W. and Skerra, A. Structural basis for the enzymatic formation of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone. J. Biol. Chem. 288 (2013) 16815–16826. [DOI] [PMID: 23589283]
4.	Uehara, K., Watanabe, J., Mogi, Y. and Tsukioka, Y. Identification and characterization of an enzyme involved in the biosynthesis of the 4-hydroxy-2(or 5)-ethyl-5(or 2)-methyl-3(2H)-furanone in yeast. J. Biosci. Bioeng. 123 (2017) 333–341. [DOI] [PMID: 27865643]

[EC 1.3.1.105 created 2013]

1.3.1.106

Accepted name:

cobalt-precorrin-6A reductase

Reaction:

cobalt-precorrin-6B + NAD⁺ = cobalt-precorrin-6A + NADH + H⁺

For diagram of anaerobic corrin biosynthesis (part 2), click here

Other name(s):

cbiJ (gene name)

Systematic name:

cobalt-precorrin-6B:NAD⁺ oxidoreductase

Comments:

The enzyme, which participates in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis, catalyses the reduction of the double bond between C-18 and C-19 of cobalt-precorrin-6A. The enzyme from the bacterium Bacillus megaterium has no activity with NADPH. See EC 1.3.1.54, precorrin-6A reductase, for the corresponding enzyme that participates in the aerobic cobalamin biosynthesis pathway.

Links to other databases:

References:

1.	Kim, W., Major, T.A. and Whitman, W.B. Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis. Archaea 1 (2005) 375–384. [PMID: 16243778]
2.	Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B₁₂). Proc. Natl. Acad. Sci. USA 110 (2013) 14906–14911. [DOI] [PMID: 23922391]

[EC 1.3.1.106 created 2014]

*EC

1.3.5.1

Accepted name:

succinate dehydrogenase

Reaction:

succinate + a quinone = fumarate + a quinol

For diagram of the citric acid cycle, click here

Other name(s):

succinate dehydrogenase (quinone); succinate dehydrogenase (ubiquinone); succinic dehydrogenase; complex II (ambiguous); succinate dehydrogenase complex; SDH (ambiguous); succinate:ubiquinone oxidoreductase; fumarate reductase (quinol); FRD; menaquinol-fumarate oxidoreductase; succinate dehydrogenase (menaquinone); succinate:menaquinone oxidoreductase; fumarate reductase (menaquinone)

Systematic name:

succinate:quinone oxidoreductase

Comments:

A complex generally comprising an FAD-containing component that also binds the carboxylate substrate (A subunit), a component that contains three different iron-sulfur centers [2Fe-2S], [4Fe-4S], and [3Fe-4S] (B subunit), and a hydrophobic membrane-anchor component (C, or C and D subunits) that is also the site of the interaction with quinones. The enzyme is found in the inner mitochondrial membrane in eukaryotes and the plasma membrane of bacteria and archaea, with the hydrophilic domain extending into the mitochondrial matrix and the cytoplasm, respectively. Under aerobic conditions the enzyme catalyses succinate oxidation, a key step in the citric acid (TCA) cycle, transferring the electrons to quinones in the membrane, thus linking the TCA cycle with the aerobic respiratory chain (where it is known as complex II). Under anaerobic conditions the enzyme functions as a fumarate reductase, transferring electrons from the quinol pool to fumarate, and participating in anaerobic respiration with fumarate as the terminal electron acceptor. The enzyme interacts with the quinone produced by the organism, such as ubiquinone, menaquinone, caldariellaquinone, thermoplasmaquinone, rhodoquinone etc. Some of the enzymes contain two heme subunits in their membrane anchor subunit. These enzymes catalyse an electrogenic reaction and are thus classified as EC 7.1.1.12, succinate dehydrogenase (electrogenic, proton-motive force generating).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9028-11-9

References:

1.	Kita, K., Vibat, C.R., Meinhardt, S., Guest, J.R. and Gennis, R.B. One-step purification from Escherichia coli of complex II (succinate: ubiquinone oxidoreductase) associated with succinate-reducible cytochrome b₅₅₆. J. Biol. Chem. 264 (1989) 2672–2677. [PMID: 2644269]
2.	Van Hellemond, J.J. and Tielens, A.G. Expression and functional properties of fumarate reductase. Biochem. J. 304 (1994) 321–331. [PMID: 7998964]
3.	Iverson, T.M., Luna-Chavez, C., Cecchini, G. and Rees, D.C. Structure of the Escherichia coli fumarate reductase respiratory complex. Science 284 (1999) 1961–1966. [DOI] [PMID: 10373108]
4.	Cecchini, G., Schroder, I., Gunsalus, R.P. and Maklashina, E. Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim. Biophys. Acta 1553 (2002) 140–157. [DOI] [PMID: 11803023]
5.	Figueroa, P., Leon, G., Elorza, A., Holuigue, L., Araya, A. and Jordana, X. The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana. Plant Mol. Biol. 50 (2002) 725–734. [PMID: 12374303]
6.	Cecchini, G. Function and structure of complex II of the respiratory chain. Annu. Rev. Biochem. 72 (2003) 77–109. [DOI] [PMID: 14527321]
7.	Oyedotun, K.S. and Lemire, B.D. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. Homology modeling, cofactor docking, and molecular dynamics simulation studies. J. Biol. Chem. 279 (2004) 9424–9431. [DOI] [PMID: 14672929]
8.	Kurokawa, T. and Sakamoto, J. Purification and characterization of succinate:menaquinone oxidoreductase from Corynebacterium glutamicum. Arch. Microbiol. 183 (2005) 317–324. [DOI] [PMID: 15883782]
9.	Iwata, F., Shinjyo, N., Amino, H., Sakamoto, K., Islam, M.K., Tsuji, N. and Kita, K. Change of subunit composition of mitochondrial complex II (succinate-ubiquinone reductase/quinol-fumarate reductase) in Ascaris suum during the migration in the experimental host. Parasitol Int 57 (2008) 54–61. [DOI] [PMID: 17933581]

[EC 1.3.5.1 created 1983 (EC 1.3.99.1 created 1961, incorporated 2014, EC 1.3.5.4 created 2010, incorporated 2022), modified 2022]

*EC

1.3.5.4

Transferred entry:

fumarate reductase (quinol), now included in EC 1.3.5.1, succinate dehydrogenase.

[EC 1.3.5.4 created 2010, modified 2013, deleted 2022]

1.3.8.10

Accepted name:

cyclohex-1-ene-1-carbonyl-CoA dehydrogenase

Reaction:

cyclohex-1-ene-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1,5-diene-1-carbonyl-CoA + reduced electron-transfer flavoprotein

Systematic name:

cyclohex-1-ene-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase

Comments:

Contains FAD. The enzyme, characterized from the strict anaerobic bacterium Syntrophus aciditrophicus, is involved in production of cyclohexane-1-carboxylate, a byproduct produced by that organism during fermentation of benzoate and crotonate to acetate.

Links to other databases:

References:

Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193–3200. [DOI] [PMID: 23667239]

[EC 1.3.8.10 created 2013]

1.3.8.11

Accepted name:

cyclohexane-1-carbonyl-CoA dehydrogenase (electron-transfer flavoprotein)

Reaction:

cyclohexane-1-carbonyl-CoA + electron-transfer flavoprotein = cyclohex-1-ene-1-carbonyl-CoA + reduced electron-transfer flavoprotein

Other name(s):

aliB (gene name); cyclohexane-1-carbonyl-CoA dehydrogenase (ambiguous)

Systematic name:

cyclohexane-1-carbonyl-CoA:electron transfer flavoprotein oxidoreductase

Comments:

Links to other databases:

References:

1.	Pelletier, D.A. and Harwood, C.S. 2-Hydroxycyclohexanecarboxyl coenzyme A dehydrogenase, an enzyme characteristic of the anaerobic benzoate degradation pathway used by Rhodopseudomonas palustris. J. Bacteriol. 182 (2000) 2753–2760. [PMID: 10781543]
2.	Kung, J.W., Seifert, J., von Bergen, M. and Boll, M. Cyclohexanecarboxyl-coenzyme A (CoA) and cyclohex-1-ene-1-carboxyl-CoA dehydrogenases, two enzymes involved in the fermentation of benzoate and crotonate in Syntrophus aciditrophicus. J. Bacteriol. 195 (2013) 3193–3200. [DOI] [PMID: 23667239]

[EC 1.3.8.11 created 2013, modified 2020]

1.3.98.2

Transferred entry:

fumarate reductase (CoM/CoB). Now EC 1.3.4.1, fumarate reductase (CoM/CoB)

[EC 1.3.98.2 created 2014, deleted 2014]

1.3.99.1

Deleted entry:

succinate dehydrogenase. The activity is included in EC 1.3.5.1, succinate dehydrogenase (quinone).

[EC 1.3.99.1 created 1961, deleted 2014]

1.3.99.35

Transferred entry:

chlorophyllide a reductase. Now EC 1.3.7.15, chlorophyllide a reductase

[EC 1.3.99.35 created 2014, deleted 2016]

1.5.3.22

Accepted name:

coenzyme F₄₂₀H₂ oxidase

Reaction:

2 reduced coenzyme F₄₂₀ + O₂ = 2 oxidized coenzyme F₄₂₀ + 2 H₂O

For diagram of coenzyme F₄₂₀ biosynthesis, click here

Glossary:

oxidized coenzyme F₄₂₀ = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate

Other name(s):

FprA

Systematic name:

reduced coenzyme F₄₂₀:oxygen oxidoreductase

Comments:

The enzyme contains FMN and a binuclear iron center. The enzyme from the archaeon Methanothermobacter marburgensis is Si-face specific with respect to C-5 of coenzyme F₄₂₀ [2].

Links to other databases:

References:

1.	Seedorf, H., Dreisbach, A., Hedderich, R., Shima, S. and Thauer, R.K. F₄₂₀H₂ oxidase (FprA) from Methanobrevibacter arboriphilus, a coenzyme F₄₂₀-dependent enzyme involved in O₂ detoxification. Arch. Microbiol. 182 (2004) 126–137. [DOI] [PMID: 15340796]
2.	Seedorf, H., Kahnt, J., Pierik, A.J. and Thauer, R.K. Si-face stereospecificity at C5 of coenzyme F₄₂₀ for F₄₂₀H₂ oxidase from methanogenic Archaea as determined by mass spectrometry. FEBS J. 272 (2005) 5337–5342. [DOI] [PMID: 16218963]
3.	Seedorf, H., Hagemeier, C.H., Shima, S., Thauer, R.K., Warkentin, E. and Ermler, U. Structure of coenzyme F₄₂₀H₂ oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O₂ to H₂O. FEBS J. 274 (2007) 1588–1599. [DOI] [PMID: 17480207]

[EC 1.5.3.22 created 2013]

1.5.7.2

Accepted name:

coenzyme F₄₂₀ oxidoreductase (ferredoxin)

Reaction:

reduced coenzyme F₄₂₀ + 2 oxidized ferredoxin = oxidized coenzyme F₄₂₀ + 2 reduced ferredoxin + 2 H⁺

Glossary:

oxidized coenzyme F₄₂₀ = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate

Other name(s):

Fd:F420 oxidoreductase; FpoF protein; ferredoxin:F420 oxidoreductase

Systematic name:

coenzyme F₄₂₀:ferredoxin oxidoreductase

Comments:

The enzyme from the archaeon Methanosarcina mazei contains iron-sulfur centres and FAD.

Links to other databases:

References:

1.	Welte, C. and Deppenmeier, U. Re-evaluation of the function of the F₄₂₀ dehydrogenase in electron transport of Methanosarcina mazei. FEBS J. 278 (2011) 1277–1287. [DOI] [PMID: 21306561]

[EC 1.5.7.2 created 2013]

1.5 Acting on the CH-NH group of donors

1.5.98 With other, known, physiological acceptors

1.5.98.1

Accepted name:

methylenetetrahydromethanopterin dehydrogenase

Reaction:

5,10-methylenetetrahydromethanopterin + oxidized coenzyme F₄₂₀ = 5,10-methenyltetrahydromethanopterin + reduced coenzyme F₄₂₀

For diagram of methane biosynthesis, click here

Other name(s):

N⁵,N¹⁰-methylenetetrahydromethanopterin dehydrogenase; 5,10-methylenetetrahydromethanopterin dehydrogenase

Systematic name:

5,10-methylenetetrahydromethanopterin:coenzyme-F₄₂₀ oxidoreductase

Comments:

Coenzyme F₄₂₀ is a 7,8-didemethyl-8-hydroxy-5-deazariboflavin derivative; methanopterin is a pterin analogue. The enzyme is involved in the formation of methane from CO₂ in the methanogen Methanothermobacter thermautotrophicus.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 100357-01-5

References:

1.	Hartzell, P.L., Zvilius, G., Escalante-Semerena, J.C. and Donnelly, M.I. Coenzyme F₄₂₀ dependence of the methylenetetrahydromethanopterin dehydrogenase of Methanobacterium thermoautotrophicum. Biochem. Biophys. Res. Commun. 133 (1985) 884–890. [DOI] [PMID: 4084309]
2.	te Brömmelstroet, B.W., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F₄₂₀-dependent enzymes, from Methanosarcina barkeri. Biochim. Biophys. Acta 1079 (1991) 293–302. [DOI] [PMID: 1911853]

[EC 1.5.98.1 created 1989 as EC 1.5.99.9, modified 2004, transferred 2014 to EC 1.5.98.1]

1.5.98.2

Accepted name:

5,10-methylenetetrahydromethanopterin reductase

Reaction:

5-methyltetrahydromethanopterin + oxidized coenzyme F₄₂₀ = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F₄₂₀

For diagram of methane biosynthesis, click here

Other name(s):

5,10-methylenetetrahydromethanopterin cyclohydrolase; N⁵,N¹⁰-methylenetetrahydromethanopterin reductase; methylene-H₄MPT reductase; coenzyme F₄₂₀-dependent N⁵,N¹⁰-methenyltetrahydromethanopterin reductase; N⁵,N¹⁰-methylenetetrahydromethanopterin:coenzyme-F₄₂₀ oxidoreductase

Systematic name:

5-methyltetrahydromethanopterin:coenzyme-F₄₂₀ oxidoreductase

Comments:

Catalyses an intermediate step in methanogenesis from CO₂ and H₂ in methanogenic archaea.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB

References:

1.	Ma, K. and Thauer, R.K. Purification and properties of N⁵,N¹⁰-methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum (strain Marburg). Eur. J. Biochem. 191 (1990) 187–193. [DOI] [PMID: 2379499]
2.	te Brömmelstroet, B.W., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F₄₂₀-dependent enzymes, from Methanosarcina barkeri. Biochim. Biophys. Acta 1079 (1991) 293–302. [DOI] [PMID: 1911853]
3.	Ma, K. and Thauer, R.K. Single step purification of methylenetetrahydromethanopterin reductase from Methanobacterium thermoautotrophicum by specific binding to blue sepharose CL-6B. FEBS Lett. 268 (1990) 59–62. [DOI] [PMID: 1696553]
4.	te Brömmelstroet, B.W., Hensgens, C.M., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methylenetetrahydromethanopterin reductase, a coenzyme F₄₂₀-dependent enzyme, from Methanobacterium thermoautotrophicum strain ΔH. J. Biol. Chem.* 265 (1990) 1852–1857. [PMID: 2298726]
5.	te Brömmelstroet, B.W., Hensgens, C.M., Geerts, W.J., Keltjens, J.T., van der Drift, C. and Vogels, G.D. Purification and properties of 5,10-methenyltetrahydromethanopterin cyclohydrolase from Methanosarcina barkeri. J. Bacteriol. 172 (1990) 564–571. [DOI] [PMID: 2298699]

[EC 1.5.98.2 created 2000 as EC 1.5.99.11, modified 2004, transferred to EC 1.5.98.2 2014]

1.5.99.9

Transferred entry:

methylenetetrahydromethanopterin dehydrogenase. As the acceptor is known the enzyme has been transferred to EC 1.5.98.1, methylenetetrahydromethanopterin dehydrogenase

[EC 1.5.99.9 created 1989, modified 2004, deleted 2014]

1.5.99.11

Transferred entry:

methylenetetrahydromethanopterin dehydrogenase. As the acceptor is known the enzyme has been transferred to EC 1.5.98.2, 5,10-methylenetetrahydromethanopterin reductase

[EC 1.5.99.11 created 2000, modified 2004, deleted 2014]

1.6.3.5

Accepted name:

renalase

Reaction:

(1) 1,2-dihydro-β-NAD(P) + H⁺ + O₂ = β-NAD(P)⁺ + H₂O₂
(2) 1,6-dihydro-β-NAD(P) + H⁺ + O₂ = β-NAD(P)⁺ + H₂O₂

Other name(s):

αNAD(P)H oxidase/anomerase (incorrect); NAD(P)H:oxygen oxidoreductase (H₂O₂-forming, epimerising) (incorrect)

Systematic name:

dihydro-NAD(P):oxygen oxidoreductase (H₂O₂-forming)

Comments:

Requires FAD. Renalase, previously thought to be a hormone, is a flavoprotein secreted into the blood by the kidney that oxidizes the 1,2-dihydro- and 1,6-dihydro- isomeric forms of β-NAD(P)H back to β-NAD(P)⁺. These isomeric forms, generated by nonspecific reduction of β-NAD(P)⁺ or by tautomerization of β-NAD(P)H, are potent inhibitors of primary metabolism dehydrogenases and pose a threat to normal respiration.

Links to other databases:

References:

1.	Xu, J., Li, G., Wang, P., Velazquez, H., Yao, X., Li, Y., Wu, Y., Peixoto, A., Crowley, S. and Desir, G.V. Renalase is a novel, soluble monoamine oxidase that regulates cardiac function and blood pressure. J. Clin. Invest. 115 (2005) 1275–1280. [DOI] [PMID: 15841207]
2.	Beaupre, B.A., Hoag, M.R., Roman, J., Forsterling, F.H. and Moran, G.R. Metabolic function for human renalase: oxidation of isomeric forms of β-NAD(P)H that are inhibitory to primary metabolism. Biochemistry 54 (2015) 795–806. [DOI] [PMID: 25531177]

[EC 1.6.3.5 created 2014, modified 2015]

*EC

1.10.2.2

Transferred entry:

quinol—cytochrome-c reductase. Now EC 7.1.1.8, quinol—cytochrome-c reductase

[EC 1.10.2.2 created 1978, modified 2013, deleted 2018]

*EC

1.10.3.11

Accepted name:

ubiquinol oxidase (non-electrogenic)

Reaction:

2 ubiquinol + O₂ = 2 ubiquinone + 2 H₂O

Other name(s):

plant alternative oxidase; cyanide-insensitive oxidase; AOX (gene name); ubiquinol oxidase; ubiquinol:O₂ oxidoreductase (non-electrogenic)

Systematic name:

ubiquinol:oxygen oxidoreductase (non-electrogenic)

Comments:

The enzyme, described from the mitochondria of plants and some fungi and protists, is an alternative terminal oxidase that is not sensitive to cyanide inhibition and does not generate a proton motive force. Unlike the electrogenic terminal oxidases that contain hemes (cf. EC 7.1.1.3 and EC 7.1.1.7), this enzyme contains a dinuclear non-heme iron complex. The function of this oxidase is believed to be dissipating excess reducing power, minimizing oxidative stress, and optimizing photosynthesis in response to changing conditions.

Links to other databases:

References:

1.	Bendall, D.S. and Bonner, W.D. Cyanide-insensitive respiration in plant mitochondria. Plant Physiol. 47 (1971) 236–245. [PMID: 16657603]
2.	Siedow, J.N., Umbach, A.L. and Moore, A.L. The active site of the cyanide-resistant oxidase from plant mitochondria contains a binuclear iron center. FEBS Lett. 362 (1995) 10–14. [DOI] [PMID: 7698344]
3.	Berthold, D.A., Andersson, M.E. and Nordlund, P. New insight into the structure and function of the alternative oxidase. Biochim. Biophys. Acta 1460 (2000) 241–254. [DOI] [PMID: 11106766]
4.	Williams, B.A., Elliot, C., Burri, L., Kido, Y., Kita, K., Moore, A.L. and Keeling, P.J. A broad distribution of the alternative oxidase in microsporidian parasites. PLoS Pathog. 6:e1000761 (2010). [DOI] [PMID: 20169184]
5.	Gandin, A., Duffes, C., Day, D.A. and Cousins, A.B. The absence of alternative oxidase AOX1A results in altered response of photosynthetic carbon assimilation to increasing CO₂ in Arabidopsis thaliana. Plant Cell Physiol. 53 (2012) 1627–1637. [DOI] [PMID: 22848123]

[EC 1.10.3.11 created 2011, modified 2014]

1.10.3.14

Transferred entry:

ubiquinol oxidase (electrogenic, non H⁺-transporting). Now EC 7.1.1.7, ubiquinol oxidase (electrogenic, proton-motive force generating)

[EC 1.10.3.14 created 2014, modified 2017, deleted 2018]

1.13.11.77

Accepted name:

oleate 10S-lipoxygenase

Reaction:

(1) oleate + O₂ = (8E,10S)-10-hydroperoxyoctadeca-8-enoate
(2) linoleate + O₂ = (8E,10S,12Z)-10-hydroperoxyoctadeca-8,12-dienoate
(3) α-linolenate + O₂ = (8E,10S,12Z,15Z)-10-hydroperoxyoctadeca-8,12,15-trienoate

Other name(s):

10S-DOX; (10S)-dioxygenase; 10S-dioxygenase

Systematic name:

oleate:oxygen (10S)-oxidoreductase

Comments:

Binds Fe²⁺. The enzyme isolated from the bacterium Pseudomonas sp. 42A2 has similar activity with all the three Δ⁹ fatty acids. cf. EC 1.13.11.62, linoleate 10R-lipoxygenase.

Links to other databases:

References:

Busquets, M., Deroncele, V., Vidal-Mas, J., Rodriguez, E., Guerrero, A. and Manresa, A. Isolation and characterization of a lipoxygenase from Pseudomonas 42A2 responsible for the biotransformation of oleic acid into (S)-(E)-10-hydroxy-8-octadecenoic acid. Antonie Van Leeuwenhoek 85 (2004) 129–139. [DOI] [PMID: 15028873]

[EC 1.13.11.77 created 2013]

*EC

1.14.11.37

Accepted name:

kanamycin B dioxygenase

Reaction:

kanamycin B + 2-oxoglutarate + O₂ = 2′-dehydrokanamycin A + succinate + NH₃ + CO₂

For diagram of kanamycin A biosynthesis, click here

Other name(s):

kanJ (gene name)

Systematic name:

kanamycin-B,2-oxoglutarate:oxygen oxidoreductase (deaminating, 2′-hydroxylating)

Comments:

Requires Fe²⁺ and ascorbate. Found in the bacterium Streptomyces kanamyceticus where it is involved in the conversion of the aminoglycoside antibiotic kanamycin B to kanamycin A.

Links to other databases:

References:

1.	Sucipto, H., Kudo, F. and Eguchi, T. The last step of kanamycin biosynthesis: unique deamination reaction catalyzed by the α-ketoglutarate-dependent nonheme iron dioxygenase KanJ and the NADPH-dependent reductase KanK. Angew. Chem. Int. Ed. Engl. 51 (2012) 3428–3431. [DOI] [PMID: 22374809]

[EC 1.14.11.37 created 2013, modified 2013]

1.14.13.60

Transferred entry:

27-hydroxycholesterol 7α-monooxygenase. Now classified as EC 1.14.14.29, 25/26-hydroxycholesterol 7α-hydroxylase

[EC 1.14.13.60 created 1999, deleted 2013]

*EC

1.14.13.100

Transferred entry:

25/26-hydroxycholesterol 7α-hydroxylase. Now classified as EC 1.14.14.29, 25/26-hydroxycholesterol 7α-hydroxylase

[EC 1.14.13.100 created 2005, modified 2013 (EC 1.14.13.60 created 1999, incorporated 2013), deleted 2016]

1.14.13.183

Transferred entry:

dammarenediol 12-hydroxylase. Now EC 1.14.14.120, dammarenediol 12-hydroxylase

[EC 1.14.13.183 created 2013, deleted 2018]

1.14.13.184

Transferred entry:

protopanaxadiol 6-hydroxylase. Now EC 1.14.14.121, protopanaxadiol 6-hydroxylase

[EC 1.14.13.184 created 2013, deleted 2018]

1.14.13.185

Transferred entry:

pikromycin synthase. Now EC 1.14.15.33, pikromycin synthase

[EC 1.14.13.185 created 2014, deleted 2018]

1.14.13.186

Transferred entry:

20-oxo-5-O-mycaminosyltylactone 23-monooxygenase. Now EC 1.14.15.34, 20-oxo-5-O-mycaminosyltylactone 23-monooxygenase

[EC 1.14.13.186 created 2014, deleted 2018]

1.14.13.187

Accepted name:

L-evernosamine nitrososynthase

Reaction:

dTDP-β-L-evernosamine + 2 NADPH + 2 H⁺ + 2 O₂ = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-β-L-arabino-hexopyranose + 2 NADP⁺ + 3 H₂O (overall reaction)
(1a) dTDP-β-L-evernosamine + NADPH + H⁺ + O₂ = dTDP-N-hydroxy-β-L-evernosamine + NADP⁺ + H₂O
(1b) dTDP-N-hydroxy-β-L-evernosamine + NADPH + H⁺ + O₂ = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitroso-β-L-arabino-hexopyranose + NADP⁺ + 2 H₂O

Glossary:

dTDP-β-L-evernosamine = dTDP-3-amino-2,3,6-trideoxy-3-C-methyl-4-O-methyl-β-L-arabino-hexopyranose
dTDP-β-L-evernitrose = dTDP-2,3,6-trideoxy-3-C-methyl-4-O-methyl-3-nitro-β-L-arabino-hexopyranose

Systematic name:

dTDP-β-L-evernosamine,NADPH:oxygen oxidoreductase (N-hydroxylating)

Comments:

Requires FAD. Isolated from the bacterium Micromonospora carbonacea var. africana. The nitroso group is probably spontaneously oxidized to a nitro group giving dTDP-β-L-evernitrose, which is involved in the biosynthesis of the antibiotic everninomycin. The reaction was studied using dTDP-β-L-4-epi-vancosamine (dTDP-4-O-desmethyl-β-L-evernitrosamine).

Links to other databases:

References:

1.	Hu, Y., Al-Mestarihi, A., Grimes, C.L., Kahne, D. and Bachmann, B.O. A unifying nitrososynthase involved in nitrosugar biosynthesis. J. Am. Chem. Soc. 130 (2008) 15756–15757. [DOI] [PMID: 18983146]
2.	Vey, J.L., Al-Mestarihi, A., Hu, Y., Funk, M.A., Bachmann, B.O. and Iverson, T.M. Structure and mechanism of ORF36, an amino sugar oxidizing enzyme in everninomicin biosynthesis. Biochemistry 49 (2010) 9306–9317. [DOI] [PMID: 20866105]

[EC 1.14.13.187 created 2014]

1.14.13.188

Transferred entry:

6-deoxyerythronolide B hydroxylase. Now EC 1.14.15.35, 6-deoxyerythronolide B hydroxylase

[EC 1.14.13.188 created 2014, deleted 2018]

*EC

1.16.1.7

Accepted name:

ferric-chelate reductase (NADH)

Reaction:

2 Fe(II)-siderophore + NAD⁺ + H⁺ = 2 Fe(III)-siderophore + NADH

Other name(s):

ferric chelate reductase (ambiguous); iron chelate reductase (ambiguous); NADH:Fe³⁺-EDTA reductase; NADH₂:Fe³⁺ oxidoreductase; ferB (gene name); Fe(II):NAD⁺ oxidoreductase

Systematic name:

Fe(II)-siderophore:NAD⁺ oxidoreductase

Comments:

Contains FAD. The enzyme catalyses the reduction of bound ferric iron in a variety of iron chelators (siderophores), resulting in the release of ferrous iron. The plant enzyme is involved in the transport of iron across plant plasma membranes. The enzyme from the bacterium Paracoccus denitrificans can also reduce chromate. cf. EC 1.16.1.9, ferric-chelate reductase (NADPH) and EC 1.16.1.10, ferric-chelate reductase [NAD(P)H].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 120720-17-4

References:

1.	Askerlund, P., Larrson, C. and Widell, S. Localization of donor and acceptor sites of NADH dehydrogenase activities using inside-out and right-side-out plasma membrane vesicles from plants. FEBS Lett. 239 (1988) 23–28.
2.	Brüggemann, W. and Moog, P.R. NADH-dependent Fe³⁺ EDTA and oxygen reduction by plasma membrane vesicles from barley roots. Physiol. Plant. 75 (1989) 245–254.
3.	Brüggemann, W., Moog, P.R., Nakagawa, H., Janiesch, P. and Kuiper, P.J.C. Plasma membrane-bound NADH:Fe³⁺-EDTA reductase and iron deficiency in tomato (Lycopersicon esculentum). Is there a Turbo reductase ? Physiol. Plant. 79 (1990) 339–346.
4.	Buckhout, T.J. and Hrubec, T.C. Pyridine nucleotide-dependent ferricyanide reduction associated with isolated plasma membranes of maize (Zea mays L.) roots. Protoplasma 135 (1986) 144–154.
5.	Sandelius, A.S., Barr, R., Crane, F.L. and Morré, D.J. Redox reactions of plasma membranes isolated from soybean hypocotyls by phase partition. Plant Sci. 48 (1986) 1–10.
6.	Mazoch, J., Tesarik, R., Sedlacek, V., Kucera, I. and Turanek, J. Isolation and biochemical characterization of two soluble iron(III) reductases from Paracoccus denitrificans. Eur. J. Biochem. 271 (2004) 553–562. [PMID: 14728682]

[EC 1.16.1.7 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, modified 2011, modified 2014]

*EC

1.16.1.9

Accepted name:

ferric-chelate reductase (NADPH)

Reaction:

2 Fe(II)-siderophore + NADP⁺ + H⁺ = 2 Fe(III)-siderophore + NADPH

Other name(s):

ferric chelate reductase (ambiguous); iron chelate reductase (ambiguous); NADPH:Fe³⁺-EDTA reductase; NADPH-dependent ferric reductase; yqjH (gene name); Fe(II):NADP⁺ oxidoreductase

Systematic name:

Fe(II)-siderophore:NADP⁺ oxidoreductase

Comments:

Contains FAD. The enzyme, which is widespread among bacteria, catalyses the reduction of ferric iron bound to a variety of iron chelators (siderophores), including ferric triscatecholates and ferric dicitrate, resulting in the release of ferrous iron. The enzyme from the bacterium Escherichia coli has the highest efficiency with the hydrolysed ferric enterobactin complex ferric N-(2,3-dihydroxybenzoyl)-L-serine [3]. cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.10, ferric-chelate reductase [NAD(P)H].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 120720-17-4

References:

1.	Bamford, V.A., Armour, M., Mitchell, S.A., Cartron, M., Andrews, S.C. and Watson, K.A. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 792–796. [DOI] [PMID: 18765906]
2.	Wang, S., Wu, Y. and Outten, F.W. Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli. J. Bacteriol. 193 (2011) 563–574. [DOI] [PMID: 21097627]
3.	Miethke, M., Hou, J. and Marahiel, M.A. The siderophore-interacting protein YqjH acts as a ferric reductase in different iron assimilation pathways of Escherichia coli. Biochemistry 50 (2011) 10951–10964. [DOI] [PMID: 22098718]

[EC 1.16.1.9 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, transferred 2011 to EC 1.16.1.9, modified 2012, modified 2014]

1.16.1.10

Accepted name:

ferric-chelate reductase [NAD(P)H]

Reaction:

2 Fe(II)-siderophore + NAD(P)⁺ + H⁺ = 2 Fe(III)-siderophore + NAD(P)H

Other name(s):

ferric reductase (ambiguous)

Systematic name:

Fe(II)-siderophore:NAD(P)⁺ oxidoreductase

Comments:

A flavoprotein. The enzyme catalyses the reduction of bound ferric iron in a variety of iron chelators (siderophores), resulting in the release of ferrous iron. The enzyme from the hyperthermophilic archaeon Archaeoglobus fulgidus is not active with uncomplexed Fe(III). cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.9, ferric-chelate reductase (NADPH).

Links to other databases:

References:

1.	Vadas, A., Monbouquette, H.G., Johnson, E. and Schroder, I. Identification and characterization of a novel ferric reductase from the hyperthermophilic Archaeon Archaeoglobus fulgidus. J. Biol. Chem. 274 (1999) 36715–36721. [DOI] [PMID: 10593977]
2.	Chiu, H.J., Johnson, E., Schroder, I. and Rees, D.C. Crystal structures of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP⁺. Structure 9 (2001) 311–319. [DOI] [PMID: 11525168]

[EC 1.16.1.10 created 2014]

1.21.99.2

Transferred entry:

EC 1.21.99.2, cyclic dehypoxanthinyl futalosine synthase. Now classified as EC 1.21.98.1, cyclic dehypoxanthinyl futalosine synthase.

[EC 1.21.99.2 created 2014, deleted 2014]

*EC

2.1.1.57

Accepted name:

methyltransferase cap1

Reaction:

S-adenosyl-L-methionine + a 5′-(N⁷-methyl 5′-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5′-(N⁷-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-[mRNA]

Other name(s):

FTSJD2 (gene name); messenger ribonucleate nucleoside 2′-methyltransferase; messenger RNA (nucleoside-2′-)-methyltransferase; MTR1; cap1-MTase; mRNA (nucleoside-2′-O)-methyltransferase (ambiguous); S-adenosyl-L-methionine:mRNA (nucleoside-2′-O)-methyltransferase

Systematic name:

S-adenosyl-L-methionine:5-(N⁷-methyl 5-triphosphoguanosine)-(ribonucleotide)-[mRNA] 2-O-methyltransferase

Comments:

This enzyme catalyses the methylation of the ribose on the first transcribed nucleotide of mRNA or snRNA molecules. This methylation event is known as cap1, and occurs in all mRNAs and snRNAs of higher eukaryotes, including insects, vertebrates and their viruses. The human enzyme can also methylate mRNA molecules that lack methylation on the capping 5′-triphosphoguanosine [6].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 61970-02-3

References:

1.	Barbosa, E. and Moss, B. mRNA(nucleoside-2′-)-methyltransferase from vaccinia virus. Purification and physical properties. J. Biol. Chem. 253 (1978) 7692–7697. [PMID: 701281]
2.	Barbosa, E. and Moss, B. mRNA(nucleoside-2′-)-methyltransferase from vaccinia virus. Characteristics and substrate specificity. J. Biol. Chem. 253 (1978) 7698–7702. [PMID: 701282]
3.	Boone, R.F., Ensinger, M.J. and Moss, B. Synthesis of mRNA guanylyltransferase and mRNA methyltransferases in cells infected with vaccinia virus. J. Virol. 21 (1977) 475–483. [PMID: 833934]
4.	Ensinger, M.J., Martin, S.A., Paoletti, E. and Moss, B. Modification of the 5′-terminus of mRNA by soluble guanylyl and methyl transferases from vaccinia virus. Proc. Natl. Acad. Sci. USA 72 (1975) 2525–2529. [DOI] [PMID: 1058472]
5.	Groner, Y., Gilbao, E. and Aviv, H. Methylation and capping of RNA polymerase II primary transcripts by HeLa nuclear homogenates. Biochemistry 17 (1978) 977–982. [PMID: 629955]
6.	Werner, M., Purta, E., Kaminska, K.H., Cymerman, I.A., Campbell, D.A., Mittra, B., Zamudio, J.R., Sturm, N.R., Jaworski, J. and Bujnicki, J.M. 2′-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res. 39 (2011) 4756–4768. [DOI] [PMID: 21310715]

[EC 2.1.1.57 created 1981 (EC 2.1.1.58 created 1981, incorporated 1984), modified 2014, modified 2021]

*EC

2.1.1.196

Accepted name:

cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating]

Reaction:

S-adenosyl-L-methionine + cobalt-precorrin-6B = S-adenosyl-L-homocysteine + cobalt-precorrin-7 + CO₂

For diagram of anaerobic corrin biosynthesis (part 2), click here

Other name(s):

cbiT (gene name); S-adenosyl-L-methionine:precorrin-7 C¹⁵-methyltransferase (C-12-decarboxylating); cobalt-precorrin-7 (C15)-methyltransferase [decarboxylating]

Systematic name:

S-adenosyl-L-methionine:precorrin-6B C¹⁵-methyltransferase (C-12-decarboxylating)

Comments:

This enzyme, which participates in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway, catalyses both methylation at C-15 and decarboxylation of the C-12 acetate side chain of cobalt-precorrin-6B. The equivalent activity in the aerobic adenosylcobalamin biosynthesis pathway is catalysed by the bifunctional enzyme EC 2.1.1.132, precorrin-6B C5,15-methyltransferase (decarboxylating).

Links to other databases:

References:

1.	Keller, J.P., Smith, P.M., Benach, J., Christendat, D., deTitta, G.T. and Hunt, J.F. The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure 10 (2002) 1475–1487. [DOI] [PMID: 12429089]
2.	Santander, P.J., Kajiwara, Y., Williams, H.J. and Scott, A.I. Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B₁₂ anaerobic pathway. Bioorg. Med. Chem. 14 (2006) 724–731. [DOI] [PMID: 16198574]
3.	Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B₁₂). Proc. Natl. Acad. Sci. USA 110 (2013) 14906–14911. [DOI] [PMID: 23922391]

[EC 2.1.1.196 created 2010, modified 2013]

*EC

2.1.1.222

Accepted name:

2-polyprenyl-6-hydroxyphenol methylase

Reaction:

S-adenosyl-L-methionine + 3-(all-trans-polyprenyl)benzene-1,2-diol = S-adenosyl-L-homocysteine + 2-methoxy-6-(all-trans-polyprenyl)phenol

For diagram of ubiquinol biosynthesis, click here

Other name(s):

ubiG (gene name, ambiguous); ubiG methyltransferase (ambiguous); 2-octaprenyl-6-hydroxyphenol methylase

Systematic name:

S-adenosyl-L-methionine:3-(all-trans-polyprenyl)benzene-1,2-diol 2-O-methyltransferase

Comments:

UbiG catalyses both methylation steps in ubiquinone biosynthesis in Escherichia coli. The second methylation is classified as EC 2.1.1.64 (3-demethylubiquinol 3-O-methyltransferase) [2]. In eukaryotes Coq3 catalyses the two methylation steps in ubiquinone biosynthesis. However, while the second methylation is common to both enzymes, the first methylation by Coq3 occurs at a different position within the pathway, and thus involves a different substrate and is classified as EC 2.1.1.114 (polyprenyldihydroxybenzoate methyltransferase). The substrate of the eukaryotic enzyme (3,4-dihydroxy-5-all-trans-polyprenylbenzoate) differs by an additional carboxylate moiety.

Links to other databases:

References:

1.	Poon, W.W., Barkovich, R.J., Hsu, A.Y., Frankel, A., Lee, P.T., Shepherd, J.N., Myles, D.C. and Clarke, C.F. Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis. J. Biol. Chem. 274 (1999) 21665–21672. [DOI] [PMID: 10419476]
2.	Hsu, A.Y., Poon, W.W., Shepherd, J.A., Myles, D.C. and Clarke, C.F. Complementation of coq3 mutant yeast by mitochondrial targeting of the Escherichia coli UbiG polypeptide: evidence that UbiG catalyzes both O-methylation steps in ubiquinone biosynthesis. Biochemistry 35 (1996) 9797–9806. [DOI] [PMID: 8703953]

[EC 2.1.1.222 created 2011, modified 2013]

*EC

2.1.1.267

Accepted name:

flavonoid 3′,5′-methyltransferase

Reaction:

(1) S-adenosyl-L-methionine + a 3′-hydroxyflavonoid = S-adenosyl-L-homocysteine + a 3′-methoxyflavonoid
(2) S-adenosyl-L-methionine + a 5′-hydroxy-3′-methoxyflavonoid = S-adenosyl-L-homocysteine + a 3′,5′-dimethoxyflavonoid

For diagram of anthocyanidin glucoside biosynthesis, click here

Glossary:

delphinidin = 3,3′,4′,5,5′,7-hexahydroxyflavylium
cyanidin = 3,3′,4′,5,7-pentahydroxyflavylium
myricetin = 3,3′,4′,5,5′,7-hexahydroxyflavone
quercetin = 3,3′,4′,5,7-pentahydroxyflavone

Other name(s):

AOMT; CrOMT2

Systematic name:

S-adenosyl-L-methionine:flavonoid 3′-O-methyltransferase

Comments:

Isolated from Vitis vinifera (grape) [2]. Most active with delphinidin 3-glucoside but also acts on cyanidin 3-glucoside, cyanidin, myricetin, quercetin and quercetin 3-glucoside. The enzyme from Catharanthus roseus was most active with myricetin [1].

Links to other databases:

References:

1.	Cacace, S., Schröder, G., Wehinger, E., Strack, D., Schmidt, J. and Schröder, J. A flavonol O-methyltransferase from Catharanthus roseus performing two sequential methylations. Phytochemistry 62 (2003) 127–137. [DOI] [PMID: 12482447]
2.	Hugueney, P., Provenzano, S., Verries, C., Ferrandino, A., Meudec, E., Batelli, G., Merdinoglu, D., Cheynier, V., Schubert, A. and Ageorges, A. A novel cation-dependent O-methyltransferase involved in anthocyanin methylation in grapevine. Plant Physiol. 150 (2009) 2057–2070. [DOI] [PMID: 19525322]

[EC 2.1.1.267 created 2013, modified 2014]

*EC

2.1.1.282

Accepted name:

tRNA^Phe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine³⁷-N⁴]-methyltransferase

Reaction:

S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine³⁷ in tRNA^Phe = S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine³⁷ in tRNA^Phe

For diagram of wyosine biosynthesis, click here

Glossary:

wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one

Other name(s):

TYW3 (gene name); tRNA-yW synthesizing enzyme-3

Systematic name:

S-adenosyl-L-methionine:tRNA^Phe 7-[(3S)-(3-amino-3-carboxypropyl)-4-demethylwyosine-N⁴]-methyltransferase

Comments:

The enzyme is involved in the biosynthesis of hypermodified tricyclic bases found at position 37 of certain tRNAs. These modifications are important for translational reading-frame maintenance. The enzyme is found in all eukaryotes and in some archaea, but not in bacteria. The eukaryotic enzyme is involved in the biosynthesis of wybutosine.

Links to other databases:

References:

1.	Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]

[EC 2.1.1.282 created 2013, modified 2014]

2.1.1.289

Accepted name:

cobalt-precorrin-7 (C5)-methyltransferase

Reaction:

S-adenosyl-L-methionine + cobalt-precorrin-7 = S-adenosyl-L-homocysteine + cobalt-precorrin-8

For diagram of anaerobic corrin biosynthesis (part 2), click here

Other name(s):

CbiE

Systematic name:

S-adenosyl-L-methionine:precorrin-7 C⁵-methyltransferase

Comments:

This enzyme catalyses the methylation at C-5 of cobalt-precorrin-7, a step in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway. The equivalent activity in the aerobic adenosylcobalamin biosynthesis pathway is catalysed by the bifunctional enzyme EC 2.1.1.132, precorrin-6B C5,15-methyltransferase (decarboxylating).

Links to other databases:

References:

1.	Santander, P.J., Kajiwara, Y., Williams, H.J. and Scott, A.I. Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B₁₂ anaerobic pathway. Bioorg. Med. Chem. 14 (2006) 724–731. [DOI] [PMID: 16198574]
2.	Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B₁₂). Proc. Natl. Acad. Sci. USA 110 (2013) 14906–14911. [DOI] [PMID: 23922391]

[EC 2.1.1.289 created 2010]

2.1.1.290

Accepted name:

tRNA^Phe [7-(3-amino-3-carboxypropyl)wyosine³⁷-O]-methyltransferase

Reaction:

S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-carboxypropyl]wyosine³⁷ in tRNA^Phe = S-adenosyl-L-homocysteine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine³⁷ in tRNA^Phe

For diagram of wyosine biosynthesis, click here

Glossary:

wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-[(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl]-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one

Other name(s):

TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)

Systematic name:

S-adenosyl-L-methionine:tRNA^Phe {7-[(3S)-3-amino-3-carboxypropyl]wyosine³⁷-O}-methyltransferase

Comments:

The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine³⁷ in tRNA^Phe as substrate. The enzyme also has the activity of EC 2.3.1.231, tRNA^Phe 7-[(3S)-4-methoxy-(3-amino-3-carboxypropyl)wyosine³⁷-O]-carbonyltransferase [2].

Links to other databases:

References:

1.	Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
2.	Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO₂ fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910–2925. [DOI] [PMID: 19287006]
3.	Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]

[EC 2.1.1.290 created 2013]

2.1.1.291

Accepted name:

(R,S)-reticuline 7-O-methyltransferase

Reaction:

(1) S-adenosyl-L-methionine + (S)-reticuline = S-adenosyl-L-homocysteine + (S)-laudanine
(2) S-adenosyl-L-methionine + (R)-reticuline = S-adenosyl-L-homocysteine + (R)-laudanine

For diagram of laudanine biosynthesis, click here

Glossary:

(S)-reticuline = (1S)-1-[(3-hydroxy-4-methoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol
(R)-reticuline = (1R)-1-[(3-hydroxy-4-methoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol
(S)-laudanine = 5-[((1S)-6,7-dimethoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl)methyl]-2-methoxyphenol
(R)-laudanine = 5-[((1R)-6,7-dimethoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-1-yl)methyl]-2-methoxyphenol

Systematic name:

S-adenosyl-L-methionine:(R,S)-reticuline 7-O-methyltransferase

Comments:

The enzyme from the plant Papaver somniferum (opium poppy) methylates (S)- and (R)-reticuline with equal efficiency and is involved in the biosynthesis of tetrahydrobenzylisoquinoline alkaloids.

Links to other databases:

References:

1.	Ounaroon, A., Decker, G., Schmidt, J., Lottspeich, F. and Kutchan, T.M. (R,S)-Reticuline 7-O-methyltransferase and (R,S)-norcoclaurine 6-O-methyltransferase of Papaver somniferum - cDNA cloning and characterization of methyl transfer enzymes of alkaloid biosynthesis in opium poppy. Plant J. 36 (2003) 808–819. [DOI] [PMID: 14675446]
2.	Weid, M., Ziegler, J. and Kutchan, T.M. The roles of latex and the vascular bundle in morphine biosynthesis in the opium poppy, Papaver somniferum. Proc. Natl. Acad. Sci. USA 101 (2004) 13957–13962. [DOI] [PMID: 15353584]

[EC 2.1.1.291 created 2013]

2.1.1.292

Accepted name:

carminomycin 4-O-methyltransferase

Reaction:

S-adenosyl-L-methionine + carminomycin = S-adenosyl-L-homocysteine + daunorubicin

For diagram of daunorubicin biosynthesis, click here

Glossary:

daunorubicin = (+)-daunomycin = (8S,10S)-8-acetyl-10-[(2S,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy-6,8,11-trihydroxy-1-methoxy-9,10-dihydro-7H-tetracene-5,12-dione
carminomycin = (1S,3S)-3-acetyl-3,5,10,12-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside = (1S,3S)-3-acetyl-3,5,10,12-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydronaphthacen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside
carubicin = (1S,3S)-3-acetyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranoside
= (8S,10S)-8-acetyl-10-[(3-amino-2,3,6-trideoxy-α-L-lyxo-hexopyranosyl)oxy]-6,8,11-trihydroxy-1-methoxy-7,8,9,10-tetrahydronaphthacene-5,12-dione

Other name(s):

DnrK; DauK

Systematic name:

S-adenosyl-L-methionine:carminomycin 4-O-methyltransferase

Comments:

The enzymes from the Gram-positive bacteria Streptomyces sp. C5 and Streptomyces peucetius are involved in the biosynthesis of the anthracycline daunorubicin. In vitro the enzyme from Streptomyces sp. C5 also catalyses the 4-O-methylation of 13-dihydrocarminomycin, rhodomycin D and 10-carboxy-13-deoxycarminomycin [3].

Links to other databases:

References:

1.	Connors, N.C. and Strohl, W.R. Partial purification and properties of carminomycin 4-O-methyltransferase from Streptomyces sp. strain C5. J. Gen. Microbiol. 139 Pt 6 (1993) 1353–1362. [DOI] [PMID: 8360627]
2.	Jansson, A., Koskiniemi, H., Mantsala, P., Niemi, J. and Schneider, G. Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products. J. Biol. Chem. 279 (2004) 41149–41156. [DOI] [PMID: 15273252]
3.	Dickens, M.L., Priestley, N.D. and Strohl, W.R. In vivo and in vitro bioconversion of ε-rhodomycinone glycoside to doxorubicin: functions of DauP, DauK, and DoxA. J. Bacteriol. 179 (1997) 2641–2650. [DOI] [PMID: 9098063]

[EC 2.1.1.292 created 2013]

2.1.1.293

Accepted name:

6-hydroxytryprostatin B O-methyltransferase

Reaction:

S-adenosyl-L-methionine + 6-hydroxytryprostatin B = S-adenosyl-L-homocysteine + tryprostatin A

For diagram of fumitremorgin alkaloid biosynthesis (part 1), click here

Glossary:

6-hydroxytryprostatin B = (3S,8aS)-3-{[6-hydroxy-2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione
tryprostatin A = (3S,8aS)-3-{[6-methoxy-2-(3-methylbut-2-en-1-yl)-1H-indol-3-yl]methyl}hexahydropyrrolo[1,2-a]pyrazine-1,4-dione

Other name(s):

ftmD (gene name)

Systematic name:

S-adenosyl-L-methionine:6-hydroxytryprostatin B O-methyltransferase

Comments:

Involved in the biosynthetic pathways of several indole alkaloids such as tryprostatins, fumitremorgins and verruculogen.

Links to other databases:

References:

1.	Kato, N., Suzuki, H., Okumura, H., Takahashi, S. and Osada, H. A point mutation in ftmD blocks the fumitremorgin biosynthetic pathway in Aspergillus fumigatus strain Af293. Biosci. Biotechnol. Biochem. 77 (2013) 1061–1067. [DOI] [PMID: 23649274]

[EC 2.1.1.293 created 2013]

2.1.1.294

Accepted name:

3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Reaction:

S-adenosyl-L-methionine + 3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = S-adenosyl-L-homocysteine + 3-O-methylphospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol

Other name(s):

WbdD; S-adenosyl-L-methionine:3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-α-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Systematic name:

S-adenosyl-L-methionine:3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase

Comments:

The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the preceding phosphorylation of α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.7.1.181, polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase).

Links to other databases:

References:

1.	Clarke, B.R., Cuthbertson, L. and Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279 (2004) 35709–35718. [DOI] [PMID: 15184370]
2.	Clarke, B.R., Greenfield, L.K., Bouwman, C. and Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284 (2009) 30662–30672. [DOI] [PMID: 19734145]
3.	Clarke, B.R., Richards, M.R., Greenfield, L.K., Hou, D., Lowary, T.L. and Whitfield, C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286 (2011) 41391–41401. [DOI] [PMID: 21990359]
4.	Liston, S.D., Clarke, B.R., Greenfield, L.K., Richards, M.R., Lowary, T.L. and Whitfield, C. Domain interactions control complex formation and polymerase specificity in the biosynthesis of the Escherichia coli O9a antigen. J. Biol. Chem. 290 (2015) 1075–1085. [DOI] [PMID: 25422321]

[EC 2.1.1.294 created 2014, modified 2018]

2.1.1.295

Accepted name:

2-methyl-6-phytyl-1,4-hydroquinone methyltransferase

Reaction:

(1) S-adenosyl-L-methionine + 2-methyl-6-phytylbenzene-1,4-diol = S-adenosyl-L-homocysteine + 2,3-dimethyl-6-phytylbenzene-1,4-diol
(2) S-adenosyl-L-methionine + 2-methyl-6-all-trans-nonaprenylbenzene-1,4-diol = S-adenosyl-L-homocysteine + plastoquinol
(3) S-adenosyl-L-methionine + 6-geranylgeranyl-2-methylbenzene-1,4-diol = S-adenosyl-L-homocysteine + 6-geranylgeranyl-2,3-dimethylbenzene-1,4-diol

For diagram of tocopherol biosynthesis, click here and for diagram of tocotrienol biosynthesis, click here

Other name(s):

VTE3 (gene name); 2-methyl-6-solanyl-1,4-hydroquinone methyltransferase; MPBQ/MSBQ methyltransferase; MPBQ/MSBQ MT

Systematic name:

S-adenosyl-L-methionine:2-methyl-6-phytyl-1,4-benzoquinol C-3-methyltransferase

Comments:

Involved in the biosynthesis of plastoquinol, as well as vitamin E (tocopherols and tocotrienols).

Links to other databases:

References:

1.	Shintani, D.K., Cheng, Z. and DellaPenna, D. The role of 2-methyl-6-phytylbenzoquinone methyltransferase in determining tocopherol composition in Synechocystis sp. PCC6803. FEBS Lett. 511 (2002) 1–5. [DOI] [PMID: 11821038]
2.	Cheng, Z., Sattler, S., Maeda, H., Sakuragi, Y., Bryant, D.A. and DellaPenna, D. Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes. Plant Cell 15 (2003) 2343–2356. [DOI] [PMID: 14508009]
3.	Van Eenennaam, A.L., Lincoln, K., Durrett, T.P., Valentin, H.E., Shewmaker, C.K., Thorne, G.M., Jiang, J., Baszis, S.R., Levering, C.K., Aasen, E.D., Hao, M., Stein, J.C., Norris, S.R. and Last, R.L. Engineering vitamin E content: from Arabidopsis mutant to soy oil. Plant Cell 15 (2003) 3007–3019. [DOI] [PMID: 14630966]

[EC 2.1.1.295 created 2014]

2.1.1.296

Accepted name:

methyltransferase cap2

Reaction:

S-adenosyl-L-methionine + a 5′-(N⁷-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5′-(N⁷-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-(2′-O-methyl-ribonucleotide)-[mRNA]

Other name(s):

CMTR2 (gene name); MTR2; cap2-MTase; mRNA (nucleoside-2′-O)-methyltransferase (ambiguous)

Systematic name:

S-adenosyl-L-methionine:5′-(N⁷-methyl 5′-triphosphoguanosine)-(2′-O-methyl-ribonucleotide)-ribonucleotide-[mRNA] 2′-O-methyltransferase

Comments:

The enzyme, found in higher eukaryotes including insects and vertebrates, and their viruses, methylates the ribose of the ribonucleotide at the second transcribed position of mRNAs and snRNAs. This methylation event is known as cap2. The human enzyme can also methylate mRNA molecules where the upstream ribonucleotide is not methylated (see EC 2.1.1.57, methyltransferase cap1), but with lower efficiency [2].

Links to other databases:

References:

1.	Arhin, G.K., Ullu, E. and Tschudi, C. 2′-O-methylation of position 2 of the trypanosome spliced leader cap 4 is mediated by a 48 kDa protein related to vaccinia virus VP39. Mol. Biochem. Parasitol. 147 (2006) 137–139. [DOI] [PMID: 16516986]
2.	Werner, M., Purta, E., Kaminska, K.H., Cymerman, I.A., Campbell, D.A., Mittra, B., Zamudio, J.R., Sturm, N.R., Jaworski, J. and Bujnicki, J.M. 2′-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res. 39 (2011) 4756–4768. [DOI] [PMID: 21310715]

[EC 2.1.1.296 created 2014, modified 2021]

2.1.1.297

Accepted name:

peptide chain release factor N⁵-glutamine methyltransferase

Reaction:

S-adenosyl-L-methionine + [peptide chain release factor 1 or 2]-L-glutamine = S-adenosyl-L-homocysteine + [peptide chain release factor 1 or 2]-N⁵-methyl-L-glutamine

Other name(s):

N⁵-glutamine S-adenosyl-L-methionine dependent methyltransferase; N⁵-glutamine MTase; HemK; PrmC

Systematic name:

S-adenosyl-L-methionine:[peptide chain release factor 1 or 2]-L-glutamine (N⁵-glutamine)-methyltransferase

Comments:

Modifies the glutamine residue in the universally conserved glycylglycylglutamine (GGQ) motif of peptide chain release factor, resulting in almost complete loss of release activity.

Links to other databases:

References:

1.	Nakahigashi, K., Kubo, N., Narita, S., Shimaoka, T., Goto, S., Oshima, T., Mori, H., Maeda, M., Wada, C. and Inokuchi, H. HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc. Natl. Acad. Sci. USA 99 (2002) 1473–1478. [DOI] [PMID: 11805295]
2.	Heurgue-Hamard, V., Champ, S., Engstrom, A., Ehrenberg, M. and Buckingham, R.H. The hemK gene in Escherichia coli encodes the N⁵-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21 (2002) 769–778. [DOI] [PMID: 11847124]
3.	Schubert, H.L., Phillips, J.D. and Hill, C.P. Structures along the catalytic pathway of PrmC/HemK, an N⁵-glutamine AdoMet-dependent methyltransferase. Biochemistry 42 (2003) 5592–5599. [DOI] [PMID: 12741815]
4.	Yoon, H.J., Kang, K.Y., Ahn, H.J., Shim, S.M., Ha, J.Y., Lee, S.K., Mikami, B. and Suh, S.W. X-ray crystallographic studies of HemK from Thermotoga maritima, an N⁵-glutamine methyltransferase. Mol. Cells 16 (2003) 266–269. [PMID: 14651272]
5.	Yang, Z., Shipman, L., Zhang, M., Anton, B.P., Roberts, R.J. and Cheng, X. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N⁵)-glutamine methyltransferase. J. Mol. Biol. 340 (2004) 695–706. [DOI] [PMID: 15223314]
6.	Pannekoek, Y., Heurgue-Hamard, V., Langerak, A.A., Speijer, D., Buckingham, R.H. and van der Ende, A. The N⁵-glutamine S-adenosyl-L-methionine-dependent methyltransferase PrmC/HemK in Chlamydia trachomatis methylates class 1 release factors. J. Bacteriol. 187 (2005) 507–511. [DOI] [PMID: 15629922]

[EC 2.1.1.297 created 2014]

2.1.1.298

Accepted name:

ribosomal protein uL3 N⁵-glutamine methyltransferase

Reaction:

S-adenosyl-L-methionine + [ribosomal protein uL3]-L-glutamine = S-adenosyl-L-homocysteine + [ribosomal protein uL3]-N⁵-methyl-L-glutamine

Other name(s):

YfcB; PrmB

Systematic name:

S-adenosyl-L-methionine:[ribosomal protein uL3]-L-glutamine (N⁵-glutamine)-methyltransferase

Comments:

Modifies the glutamine residue in the glycylglycylglutamine (GGQ) motif of ribosomal protein uL3 (Gln¹⁵⁰ in the protein from the bacterium Escherichia coli). The enzyme does not act on peptide chain release factor 1 or 2.

Links to other databases:

References:

1.	Heurgue-Hamard, V., Champ, S., Engstrom, A., Ehrenberg, M. and Buckingham, R.H. The hemK gene in Escherichia coli encodes the N⁵-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21 (2002) 769–778. [DOI] [PMID: 11847124]

[EC 2.1.1.298 created 2014, modified 2023]

2.1.1.299

Accepted name:

protein N-terminal monomethyltransferase

Reaction:

S-adenosyl-L-methionine + N-terminal-(A,P,S)PK-[protein] = S-adenosyl-L-homocysteine + N-terminal-N-methyl-N-(A,P,S)PK-[protein]

Other name(s):

NRMT2 (gene name); METTL11B (gene name); N-terminal monomethylase

Systematic name:

S-adenosyl-L-methionine:N-terminal-(A,P,S)PK-[protein] monomethyltransferase

Comments:

This enzyme methylates the N-terminus of target proteins containing the N-terminal motif [Ala/Pro/Ser]-Pro-Lys after the initiator L-methionine is cleaved. In contrast to EC 2.1.1.244, protein N-terminal methyltransferase, the protein only adds one methyl group to the N-terminal.

Links to other databases:

References:

1.	Petkowski, J.J., Bonsignore, L.A., Tooley, J.G., Wilkey, D.W., Merchant, M.L., Macara, I.G. and Schaner Tooley, C.E. NRMT2 is an N-terminal monomethylase that primes for its homologue NRMT1. Biochem. J. 456 (2013) 453–462. [DOI] [PMID: 24090352]

[EC 2.1.1.299 created 2014]

2.1.1.300

Accepted name:

pavine N-methyltransferase

Reaction:

S-adenosyl-L-methionine + (±)-pavine = S-adenosyl-L-homocysteine + N-methylpavine

Other name(s):

PavNMT

Systematic name:

S-adenosyl-L-methionine:(±)-pavine N-methyltransferase

Comments:

The enzyme, isolated from the plant Thalictrum flavum, also methylates (R,S)-stylopine and (S)-scoulerine (11%) with lower activity (14% and 11%, respectively).

Links to other databases:

References:

1.	Jain, A., Ziegler, J., Liscombe, D.K., Facchini, P.J., Tucker, P.A. and Panjikar, S. Purification, crystallization and X-ray diffraction analysis of pavine N-methyltransferase from Thalictrum flavum. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 1066–1069. [DOI] [PMID: 18997344]
2.	Liscombe, D.K., Ziegler, J., Schmidt, J., Ammer, C. and Facchini, P.J. Targeted metabolite and transcript profiling for elucidating enzyme function: isolation of novel N-methyltransferases from three benzylisoquinoline alkaloid-producing species. Plant J. 60 (2009) 729–743. [DOI] [PMID: 19624470]

[EC 2.1.1.300 created 2014]

*EC

2.3.1.86

Accepted name:

fatty-acyl-CoA synthase system

Reaction:

acetyl-CoA + n malonyl-CoA + 2n NADPH + 4n H⁺ = long-chain-acyl-CoA + n CoA + n CO₂ + 2n NADP⁺

Other name(s):

yeast fatty acid synthase; FAS1 (gene name); FAS2 (gene name); fatty-acyl-CoA synthase

Systematic name:

acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing)

Comments:

The enzyme from yeasts (Ascomycota and Basidiomycota) is a multi-functional protein complex composed of two subunits. One subunit catalyses the reactions EC 1.1.1.100, 3-oxoacyl-[acyl-carrier-protein] reductase and EC 2.3.1.41, β-ketoacyl-[acyl-carrier-protein] synthase I, while the other subunit catalyses the reactions of EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, EC 2.3.1.39, [acyl-carrier-protein] S-malonyltransferase, EC 4.2.1.59, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, EC 1.3.1.10, enoyl-[acyl-carrier-protein] reductase (NADPH, Si-specific) and EC 1.1.1.279, (R)-3-hydroxyacid-ester dehydrogenase. The enzyme system differs from the animal system (EC 2.3.1.85, fatty-acid synthase system) in that the enoyl reductase domain requires FMN as a cofactor, and the ultimate product is an acyl-CoA (usually palmitoyl-CoA) instead of a free fatty acid.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 94219-29-1

References:

1.	Schweitzer, E., Kniep, B., Castorph, H. and Holzner, U. Pantetheine-free mutants of the yeast fatty-acid-synthetase complex. Eur. J. Biochem. 39 (1973) 353–362. [DOI] [PMID: 4590449]
2.	Wakil, S.J., Stoops, J.K. and Joshi, V.C. Fatty acid synthesis and its regulation. Annu. Rev. Biochem. 52 (1983) 537–579. [DOI] [PMID: 6137188]
3.	Tehlivets, O., Scheuringer, K. and Kohlwein, S.D. Fatty acid synthesis and elongation in yeast. Biochim. Biophys. Acta 1771 (2007) 255–270. [DOI] [PMID: 16950653]

[EC 2.3.1.86 created 1984, modified 2003, modified 2013, modified 2019]

2.3.1.230

Accepted name:

2-heptyl-4(1H)-quinolone synthase

Reaction:

octanoyl-CoA + (2-aminobenzoyl)acetate = 2-heptyl-4-quinolone + CoA + CO₂ + H₂O (overall reaction)
(1a) octanoyl-CoA + L-cysteinyl-[PqsC protein] = S-octanoyl-L-cysteinyl-[PqsC protein] + CoA
(1b) S-octanoyl-L-cysteinyl-[PqsC protein] + (2-aminobenzoyl)acetate = 1-(2-aminophenyl)decane-1,3-dione + CO₂ + L-cysteinyl-[PqsC protein]
(1c) 1-(2-aminophenyl)decane-1,3-dione = 2-heptyl-4-quinolone + H₂O

Glossary:

2-heptyl-4-quinolone = 2-heptylquinolin-4(1H)-one

Other name(s):

pqsBC (gene names); malonyl-CoA:anthraniloyl-CoA C-acetyltransferase (decarboxylating)

Systematic name:

octanoyl-CoA:(2-aminobenzoyl)acetate octanoyltransferase

Comments:

The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is a heterodimeric complex. The PqsC subunit acquires an octanoyl group from octanoyl-CoA and attaches it to an internal cysteine residue. Together with the PqsB subunit, the proteins catalyse the coupling of the octanoyl group with (2-aminobenzoyl)acetate, leading to decarboxylation and dehydration events that result in closure of the quinoline ring.

Links to other databases:

References:

1.	Dulcey, C.E., Dekimpe, V., Fauvelle, D.A., Milot, S., Groleau, M.C., Doucet, N., Rahme, L.G., Lepine, F. and Deziel, E. The end of an old hypothesis: the pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines derive from fatty acids, not 3-ketofatty acids. Chem. Biol. 20 (2013) 1481–1491. [DOI] [PMID: 24239007]
2.	Drees, S.L., Li, C., Prasetya, F., Saleem, M., Dreveny, I., Williams, P., Hennecke, U., Emsley, J. and Fetzner, S. PqsBC, a condensing enzyme in the biosynthesis of the Pseudomonas aeruginosa quinolone signal: crystal structure, inhibition, and reaction mechanism. J. Biol. Chem. 291 (2016) 6610–6624. [DOI] [PMID: 26811339]

[EC 2.3.1.230 created 2013, modified 2017]

2.3.1.231

Accepted name:

tRNA^Phe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine³⁷-N}-methoxycarbonyltransferase

Reaction:

S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine³⁷ in tRNA^Phe + CO₂ = S-adenosyl-L-homocysteine + wybutosine³⁷ in tRNA^Phe

For diagram of wyosine biosynthesis, click here

Glossary:

wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one

Other name(s):

TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)

Systematic name:

S-adenosyl-L-methionine:tRNA^Phe {7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine³⁷-N}-methyltransferase (carbon dioxide-adding)

Comments:

The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-[2-hydroxy-3-amino-3-(methoxycarbonyl)propyl]wyosine³⁷ in tRNA^Phe as substrate. The enzyme also has the activity of EC 2.1.1.290, tRNA^Phe [7-(3-amino-3-carboxypropyl)wyosine³⁷-O]-methyltransferase [2].

Links to other databases:

References:

1.	Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
2.	Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO₂ fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910–2925. [DOI] [PMID: 19287006]
3.	Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]

[EC 2.3.1.231 created 2013]

2.3.1.232

Accepted name:

methanol O-anthraniloyltransferase

Reaction:

anthraniloyl-CoA + methanol = CoA + O-methyl anthranilate

Glossary:

anthraniloyl-CoA = 2-aminobenzoyl-CoA

Other name(s):

AMAT; anthraniloyl-coenzyme A (CoA):methanol acyltransferase

Systematic name:

anthraniloyl-CoA:methanol O-anthraniloyltransferase

Comments:

The enzyme from Concord grape (Vitis labrusca) is solely responsible for the production of O-methyl anthranilate, an important aroma and flavor compound in the grape. The enzyme has a broad substrate specificity, and can use a range of alcohols with substantial activity, the best being butanol, benzyl alcohol, iso-pentanol, octanol and 2-propanol. It can use benzoyl-CoA and acetyl-CoA as acyl donors with lower efficiency. In addition to O-methyl anthranilate, the enzyme might be responsible for the production of ethyl butanoate, methyl-3-hydroxy butanoate and ethyl-3-hydroxy butanoate, which are present in large quantities in the grapes. Also catalyses EC 2.3.1.196, benzyl alcohol O-benzoyltransferase.

Links to other databases:

References:

1.	Wang, J. and De Luca, V. The biosynthesis and regulation of biosynthesis of Concord grape fruit esters, including ’foxy’ methylanthranilate. Plant J. 44 (2005) 606–619. [DOI] [PMID: 16262710]

[EC 2.3.1.232 created 2014]

*EC

2.3.3.1

Accepted name:

citrate (Si)-synthase

Reaction:

acetyl-CoA + H₂O + oxaloacetate = citrate + CoA

For diagram of the citric acid cycle, click here and for diagram of the glyoxylate cycle, click here

Other name(s):

(R)-citric synthase; citrate oxaloacetate-lyase [(pro-3S)-CH₂COO^-→acetyl-CoA]

Systematic name:

acetyl-CoA:oxaloacetate C-acetyltransferase [thioester-hydrolysing, (pro-S)-carboxymethyl-forming]

Comments:

The stereospecificity of this enzyme is opposite to that of EC 2.3.3.3, citrate (Re)-synthase, which is found in some anaerobes. Citrate synthase for which the stereospecificity with respect to C-2 of oxaloacetate has not been established are included in EC 2.3.3.16, citrate synthase (unknown stereospecificity).

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9027-96-7

References:

1.	Lenz, H., Buckel, W., Wunderwald, P., Biedermann, G., Buschmeier, V., Eggerer, H., Cornforth, J.W., Redmond, J.W. and Mallaby, R. Stereochemistry of si-citrate synthase and ATP-citrate-lyase reactions. Eur. J. Biochem. 24 (1971) 207–215. [DOI] [PMID: 5157292]
2.	Karpusas, M., Branchaud, B. and Remington, S.J. Proposed mechanism for the condensation reaction of citrate synthase: 1.9-Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A. Biochemistry 29 (1990) 2213–2219. [PMID: 2337600]
3.	van Rooyen, J.P., Mienie, L.J., Erasmus, E., De Wet, W.J., Ketting, D., Duran, M. and Wadman, S.K. Identification of the stereoisomeric configurations of methylcitric acid produced by si-citrate synthase and methylcitrate synthase using capillary gas chromatography-mass spectrometry. J. Inherit. Metab. Dis. 17 (1994) 738–747. [PMID: 7707698]

[EC 2.3.3.1 created 1961 as EC 4.1.3.7, transferred 2002 to EC 2.3.3.1, modified 2014]

2.3.3.16

Accepted name:

citrate synthase (unknown stereospecificity)

Reaction:

acetyl-CoA + H₂O + oxaloacetate = citrate + CoA

Other name(s):

citrate condensing enzyme; CoA-acetylating citrate oxaloacetate-lyase; citrate synthetase; citric synthase; citric-condensing enzyme; citrogenase; condensing enzyme (ambiguous); oxaloacetate transacetase; oxalacetic transacetase

Systematic name:

acetyl-CoA:oxaloacetate C-acetyltransferase (thioester-hydrolysing)

Comments:

This entry has been included to accommodate those citrate synthases for which the stereospecificity with respect to C-2 of oxaloacetate has not been established [cf. EC 2.3.3.1, citrate (Si)-synthase and EC 2.3.3.3, citrate (Re)-synthase].

Links to other databases:

References:

1.	Lohlein-Werhahn, G., Goepfert, P. and Eggerer, H. Purification and properties of an archaebacterial enzyme: citrate synthase from Sulfolobus solfataricus. Biol. Chem. Hoppe Seyler 369 (1988) 109–113. [PMID: 3130075]
2.	Sievers, M., Stockli, M. and Teuber, M. Purification and properties of citrate synthase from Acetobacter europaeus. FEMS Microbiol. Lett. 146 (1997) 53–58. [DOI] [PMID: 8997706]
3.	Belova, L.L., Sokolov, A.P., Morgunov, I.G. and Trotsenko YuA. Purification and characterization of citrate synthase from Methylobacterium extorquens—a methylotrophic producer of polyhydroxybutyrate. Biochemistry (Mosc.) 62 (1997) 71–76. [PMID: 9113733]
4.	Lee, S., Park, C. and Yim, J. Characterization of citrate synthase purified from Drosophila melanogaster. Mol. Cells 7 (1997) 599–604. [PMID: 9387145]
5.	Maurus, R., Nguyen, N.T., Stokell, D.J., Ayed, A., Hultin, P.G., Duckworth, H.W. and Brayer, G.D. Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases. Biochemistry 42 (2003) 5555–5565. [DOI] [PMID: 12741811]

[EC 2.3.3.16 created 2014]

*EC

2.4.1.161

Accepted name:

oligosaccharide 4-α-D-glucosyltransferase

Reaction:

Transfers the non-reducing terminal α-D-glucose residue from a (1→4)-α-D-glucan to the 4-position of a free glucose or of a glucosyl residue at the non-reducing terminus of a (1→4)-α-D-glucan, thus bringing about the rearrangement of oligosaccharides

Other name(s):

amylase III; 1,4-α-glucan:1,4-α-glucan 4-α-glucosyltransferase; 1,4-α-D-glucan:1,4-α-D-glucan 4-α-D-glucosyltransferase; α-1,4-transglucosylase

Systematic name:

(1→4)-α-D-glucan:(1→4)-α-D-glucan 4-α-D-glucosyltransferase

Comments:

The enzyme acts on amylose, amylopectin, glycogen and maltooligosaccharides. No detectable free glucose is formed, indicating the enzyme does not act as a hydrolase. The enzyme from the bacterium Cellvibrio japonicus has the highest activity with maltotriose as a donor, and also accepts maltose [3], while the enzyme from amoeba does not accept maltose [1,2]. Oligosaccharides with 1→6 linkages cannot function as donors, but can act as acceptors [3]. Unlike EC 2.4.1.25, 4-α-glucanotransferase, this enzyme can transfer only a single glucosyl residue.

Links to other databases:

BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9000-92-4

References:

1.	Nebinger, P. Separation and characterization of four different amylases of Entamoeba histolytica. I. Purification and properties. Biol. Chem. Hoppe-Seyler 367 (1986) 161–167. [PMID: 2423097]
2.	Nebinger, P. Separation and characterization of four different amylases of Entamoeba histolytica. II. Characterization of amylases. Biol. Chem. Hoppe-Seyler 367 (1986) 169–176. [PMID: 2423098]
3.	Larsbrink, J., Izumi, A., Hemsworth, G.R., Davies, G.J. and Brumer, H. Structural enzymology of Cellvibrio japonicus Agd31B protein reveals α-transglucosylase activity in glycoside hydrolase family 31. J. Biol. Chem. 287 (2012) 43288–43299. [DOI] [PMID: 23132856]

[EC 2.4.1.161 created 1989, modified 2013]

*EC

2.4.1.277

Accepted name:

10-deoxymethynolide desosaminyltransferase

Reaction:

dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose + 10-deoxymethynolide = dTDP + 10-deoxymethymycin

For diagram of methymycin biosynthesis, click here and for diagram of pikromycin biosynthesis, click here

Glossary:

dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose = dTDP-D-desosamine

Other name(s):

glycosyltransferase DesVII; DesVII

Systematic name:

dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose:10-deoxymethynolide 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase

Comments:

DesVII is the glycosyltransferase responsible for the attachment of dTDP-D-desosamine to 10-deoxymethynolide or narbonolide during the biosynthesis of methymycin, neomethymycin, narbomycin, and pikromycin in the bacterium Streptomyces venezuelae. Activity requires an additional protein partner, DesVIII.

Links to other databases:

References:

1.	Borisova, S.A. and Liu, H.W. Characterization of glycosyltransferase DesVII and its auxiliary partner protein DesVIII in the methymycin/picromycin biosynthetic pathway. Biochemistry 49 (2010) 8071–8084. [DOI] [PMID: 20695498]
2.	Borisova, S.A., Kim, H.J., Pu, X. and Liu, H.W. Glycosylation of acyclic and cyclic aglycone substrates by macrolide glycosyltransferase DesVII/DesVIII: analysis and implications. ChemBioChem 9 (2008) 1554–1558. [DOI] [PMID: 18548476]
3.	Hong, J.S., Park, S.J., Parajuli, N., Park, S.R., Koh, H.S., Jung, W.S., Choi, C.Y. and Yoon, Y.J. Functional analysis of DesVIII homologues involved in glycosylation of macrolide antibiotics by interspecies complementation. Gene 386 (2007) 123–130. [DOI] [PMID: 17049185]

[EC 2.4.1.277 created 2011, modified 2014]

*EC

2.4.1.278

Accepted name:

3-α-mycarosylerythronolide B desosaminyl transferase

Reaction:

dTDP-D-desosamine + 3-α-L-mycarosylerythronolide B = dTDP + erythromycin D

For diagram of erythromycin biosynthesis, click here

Glossary:

dTDP-D-desosamine = dTDP-3,4,6-trideoxy-3-(dimethylamino)-α-D-xylo-hexopyranose
erythromycin D = (3R,4S,5S,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12-dihydroxy-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione
3-O-α-mycarosylerythronolide B = (3R,4S,5R,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-6,7,12-trihydroxy-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione

Other name(s):

EryCIII; dTDP-3-dimethylamino-4,6-dideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase

Systematic name:

dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-3,4,6-trideoxy-β-D-glucosyltransferase

Comments:

The enzyme is involved in erythromycin biosynthesis.

Links to other databases:

References:

1.	Yuan, Y., Chung, H.S., Leimkuhler, C., Walsh, C.T., Kahne, D. and Walker, S. In vitro reconstitution of EryCIII activity for the preparation of unnatural macrolides. J. Am. Chem. Soc. 127 (2005) 14128–14129. [DOI] [PMID: 16218575]
2.	Lee, H.Y., Chung, H.S., Hang, C., Khosla, C., Walsh, C.T., Kahne, D. and Walker, S. Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway. J. Am. Chem. Soc. 126 (2004) 9924–9925. [DOI] [PMID: 15303858]
3.	Moncrieffe, M.C., Fernandez, M.J., Spiteller, D., Matsumura, H., Gay, N.J., Luisi, B.F. and Leadlay, P.F. Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII. J. Mol. Biol. 415 (2012) 92–101. [DOI] [PMID: 22056329]

[EC 2.4.1.278 created 2012, modified 2014]

2.4.1.310

Accepted name:

vancomycin aglycone glucosyltransferase

Reaction:

UDP-α-D-glucose + vancomycin aglycone = UDP + devancosaminyl-vancomycin

For diagram of chloroorienticin biosynthesis, click here

Glossary:

devancosaminyl-vancomycin = vancomycin pseudoaglycone

Other name(s):

GtfB (ambiguous)

Systematic name:

UDP-α-D-glucose:vancomycin aglycone 48-O-β-glucosyltransferase

Comments:

The enzyme from the bacterium Amycolatopsis orientalis is involved in the biosynthesis of the glycopeptide antibiotic chloroeremomycin.

Links to other databases:

References:

1.	Losey, H.C., Peczuh, M.W., Chen, Z., Eggert, U.S., Dong, S.D., Pelczer, I., Kahne, D. and Walsh, C.T. Tandem action of glycosyltransferases in the maturation of vancomycin and teicoplanin aglycones: novel glycopeptides. Biochemistry 40 (2001) 4745–4755. [DOI] [PMID: 11294642]
2.	Mulichak, A.M., Losey, H.C., Walsh, C.T. and Garavito, R.M. Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics. Structure 9 (2001) 547–557. [DOI] [PMID: 11470430]

[EC 2.4.1.310 created 2013]

2.4.1.311

Accepted name:

chloroorienticin B synthase

Reaction:

dTDP-β-L-4-epi-vancosamine + desvancosaminyl-vancomycin = dTDP + chloroorienticin B

For diagram of chloroorienticin biosynthesis, click here

Glossary:

dTDP-β-L-4-epi-vancosamine = dTDP-3-amino-2,3,6-trideoxy-3-methyl-β-L-arabino-hexopyranose
desvancosaminyl-vancomycin = vanomycin pseudoaglycone

Other name(s):

GtfA

Systematic name:

dTDP-L-4-epi-vancosamine:desvancosaminyl-vancomycin vancosaminyltransferase

Comments:

The enzyme from the bacterium Amycolatopsis orientalis is involved in the biosynthesis of the glycopeptide antibiotic chloroeremomycin.

Links to other databases:

References:

1.	Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T. and Garavito, R.M. Structure of the TDP-epi-vancosaminyltransferase GtfA from the chloroeremomycin biosynthetic pathway. Proc. Natl. Acad. Sci. USA 100 (2003) 9238–9243. [DOI] [PMID: 12874381]
2.	Lu, W., Oberthur, M., Leimkuhler, C., Tao, J., Kahne, D. and Walsh, C.T. Characterization of a regiospecific epivancosaminyl transferase GtfA and enzymatic reconstitution of the antibiotic chloroeremomycin. Proc. Natl. Acad. Sci. USA 101 (2004) 4390–4395. [DOI] [PMID: 15070728]

[EC 2.4.1.311 created 2013]

2.4.1.312

Accepted name:

protein O-mannose β-1,4-N-acetylglucosaminyltransferase

Reaction:

UDP-N-acetyl-α-D-glucosamine + 3-O-(α-D-mannosyl)-L-threonyl-[protein] = UDP + 3-O-[N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl-[protein]

For diagram of glycoprotein biosynthesis, click here

Other name(s):

GTDC2 (gene name); POMGNT2

Systematic name:

UDP-N-acetyl-α-D-glucosamine:α-D-mannosyl-threonyl-[protein] 4-β-N-acetyl-D-glucosaminyltransferase

Comments:

The human protein is involved in the formation of a phosphorylated trisaccharide on a threonine residue of α-dystroglycan, an extracellular peripheral glycoprotein that acts as a receptor for extracellular matrix proteins containing laminin-G domains.

Links to other databases:

References:

1.	Yoshida-Moriguchi, T., Willer, T., Anderson, M.E., Venzke, D., Whyte, T., Muntoni, F., Lee, H., Nelson, S.F., Yu, L. and Campbell, K.P. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science 341 (2013) 896–899. [DOI] [PMID: 23929950]

[EC 2.4.1.312 created 2013]

2.4.1.313

Accepted name:

protein O-mannose β-1,3-N-acetylgalactosaminyltransferase

Reaction:

UDP-N-acetyl-α-D-galactosamine + 3-O-[N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl-[protein] = UDP + 3-O-[N-acetyl-β-D-galactosaminyl-(1→3)-N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl]-L-threonyl-[protein]

For diagram of glycoprotein biosynthesis, click here

Other name(s):

B3GALNT2

Systematic name:

UDP-N-acetyl-α-D-galactosamine:N-acetyl-β-D-glucosaminyl-(1→4)-α-D-mannosyl-threonyl-[protein] 3-β-N-acetyl-D-galactosaminyltransferase

Comments:

The human protein is specific for UDP-N-acetyl-α-D-galactosamine as donor [1]. The enzyme is involved in the formation of a phosphorylated trisaccharide on a threonine residue of α-dystroglycan, an extracellular peripheral glycoprotein that acts as a receptor for extracellular matrix proteins containing laminin-G domains.

Links to other databases:

References:

1.	Hiruma, T., Togayachi, A., Okamura, K., Sato, T., Kikuchi, N., Kwon, Y.D., Nakamura, A., Fujimura, K., Gotoh, M., Tachibana, K., Ishizuka, Y., Noce, T., Nakanishi, H. and Narimatsu, H. A novel human β1,3-N-acetylgalactosaminyltransferase that synthesizes a unique carbohydrate structure, GalNAcβ1-3GlcNAc. J. Biol. Chem. 279 (2004) 14087–14095. [DOI] [PMID: 14724282]
2.	Yoshida-Moriguchi, T., Willer, T., Anderson, M.E., Venzke, D., Whyte, T., Muntoni, F., Lee, H., Nelson, S.F., Yu, L. and Campbell, K.P. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. Science 341 (2013) 896–899. [DOI] [PMID: 23929950]

[EC 2.4.1.313 created 2013]

2.4.1.314

Accepted name:

ginsenoside Rd glucosyltransferase

Reaction:

UDP-α-D-glucose + ginsenoside Rd = UDP + ginsenoside Rb1

For diagram of protopanaxadiol ginsenosides ginsenosidases, click here

Glossary:

ginsenoside Rd = 20-(β-D-glucopyranosyl)oxy-3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol

Other name(s):

UDPG:ginsenoside Rd glucosyltransferase; UDP-glucose:ginsenoside Rd glucosyltransferase; UGRdGT

Systematic name:

UDP-glucose:ginsenoside-Rd β-1,6-glucosyltransferase

Comments:

The glucosyl group forms a 1→6 bond to the glucosyloxy moiety at C-20 of ginsenoside Rd. Isolated from sanchi ginseng (Panax notoginseng).

Links to other databases:

References:

1.	Yue, C.-J. and Zhong J.-J. Purification and characterization of UDPG:ginsenoside Rd glucosyltransferase from suspended cells of Panax notoginseng. Process Biochem. 40 (2005) 3742–3748.

[EC 2.4.1.314 created 2013]

2.4.1.315

Accepted name:

diglucosyl diacylglycerol synthase (1,6-linking)

Reaction:

(1) UDP-α-D-glucose + 1,2-diacyl-3-O-(β-D-glucopyranosyl)-sn-glycerol = 1,2-diacyl-3-O-[β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl]-sn-glycerol + UDP
(2) UDP-α-D-glucose + 1,2-diacyl-3-O-[β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl]-sn-glycerol = 1,2-diacyl-3-O-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl]-sn-glycerol + UDP

Other name(s):

monoglucosyl diacylglycerol (1→6) glucosyltransferase; MGlcDAG (1→6) glucosyltransferase; DGlcDAG synthase (ambiguous); UGT106B1; ypfP (gene name)

Systematic name:

UDP-α-D-glucose:1,2-diacyl-3-O-(β-D-glucopyranosyl)-sn-glycerol 6-glucosyltransferase

Comments:

The enzyme is found in several bacterial species. The enzyme from Bacillus subtilis is specific for glucose [1]. The enzyme from Mycoplasma genitalium can incoporate galactose with similar efficiency, but forms mainly 1,2-diacyl-diglucopyranosyl-sn-glycerol in vivo [3]. The enzyme from Staphylococcus aureus can also form glucosyl-glycero-3-phospho-(1′-sn-glycerol) [2].

Links to other databases:

References:

1.	Jorasch, P., Wolter, F.P., Zahringer, U. and Heinz, E. A UDP glucosyltransferase from Bacillus subtilis successively transfers up to four glucose residues to 1,2-diacylglycerol: expression of ypfP in Escherichia coli and structural analysis of its reaction products. Mol. Microbiol. 29 (1998) 419–430. [DOI] [PMID: 9720862]
2.	Jorasch, P., Warnecke, D.C., Lindner, B., Zahringer, U. and Heinz, E. Novel processive and nonprocessive glycosyltransferases from Staphylococcus aureus and Arabidopsis thaliana synthesize glycoglycerolipids, glycophospholipids, glycosphingolipids and glycosylsterols. Eur. J. Biochem. 267 (2000) 3770–3783. [DOI] [PMID: 10848996]
3.	Andres, E., Martinez, N. and Planas, A. Expression and characterization of a Mycoplasma genitalium glycosyltransferase in membrane glycolipid biosynthesis: potential target against mycoplasma infections. J. Biol. Chem. 286 (2011) 35367–35379. [DOI] [PMID: 21835921]

[EC 2.4.1.315 created 2014]

2.4.1.316

Accepted name:

tylactone mycaminosyltransferase

Reaction:

tylactone + dTDP-α-D-mycaminose = dTDP + 5-O-β-D-mycaminosyltylactone

For diagram of tylactone biosynthesis, click here

Glossary:

tylactone = (4R,5S,6S,7S,9R,11E,13E,15S,16R)-7,16-diethyl-4,6-dihydroxy-5,9,13,15-tetramethyloxacyclohexadeca-11,13-diene-2,10-dione
dTDP-α-D-mycaminose = dTDP-3,6-dideoxy-3-dimethylamino-α-D-glucopyranose

Other name(s):

tylM2 (gene name)

Systematic name:

dTDP-α-D-mycaminose:tylactone 5-O-β-D-mycaminosyltransferase

Comments:

The enzyme participates in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria. Activity is significantly enhanced by the presence of an accessory protein encoded by the tylM3 gene.

Links to other databases:

References:

1.	Gandecha, A.R., Large, S.L. and Cundliffe, E. Analysis of four tylosin biosynthetic genes from the tylLM region of the Streptomyces fradiae genome. Gene 184 (1997) 197–203. [DOI] [PMID: 9031628]
2.	Melancon, C.E., 3rd, Takahashi, H. and Liu, H.W. Characterization of tylM3/tylM2 and mydC/mycB pairs required for efficient glycosyltransfer in macrolide antibiotic biosynthesis. J. Am. Chem. Soc. 126 (2004) 16726–16727. [DOI] [PMID: 15612702]

[EC 2.4.1.316 created 2014]

2.4.1.317

Accepted name:

O-mycaminosyltylonolide 6-deoxyallosyltransferase

Reaction:

5-O-β-D-mycaminosyltylonolide + dTDP-6-deoxy-α-D-allose = dTDP + demethyllactenocin

For diagram of tylosin biosynthesis, click here

Glossary:

mycaminose = 3,6-dideoxy-3-dimethylamino-glucopyranose
tylonolide = 2-[(4R,5S,6S,7R,9R,11E,13E,15R,16R)-16-ethyl-4,6-dihydroxy-15-(hydroxymethyl)-5,9,13-trimethyl-2,10-dioxooxacyclohexadeca-11,13-dien-7-yl]acetaldehyde
demethyllactenocin = [(2R,3R,4E,6E,9R,11R,12S,13S,14R)-12-{[3,6-dideoxy-3-(dimethylamino)-D-glucopyranosyl]oxy}-2-ethyl-14-hydroxy-5,9,13-trimethyl-8,16-dioxo-11-(2-oxoethyl)oxacyclohexadeca-4,6-dien-3-yl]methyl 6-deoxy-β-D-allopyranoside

Other name(s):

tylN (gene name)

Systematic name:

dTDP-6-deoxy-α-D-allose:5-O-β-D-mycaminosyltylonolide 23-O-6-deoxy-α-D-allosyltransferase

Comments:

The enzyme participates in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria.

Links to other databases:

References:

1.	Wilson, V.T. and Cundliffe, E. Characterization and targeted disruption of a glycosyltransferase gene in the tylosin producer, Streptomyces fradiae. Gene 214 (1998) 95–100. [DOI] [PMID: 9651492]

[EC 2.4.1.317 created 2014]

2.4.1.318

Accepted name:

demethyllactenocin mycarosyltransferase

Reaction:

dTDP-β-L-mycarose + demethyllactenocin = dTDP + demethylmacrocin

For diagram of tylosin biosynthesis, click here

Glossary:

dTDP-β-L-mycarose = dTDP-2,6-dideoxy-3-C-methyl-β-L-ribo-hexose
demethyllactenocin = [(2R,3R,4E,6E,9R,11R,12S,13S,14R)-12-{[3,6-dideoxy-3-(dimethylamino)-D-glucopyranosyl]oxy}-2-ethyl-14-hydroxy-5,9,13-trimethyl-8,16-dioxo-11-(2-oxoethyl)oxacyclohexadeca-4,6-dien-3-yl]methyl 6-deoxy-D-allopyranoside

Other name(s):

tylCV (gene name); tylC5 (gene name)

Systematic name:

dTDP-β-L-mycarose:demethyllactenocin 4′-O-α-L-mycarosyltransferase

Comments:

The enzyme participates in the biosynthetic pathway of the macrolide antibiotic tylosin, which is produced by several species of Streptomyces bacteria.

Links to other databases:

References:

1.	Bate, N., Butler, A.R., Smith, I.P. and Cundliffe, E. The mycarose-biosynthetic genes of Streptomyces fradiae, producer of tylosin. Microbiology 146 (2000) 139–146. [DOI] [PMID: 10658660]

[EC 2.4.1.318 created 2014]

2.4.1.319

Accepted name:

β-1,4-mannooligosaccharide phosphorylase

Reaction:

[(1→4)-β-D-mannosyl]_n + phosphate = [(1→4)-β-D-mannosyl]_n-1 + α-D-mannose 1-phosphate

Other name(s):

RaMP2

Systematic name:

1,4-β-D-mannooligosaccharide:phosphate α-D-mannosyltransferase

Comments:

The enzyme, isolated from the ruminal bacterium Ruminococcus albus, catalyses the reversible phosphorolysis of β-1,4-mannooligosaccharide with a minimum size of three monomers.

Links to other databases:

References:

Kawahara, R., Saburi, W., Odaka, R., Taguchi, H., Ito, S., Mori, H. and Matsui, H. Metabolic mechanism of mannan in a ruminal bacterium, Ruminococcus albus, involving two mannoside phosphorylases and cellobiose 2-epimerase: discovery of a new carbohydrate phosphorylase, β-1,4-mannooligosaccharide phosphorylase. J. Biol. Chem. 287 (2012) 42389–42399. [DOI] [PMID: 23093406]

[EC 2.4.1.319 created 2014]

2.4.1.320

Accepted name:

1,4-β-mannosyl-N-acetylglucosamine phosphorylase

Reaction:

4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine + phosphate = N-acetyl-D-glucosamine + α-D-mannose 1-phosphate

Other name(s):

BT1033

Systematic name:

4-O-β-D-mannopyranosyl-N-acetyl-D-glucosamine:phosphate α-D-mannosyltransferase

Comments:

The enzyme isolated from the anaerobic bacterium Bacteroides thetaiotaomicron is involved in the degradation of host-derived N-glycans.

Links to other databases:

References:

1.	Nihira, T., Suzuki, E., Kitaoka, M., Nishimoto, M., Ohtsubo, K. and Nakai, H. Discovery of β-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans. J. Biol. Chem. 288 (2013) 27366–27374. [DOI] [PMID: 23943617]

[EC 2.4.1.320 created 2014]

2.4.1.321

Accepted name:

cellobionic acid phosphorylase

Reaction:

4-O-β-D-glucopyranosyl-D-gluconate + phosphate = α-D-glucose 1-phosphate + D-gluconate

Glossary:

4-O-β-D-glucopyranosyl-D-gluconate = cellobionate

Systematic name:

4-O-β-D-glucopyranosyl-D-gluconate:phosphate α-D-glucosyltransferase

Comments:

The enzyme occurs in cellulolytic bacteria and fungi. It catalyses the reversible phosphorolysis of cellobionic acid. In the synthetic direction it produces 4-O-β-D-glucopyranosyl-D-glucuronate from α-D-glucose 1-phosphate and D-glucuronate with low activity.

Links to other databases:

References:

1.	Nihira, T., Saito, Y., Nishimoto, M., Kitaoka, M., Igarashi, K., Ohtsubo, K. and Nakai, H. Discovery of cellobionic acid phosphorylase in cellulolytic bacteria and fungi. FEBS Lett. 587 (2013) 3556–3561. [DOI] [PMID: 24055472]

[EC 2.4.1.321 created 2014]

2.4.1.322

Accepted name:

devancosaminyl-vancomycin vancosaminetransferase

Reaction:

dTDP-β-L-vancosamine + devancosaminyl-vancomycin = dTDP + vancomycin

For diagram of chloroorienticin biosynthesis, click here

Glossary:

dTDP-β-L-vancosamine = dTDP-3-amino-2,3,6-trideoxy-3-C-methyl-β-L-lyxo-hexopyranose

Other name(s):

devancosaminyl-vancomycin TDP-vancosaminyltransferase; GtfD; dTDP-β-L-vancomycin:desvancosaminyl-vancomycin β-L-vancosaminetransferase; desvancosaminyl-vancomycin vancosaminetransferase

Systematic name:

dTDP-β-L-vancomycin:devancosaminyl-vancomycin β-L-vancosaminetransferase

Comments:

The enzyme, isolated from the bacterium Amycolatopsis orientalis, catalyses the ultimate step in the biosynthesis of the antibiotic vancomycin.

Links to other databases:

References:

1.	Losey, H.C., Peczuh, M.W., Chen, Z., Eggert, U.S., Dong, S.D., Pelczer, I., Kahne, D. and Walsh, C.T. Tandem action of glycosyltransferases in the maturation of vancomycin and teicoplanin aglycones: novel glycopeptides. Biochemistry 40 (2001) 4745–4755. [DOI] [PMID: 11294642]
2.	Mulichak, A.M., Lu, W., Losey, H.C., Walsh, C.T. and Garavito, R.M. Crystal structure of vancosaminyltransferase GtfD from the vancomycin biosynthetic pathway: interactions with acceptor and nucleotide ligands. Biochemistry 43 (2004) 5170–5180. [DOI] [PMID: 15122882]

[EC 2.4.1.322 created 2014]

2.4.1.323

Accepted name:

7-deoxyloganetic acid glucosyltransferase

Reaction:

UDP-α-D-glucose + 7-deoxyloganetate = UDP + 7-deoxyloganate

For diagram of secologanin biosynthesis, click here

Other name(s):

UGT8

Systematic name:

UDP-α-D-glucose:7-deoxyloganetate O-D-glucosyltransferase

Comments:

Isolated from the plant Catharanthus roseus (Madagascar periwinkle). Involved in loganin and secologanin biosynthesis. Does not react with 7-deoxyloganetin. cf. EC 2.4.1.324 7-deoxyloganetin glucosyltransferase.

Links to other databases:

References:

1.	Asada, K., Salim, V., Masada-Atsumi, S., Edmunds, E., Nagatoshi, M., Terasaka, K., Mizukami, H. and De Luca, V. A 7-deoxyloganetic acid glucosyltransferase contributes a key step in secologanin biosynthesis in madagascar periwinkle. Plant Cell 25 (2013) 4123–4134. [DOI] [PMID: 24104568]

[EC 2.4.1.323 created 2014]

2.4.1.324

Accepted name:

7-deoxyloganetin glucosyltransferase

Reaction:

UDP-α-D-glucose + 7-deoxyloganetin = UDP + 7-deoxyloganin

For diagram of secologanin biosynthesis, click here

Other name(s):

UDPglucose:iridoid glucosyltransferase; UGT6; UGT85A24

Systematic name:

UDP-α-D-glucose:7-deoxyloganetin O-D-glucosyltransferase

Comments:

Isolated from the plants Catharanthus roseus (Madagascar periwinkle) and Gardenia jasminoides (cape jasmine). With Gardenia it also acts on genipin. Involved in loganin and secologanin biosynthesis. Does not react with 7-deoxyloganetate. cf. EC 2.4.1.323 7-deoxyloganetic acid glucosyltransferase.

Links to other databases:

References:

1.	Nagatoshi, M., Terasaka, K., Nagatsu, A. and Mizukami, H. Iridoid-specific glucosyltransferase from Gardenia jasminoides. J. Biol. Chem. 286 (2011) 32866–32874. [DOI] [PMID: 21799001]
2.	Asada, K., Salim, V., Masada-Atsumi, S., Edmunds, E., Nagatoshi, M., Terasaka, K., Mizukami, H. and De Luca, V. A 7-deoxyloganetic acid glucosyltransferase contributes a key step in secologanin biosynthesis in madagascar periwinkle. Plant Cell 25 (2013) 4123–4134. [DOI] [PMID: 24104568]

[EC 2.4.1.324 created 2014]

*EC

2.4.2.35

Accepted name:

flavonol-3-O-glycoside xylosyltransferase

Reaction:

UDP-α-D-xylose + a flavonol 3-O-glycoside = UDP + a flavonol 3-[β-D-xylosyl-(1→2)-β-D-glycoside]

For diagram of quercetin 3-o-glycoside derivatives biosynthesis, click here

Other name(s):

UDP-D-xylose:flavonol-3-O-glycoside 2′′-O-β-D-xylosyltransferase

Systematic name:

UDP-α-D-xylose:flavonol-3-O-glycoside 2′′-O-β-D-xylosyltransferase

Comments:

Flavonol 3-O-glucoside, flavonol 3-O-galactoside and, more slowly, rutin, can act as acceptors.

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 83380-90-9

References:

Kleinehollenhorst, G., Behrens, H., Pegels, G., Srunk, N. and Wiermann, R. Formation of flavonol 3-O-diglycosides and flavonol 3-O-triglycosides by enzyme extracts from anthers of Tulipa cv apeldoorn - characterization and activity of 3 different O-glycosyltransferases during anther development. Z. Natursforsch. C: Biosci. 37 (1982) 587–599.

[EC 2.4.2.35 created 1986, modified 2014]

2.4.2.55

Accepted name:

nicotinate D-ribonucleotide:phenol phospho-D-ribosyltransferase

Reaction:

nicotinate D-ribonucleotide + phenol = nicotinate + phenyl 5-phospho-α-D-ribofuranoside

Other name(s):

ArsAB

Systematic name:

nicotinate D-ribonucleotide:phenol phospho-D-ribosyltransferase

Comments:

The enzyme is involved in the biosynthesis of phenolic cobamides in the Gram-positive bacterium Sporomusa ovata. It can also transfer the phospho-D-ribosyl group to 4-methylphenol and 5,6-dimethylbenzimidazole. The related EC 2.4.2.21, nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase, also transfers the phospho-D-ribosyl group from nicotinate D-ribonucleotide to 5,6-dimethylbenzimidazole, but shows no activity with 4-methylphenol or phenol.

Links to other databases:

References:

1.	Chan, C.H. and Escalante-Semerena, J.C. ArsAB, a novel enzyme from Sporomusa ovata activates phenolic bases for adenosylcobamide biosynthesis. Mol. Microbiol. 81 (2011) 952–967. [DOI] [PMID: 21696461]

[EC 2.4.2.55 created 2013]

2.4.2.56

Accepted name:

kaempferol 3-O-xylosyltransferase

Reaction:

UDP-α-D-xylose + kaempferol = UDP + kaempferol 3-O-β-D-xyloside

For diagram of kaempferol biosynthesis, click here

Other name(s):

F3XT; UDP-D-xylose:flavonol 3-O-xylosyltransferase; flavonol 3-O-xylosyltransferase

Systematic name:

UDP-α-D-xylose:kaempferol 3-O-D-xylosyltransferase

Comments:

The enzyme from the plant Euonymus alatus also catalyses the 3-O-D-xylosylation of other flavonols (e.g. quercetin, isorhamnetin, rhamnetin, myricetin, fisetin) with lower activity.

Links to other databases:

References:

1.	Ishikura, N. and Yang, Z.Q. UDP-D-xylose: flavonol 3-O-xylosyltransferase from young leaves of Euonymus alatus f. ciliato-dentatus. Z. Naturforsch. C: Biosci. 46 (1991) 1003–1010.

[EC 2.4.2.56 created 2013]

2.4.2.57

Accepted name:

AMP phosphorylase

Reaction:

(1) AMP + phosphate = adenine + α-D-ribose 1,5-bisphosphate
(2) CMP + phosphate = cytosine + α-D-ribose 1,5-bisphosphate
(3) UMP + phosphate = uracil + α-D-ribose 1,5-bisphosphate

For diagram of AMP catabolism, click here

Other name(s):

AMPpase; nucleoside monophosphate phosphorylase; deoA (gene name)

Systematic name:

AMP:phosphate α-D-ribosyl 5′-phosphate-transferase

Comments:

The enzyme from archaea is involved in AMP metabolism and CO₂ fixation through type III RubisCO enzymes. The activity with CMP and UMP requires activation by cAMP [2].

Links to other databases:

References:

1.	Sato, T., Atomi, H. and Imanaka, T. Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315 (2007) 1003–1006. [DOI] [PMID: 17303759]
2.	Aono, R., Sato, T., Yano, A., Yoshida, S., Nishitani, Y., Miki, K., Imanaka, T. and Atomi, H. Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J. Bacteriol. 194 (2012) 6847–6855. [DOI] [PMID: 23065974]
3.	Nishitani, Y., Aono, R., Nakamura, A., Sato, T., Atomi, H., Imanaka, T. and Miki, K. Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization. J. Mol. Biol. 425 (2013) 2709–2721. [DOI] [PMID: 23659790]

[EC 2.4.2.57 created 2014]

2.4.99.20

Accepted name:

2′-phospho-ADP-ribosyl cyclase/2′-phospho-cyclic-ADP-ribose transferase

Reaction:

NADP⁺ + nicotinate = nicotinate-adenine dinucleotide phosphate + nicotinamide (overall reaction)
(1a) NADP⁺ = 2′-phospho-cyclic ADP-ribose + nicotinamide
(1b) 2′-phospho-cyclic ADP-ribose + nicotinate = nicotinate-adenine dinucleotide phosphate

For diagram of cyclic ADP-ribose biosynthesis, click here

Glossary:

2′-phospho-cyclic ADP-ribose = cADPRP
nicotinic acid-adenine dinucleotide phosphate = NAADP⁺

Other name(s):

diphosphopyridine nucleosidase (ambiguous); CD38 (gene name); BST1 (gene name)

Systematic name:

NADP⁺:nicotinate ADP-ribosyltransferase

Comments:

This multiunctional enzyme catalyses both the removal of nicotinamide from NADP⁺, forming 2′-phospho-cyclic ADP-ribose, and the addition of nicotinate to the cyclic product, forming NAADP⁺, a calcium messenger that can mobilize intracellular Ca²⁺ stores and activate Ca²⁺ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 3.2.2.6, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.

Links to other databases:

References:

1.	Chini, E.N., Chini, C.C., Kato, I., Takasawa, S. and Okamoto, H. CD38 is the major enzyme responsible for synthesis of nicotinic acid-adenine dinucleotide phosphate in mammalian tissues. Biochem. J. 362 (2002) 125–130. [PMID: 11829748]
2.	Moreschi, I., Bruzzone, S., Melone, L., De Flora, A. and Zocchi, E. NAADP⁺ synthesis from cADPRP and nicotinic acid by ADP-ribosyl cyclases. Biochem. Biophys. Res. Commun. 345 (2006) 573–580. [DOI] [PMID: 16690024]

[EC 2.4.99.20 created 2014]

2.5.1.112

Accepted name:

adenylate dimethylallyltransferase (ADP/ATP-dependent)

Reaction:

(1) prenyl diphosphate + ADP = diphosphate + N⁶-prenyladenosine 5′-diphosphate
(2) prenyl diphosphate + ATP = diphosphate + N⁶-prenyladenosine 5′-triphosphate

For diagram of N⁶-(Dimethylallyl)adenosine phosphates biosynthesis, click here

Other name(s):

cytokinin synthase (ambiguous); isopentenyltransferase (ambiguous); 2-isopentenyl-diphosphate:ADP/ATP Δ²-isopentenyltransferase; adenylate isopentenyltransferase (ambiguous); dimethylallyl diphosphate:ATP/ADP isopentenyltransferase: IPT; dimethylallyl-diphosphate:ADP/ATP dimethylallyltransferase

Systematic name:

prenyl-diphosphate:ADP/ATP prenyltransferase

Comments:

Involved in the biosynthesis of cytokinins in plants. The IPT4 isoform from the plant Arabidopsis thaliana is specific for ADP and ATP [1]. Other isoforms, such as IPT1 from Arabidopsis thaliana [1,2] and the enzyme from the common hop, Humulus lupulus [3], also have a lower activity with AMP (cf. EC 2.5.1.27, adenylate dimethylallyltransferase).

Links to other databases:

References:

1.	Kakimoto, T. Identification of plant cytokinin biosynthetic enzymes as dimethylallyl diphosphate:ATP/ADP isopentenyltransferases. Plant Cell Physiol. 42 (2001) 677–685. [PMID: 11479373]
2.	Takei, K., Sakakibara, H. and Sugiyama, T. Identification of genes encoding adenylate isopentenyltransferase, a cytokinin biosynthesis enzyme, in Arabidopsis thaliana. J. Biol. Chem. 276 (2001) 26405–26410. [DOI] [PMID: 11313355]
3.	Sakano, Y., Okada, Y., Matsunaga, A., Suwama, T., Kaneko, T., Ito, K., Noguchi, H. and Abe, I. Molecular cloning, expression, and characterization of adenylate isopentenyltransferase from hop (Humulus lupulus L.). Phytochemistry 65 (2004) 2439–2446. [DOI] [PMID: 15381407]

[EC 2.5.1.112 created 2013]

2.5.1.113

Accepted name:

[CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase

Reaction:

O-phospho-L-serine + [CysO sulfur-carrier protein]-Gly-NH-CH₂-C(O)SH = [CysO sulfur-carrier protein]-Gly-NH-CH₂-C(O)-S-L-cysteine + phosphate

Other name(s):

CysM

Systematic name:

O-phospho-L-serine:thiocarboxylated [CysO sulfur-carrier protein] 2-amino-2-carboxyethyltransferase

Comments:

A pyridoxal-phosphate protein. The enzyme participates in an alternative pathway for L-cysteine biosynthesis that involves a protein-bound thiocarboxylate as the sulfide donor. The enzyme from the bacterium Mycobacterium tuberculosis also has very low activity with O³-acetyl-L-serine (cf. EC 2.5.1.65, O-phosphoserine sulfhydrylase).

Links to other databases:

References:

1.	O'Leary, S.E., Jurgenson, C.T., Ealick, S.E. and Begley, T.P. O-Phospho-L-serine and the thiocarboxylated sulfur carrier protein CysO-COSH are substrates for CysM, a cysteine synthase from Mycobacterium tuberculosis. Biochemistry 47 (2008) 11606–11615. [DOI] [PMID: 18842002]
2.	Jurgenson, C.T., Burns, K.E., Begley, T.P. and Ealick, S.E. Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis. Biochemistry 47 (2008) 10354–10364. [DOI] [PMID: 18771296]
3.	Ågren, D., Schnell, R., Oehlmann, W., Singh, M. and Schneider, G. Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria. J. Biol. Chem. 283 (2008) 31567–31574. [DOI] [PMID: 18799456]
4.	Ågren, D., Schnell, R. and Schneider, G. The C-terminal of CysM from Mycobacterium tuberculosis protects the aminoacrylate intermediate and is involved in sulfur donor selectivity. FEBS Lett. 583 (2009) 330–336. [DOI] [PMID: 19101553]

[EC 2.5.1.113 created 2013]

2.5.1.114

Accepted name:

tRNA^Phe (4-demethylwyosine³⁷-C7) aminocarboxypropyltransferase

Reaction:

S-adenosyl-L-methionine + 4-demethylwyosine³⁷ in tRNA^Phe = S-methyl-5′-thioadenosine + 7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine³⁷ in tRNA^Phe

For diagram of wyosine biosynthesis, click here

Glossary:

4-demethylwyosine = imG-14 = 6-methyl-3-(β-D-ribofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine = yW-89

Other name(s):

TYW2; tRNA-yW synthesizing enzyme-2; TRM12 (gene name); taw2 (gene name)

Systematic name:

S-adenosyl-L-methionine:tRNA^Phe (4-demethylwyosine³⁷-C7)-[(3S)-3-amino-3-carboxypropyl]transferase

Comments:

The enzyme, which is found in all eukaryotes and in the majority of Euryarchaeota (but not in the Crenarchaeota), is involved in the hypermodification of the guanine nucleoside at position 37 of tRNA leading to formation of assorted wye bases. This modification is essential for translational reading-frame maintenance. The eukaryotic enzyme is involved in biosynthesis of the tricyclic base wybutosine, which is found only in tRNA^Phe.

Links to other databases:

References:

1.	Umitsu, M., Nishimasu, H., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc. Natl. Acad. Sci. USA 106 (2009) 15616–15621. [DOI] [PMID: 19717466]
2.	Rodriguez, V., Vasudevan, S., Noma, A., Carlson, B.A., Green, J.E., Suzuki, T. and Chandrasekharappa, S.C. Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PLoS One 7:e39297 (2012). [DOI] [PMID: 22761755]
3.	de Crecy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J. and Grosjean, H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol. Biol. Evol. 27 (2010) 2062–2077. [DOI] [PMID: 20382657]

[EC 2.5.1.114 created 2013]

2.5.1.115

Accepted name:

homogentisate phytyltransferase

Reaction:

phytyl diphosphate + homogentisate = diphosphate + 2-methyl-6-phytylbenzene-1,4-diol + CO₂

For diagram of the homogentisate pathways, click here

Glossary:

2-methyl-6-phytylbenzene-1,4-diol = MPBQ

Other name(s):

HPT; VTE2 (gene name)

Systematic name:

phytyl-diphosphate:homogentisate phytyltransferase

Comments:

Requires Mg²⁺ for activity [3]. Involved in the biosynthesis of the vitamin E tocopherols. While the enzyme from the cyanobacterium Synechocystis PCC 6803 has an appreciable activity with geranylgeranyl diphosphate (EC 2.5.1.116, homogentisate geranylgeranyltransferase), the enzyme from the plant Arabidopsis thaliana has only a low activity with that substrate [1,3,4].

Links to other databases:

References:

1.	Collakova, E. and DellaPenna, D. Isolation and functional analysis of homogentisate phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 127 (2001) 1113–1124. [PMID: 11706191]
2.	Savidge, B., Weiss, J.D., Wong, Y.H., Lassner, M.W., Mitsky, T.A., Shewmaker, C.K., Post-Beittenmiller, D. and Valentin, H.E. Isolation and characterization of homogentisate phytyltransferase genes from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 129 (2002) 321–332. [DOI] [PMID: 12011362]
3.	Sadre, R., Gruber, J. and Frentzen, M. Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis. FEBS Lett. 580 (2006) 5357–5362. [DOI] [PMID: 16989822]
4.	Yang, W., Cahoon, R.E., Hunter, S.C., Zhang, C., Han, J., Borgschulte, T. and Cahoon, E.B. Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase. Plant J. 65 (2011) 206–217. [DOI] [PMID: 21223386]

[EC 2.5.1.115 created 2014]

2.5.1.116

Accepted name:

homogentisate geranylgeranyltransferase

Reaction:

geranylgeranyl diphosphate + homogentisate = diphosphate + 6-geranylgeranyl-2-methylbenzene-1,4-diol + CO₂

For diagram of the homogentisate pathways, click here

Glossary:

6-geranylgeranyl-2-methylbenzene-1,4-diol = MGGBQ

Other name(s):

HGGT; slr1736 (gene name)

Systematic name:

geranylgeranyl-diphosphate:homogentisate geranylgeranyltransferase

Comments:

Requires Mg²⁺ for activity. Involved in the biosynthesis of the vitamin E, tocotrienols. While the enzyme from the bacterium Synechocystis PCC 6803 has higher activity with phytyl diphosphate (EC 2.5.1.115, homogentisate phytyltransferase), the enzymes from barley, rice and wheat have only a low activity with that substrate [2].

Links to other databases:

References:

1.	Collakova, E. and DellaPenna, D. Isolation and functional analysis of homogentisate phytyltransferase from Synechocystis sp. PCC 6803 and Arabidopsis. Plant Physiol. 127 (2001) 1113–1124. [PMID: 11706191]
2.	Cahoon, E.B., Hall, S.E., Ripp, K.G., Ganzke, T.S., Hitz, W.D. and Coughlan, S.J. Metabolic redesign of vitamin E biosynthesis in plants for tocotrienol production and increased antioxidant content. Nat. Biotechnol. 21 (2003) 1082–1087. [DOI] [PMID: 12897790]
3.	Yang, W., Cahoon, R.E., Hunter, S.C., Zhang, C., Han, J., Borgschulte, T. and Cahoon, E.B. Vitamin E biosynthesis: functional characterization of the monocot homogentisate geranylgeranyl transferase. Plant J. 65 (2011) 206–217. [DOI] [PMID: 21223386]

[EC 2.5.1.116 created 2014]

2.5.1.117

Accepted name:

homogentisate solanesyltransferase

Reaction:

all-trans-nonaprenyl diphosphate + homogentisate = diphosphate + 2-methyl-6-all-trans-nonaprenylbenzene-1,4-diol + CO₂

For diagram of the homogentisate pathways, click here

Glossary:

2-methyl-6-all-trans-nonaprenylbenzene-1,4-diol = 2-methyl-6-solanesylbenzene-1,4-diol = MSBQ

Other name(s):

HST; PDS2 (gene name)

Systematic name:

all-trans-nonaprenyl-diphosphate:homogentisate nonaprenyltransferase

Comments:

Requires Mg²⁺ for activity. Part of the biosynthesis pathway of plastoquinol-9. The enzymes purified from the plant Arabidopsis thaliana and the alga Chlamydomonas reinhardtii are also active in vitro with unsaturated C₁₀ to C₂₀ prenyl diphosphates, producing main products that are not decarboxylated [2].

Links to other databases:

References:

1.	Sadre, R., Gruber, J. and Frentzen, M. Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis. FEBS Lett. 580 (2006) 5357–5362. [DOI] [PMID: 16989822]
2.	Sadre, R., Frentzen, M., Saeed, M. and Hawkes, T. Catalytic reactions of the homogentisate prenyl transferase involved in plastoquinone-9 biosynthesis. J. Biol. Chem. 285 (2010) 18191–18198. [DOI] [PMID: 20400515]

[EC 2.5.1.117 created 2014]

2.5.1.118

Accepted name:

β-(isoxazolin-5-on-2-yl)-L-alanine synthase

Reaction:

O-acetyl-L-serine + isoxazolin-5-one = 3-(5-oxoisoxazolin-2-yl)-L-alanine + acetate

For diagram of O³-Acetyl-L-serine metabolism, click here

Systematic name:

O-acetyl-L-serine:isoxazolin-5-one 2-(2-amino-2-carboxyethyl)transferase

Comments:

The enzyme from the plants Lathyrus odoratus (sweet pea) and L. sativus (grass pea) also forms 3-(5-oxoisoxazolin-4-yl)-L-alanine in vitro (cf. EC 2.5.1.119). However, only 3-(5-oxoisoxazolin-2-yl)-L-alanine is formed in vivo. 3-(5-oxoisoxazolin-2-yl)-L-alanine is the biosynthetic precursor of the neurotoxin N³-oxalyl-L-2,3-diaminopropanoic acid, the cause of lathyrism. Closely related and possibly identical to EC 2.5.1.47, cysteine synthase, and EC 2.5.1.51, β-pyrazolylalanine synthase.

Links to other databases:

References:

1.	Ikegami, F., Kamiya, M., Kuo, Y.H., Lambein, F. and Murakoshi, I. Enzymatic synthesis of two isoxazolylalanine isomers by cysteine synthases in Lathyrus species. Biol. Pharm. Bull. 19 (1996) 1214–1215. [PMID: 8889043]

[EC 2.5.1.118 created 2014]

2.5.1.119

Accepted name:

β-(isoxazolin-5-on-4-yl)-L-alanine synthase

Reaction:

O-acetyl-L-serine + isoxazolin-5-one = 3-(5-oxoisoxazolin-4-yl)-L-alanine + acetate

For diagram of O³-Acetyl-L-serine metabolism, click here

Systematic name:

O-acetyl-L-serine:isoxazolin-5-one 4-(2-amino-2-carboxyethyl)transferase

Comments:

3-(5-Oxoisoxazolin-4-yl)-L-alanine is an antifungal antibiotic produced by the bacterium Streptomyces platensis. The enzymes from the plants Lathyrus odoratus (sweet pea), L. sativus (grass pea) and Citrullus vulgaris (watermelon) that catalyse EC 2.5.1.118 (β-(isoxazolin-5-on-2-yl)-L-alanine synthase) also catalyse this reaction in vitro, but not in vivo. Closely related and possibly identical to EC 2.5.1.47, cysteine synthase, and EC 2.5.1.51, β-pyrazolylalanine synthase.

Links to other databases:

References:

1.	Ikegami, F., Kamiya, M., Kuo, Y.H., Lambein, F. and Murakoshi, I. Enzymatic synthesis of two isoxazolylalanine isomers by cysteine synthases in Lathyrus species. Biol. Pharm. Bull. 19 (1996) 1214–1215. [PMID: 8889043]

[EC 2.5.1.119 created 2014]

2.5.1.120

Accepted name:

aminodeoxyfutalosine synthase

Reaction:

S-adenosyl-L-methionine + 3-[(1-carboxyvinyl)oxy]benzoate + H₂O = 6-amino-6-deoxyfutalosine + L-methionine + HCO₃^-

For diagram of the futalosine pathway, click here

Glossary:

6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s):

MqnE; AFL synthase; aminofutalosine synthase; S-adenosyl-L-methionine:3-[(1-carboxyvinyl)-oxy]benzoate adenosyltransferase (bicarbonate-hydrolysing, 6-amino-6-deoxyfutalosine-forming)

Systematic name:

S-adenosyl-L-methionine:3-[(1-carboxyvinyl)-oxy]benzoate adenosyltransferase (HCO₃^--hydrolysing, 6-amino-6-deoxyfutalosine-forming)

Comments:

This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the transferred adenosyl group. The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

Links to other databases:

References:

1.	Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318–15321. [DOI] [PMID: 24083939]

[EC 2.5.1.120 created 2014]

2.6.1.103

Accepted name:

(S)-3,5-dihydroxyphenylglycine transaminase

Reaction:

(S)-3,5-dihydroxyphenylglycine + 2-oxoglutarate = 2-(3,5-dihydroxyphenyl)-2-oxoacetate + L-glutamate

Glossary:

(S)-3,5-dihydroxyphenylglycine = (2S)-2-amino-2-(3,5-dihydroxyphenyl)acetic acid

Other name(s):

HpgT

Systematic name:

(S)-3,5-dihydroxyphenylglycine:2-oxoglutarate aminotransferase

Comments:

A pyridoxal-5′-phosphate protein. The enzyme from the bacterium Amycolatopsis orientalis catalyses the reaction in the reverse direction as part of the biosynthesis of the (S)-3,5-dihydroxyphenylglycine constituent of the glycopeptide antibiotic chloroeremomycin.

Links to other databases:

References:

1.	Sandercock, A.M., Charles, E.H., Scaife, W., Kirkpatrick, P.N., O'Brien, S.W., Papageorgiou, E.A., Spencer, J.B. and Williams, D.H. Biosynthesis of the di-meta-hydroxyphenylglycine constituent of the vancomycin-group antibiotic chloroeremomycin. Chem. Comm. (2001) 1252–1253.

[EC 2.6.1.103 created 2013]

2.6.1.104

Accepted name:

3-dehydro-glucose-6-phosphate—glutamate transaminase

Reaction:

kanosamine 6-phosphate + 2-oxoglutarate = 3-dehydro-D-glucose 6-phosphate + L-glutamate

For diagram of kanosamine biosynthesis, click here

Glossary:

kanosamine = 3-amino-3-deoxy-D-glucose

Other name(s):

3-oxo-glucose-6-phosphate:glutamate aminotransferase; ntdA (gene name)

Systematic name:

kanosamine 6-phosphate:2-oxoglutarate aminotransferase

Comments:

A pyridoxal-phosphate protein. The enzyme, found in the bacterium Bacillus subtilis, is involved in a kanosamine biosynthesis pathway.

Links to other databases:

References:

1.	van Straaten, K.E., Langill, D.M., Palmer, D.R. and Sanders, D.A. Purification, crystallization and preliminary X-ray analysis of NtdA, a putative pyridoxal phosphate-dependent aminotransferase from Bacillus subtilis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 65 (2009) 426–429. [DOI] [PMID: 19342798]
2.	Vetter, N.D., Langill, D.M., Anjum, S., Boisvert-Martel, J., Jagdhane, R.C., Omene, E., Zheng, H., van Straaten, K.E., Asiamah, I., Krol, E.S., Sanders, D.A. and Palmer, D.R. A previously unrecognized kanosamine biosynthesis pathway in Bacillus subtilis. J. Am. Chem. Soc. 135 (2013) 5970–5973. [DOI] [PMID: 23586652]

[EC 2.6.1.104 created 2014]

2.6.1.105

Accepted name:

lysine—8-amino-7-oxononanoate transaminase

Reaction:

L-lysine + 8-amino-7-oxononanoate = (S)-2-amino-6-oxohexanoate + 7,8-diaminononanoate

Glossary:

(S)-2-amino-6-oxohexanoate = L-2-aminoadipate 6-semialdehyde = L-allysine

Other name(s):

DAPA aminotransferase (ambiguous); bioA (gene name) (ambiguous); bioK (gene name)

Systematic name:

L-lysine:8-amino-7-oxononanoate aminotransferase

Comments:

A pyridoxal 5′-phosphate enzyme [2]. Participates in the pathway for biotin biosynthesis. The enzyme from the bacterium Bacillus subtilis cannot use S-adenosyl-L-methionine as amino donor and catalyses an alternative reaction for the conversion of 8-amino-7-oxononanoate to 7,8-diaminononanoate (cf. EC 2.6.1.62, adenosylmethionine—8-amino-7-oxononanoate transaminase).

Links to other databases:

References:

1.	Van Arsdell, S.W., Perkins, J.B., Yocum, R.R., Luan, L., Howitt, C.L., Chatterjee, N.P. and Pero, J.G. Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction. Biotechnol. Bioeng. 91 (2005) 75–83. [DOI] [PMID: 15880481]
2.	Dey, S., Lane, J.M., Lee, R.E., Rubin, E.J. and Sacchettini, J.C. Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase. Biochemistry 49 (2010) 6746–6760. [DOI] [PMID: 20565114]

[EC 2.6.1.105 created 2014]

2.6.1.106

Accepted name:

dTDP-3-amino-3,4,6-trideoxy-α-D-glucose transaminase

Reaction:

dTDP-3-amino-3,4,6-trideoxy-α-D-glucose + 2-oxoglutarate = dTDP-3-dehydro-4,6-deoxy-α-D-glucose + L-glutamate

For diagram of dTDP-D-desosamine biosynthesis, click here

Glossary:

dTDP-α-D-desosamine = dTDP-3-(dimethylamino)-3,4,6-trideoxy-α-D-glucose

Other name(s):

desV (gene name); megDII (gene name); eryCI (gene name)

Systematic name:

dTDP-3-amino-3,4,6-trideoxy-α-D-glucose:2-oxoglutarate aminotransferase

Comments:

A pyridoxal-phosphate protein. The enzyme is involved in the biosynthesis of dTDP-α-D-desosamine, a sugar found in several bacterial macrolide antibiotics including erythromycin, megalomicin A, mycinamicin II, and oleandomycin. The reaction occurs in the reverse direction.

Links to other databases:

References:

1.	Burgie, E.S., Thoden, J.B. and Holden, H.M. Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci. 16 (2007) 887–896. [DOI] [PMID: 17456741]

[EC 2.6.1.106 created 2014]

2.6.1.107

Accepted name:

β-methylphenylalanine transaminase

Reaction:

(2S,3S)-3-methylphenylalanine + 2-oxoglutarate = (3S)-2-oxo-3-phenylbutanoate + L-glutamate

Glossary:

(3S)-2-oxo-3-phenylbutanoate = (3S)-β-methyl-phenylpyruvate

Other name(s):

TyrB

Systematic name:

(2S,3S)-3-methylphenylalanine:2-oxoglutarate aminotransferase

Comments:

Requires pyridoxal phosphate. Isolated from the bacterium Streptomyces hygroscopicus NRRL3085. It is involved in the biosynthesis of the glycopeptide antibiotic mannopeptimycin.

Links to other databases:

References:

Huang, Y.T., Lyu, S.Y., Chuang, P.H., Hsu, N.S., Li, Y.S., Chan, H.C., Huang, C.J., Liu, Y.C., Wu, C.J., Yang, W.B. and Li, T.L. In vitro characterization of enzymes involved in the synthesis of nonproteinogenic residue (2S,3S)-β-methylphenylalanine in glycopeptide antibiotic mannopeptimycin. ChemBioChem 10 (2009) 2480–2487. [DOI] [PMID: 19731276]

[EC 2.6.1.107 created 2014]

2.6.99.4

Transferred entry:

N⁶-L-threonylcarbamoyladenine synthase. Now EC 2.3.1.234, N⁶-L-threonylcarbamoyladenine synthase.

[EC 2.6.99.4 created 2014, deleted 2014]

*EC

2.7.1.107

Accepted name:

diacylglycerol kinase (ATP)

Reaction:

ATP + 1,2-diacyl-sn-glycerol = ADP + 1,2-diacyl-sn-glycerol 3-phosphate

Glossary:

1,2-diacyl-sn-glycerol 3-phosphate = phosphatidate

Other name(s):

diglyceride kinase (ambiguous); 1,2-diacylglycerol kinase (phosphorylating) (ambiguous); 1,2-diacylglycerol kinase (ambiguous); sn-1,2-diacylglycerol kinase (ambiguous); DG kinase (ambiguous); DGK (ambiguous); ATP:diacylglycerol phosphotransferase; arachidonoyl-specific diacylglycerol kinase; diacylglycerol:ATP kinase; ATP:1,2-diacylglycerol 3-phosphotransferase; diacylglycerol kinase (ATP dependent)

Systematic name:

ATP:1,2-diacyl-sn-glycerol 3-phosphotransferase

Comments:

Involved in synthesis of membrane phospholipids and the neutral lipid triacylglycerol. Activity is stimulated by certain phospholipids [4,7]. In plants and animals the product 1,2-diacyl-sn-glycerol 3-phosphate is an important second messenger. cf. EC 2.7.1.174, diacylglycerol kinase (CTP).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 60382-71-0

References:

1.	Hokin, L.E. and Hokin, M.R. Diglyceride kinase and other pathways for phosphatidic acid synthesis in the erythrocyte membrane. Biochim. Biophys. Acta 67 (1963) 470–484. [PMID: 13961253]
2.	Weissbach, H., Thomas, E. and Kaback, H.R. Studies on the metabolism of ATP by isolated bacterial membranes: formation and metabolism of membrane-bound phosphatidic acid. Arch. Biochem. Biophys. 147 (1971) 249–254. [DOI] [PMID: 4940043]
3.	Daleo, G.R., Piras, M.M. and Piras, R. Diglyceride kinase activity of microtubules. Characterization and comparison with the protein kinase and ATPase activities associated with vinblastine-isolated tubulin of chick embryonic muscles. Eur. J. Biochem. 68 (1976) 339–346. [DOI] [PMID: 185051]
4.	Walsh, J.P. and Bell, R.M. sn-1,2-Diacylglycerol kinase of Escherichia coli. Structural and kinetic analysis of the lipid cofactor dependence. J. Biol. Chem. 261 (1986) 15062–15069. [PMID: 3021764]
5.	Russ, E., Kaiser, U. and Sandermann, H., Jr. Lipid-dependent membrane enzymes. Purification to homogeneity and further characterization of diacylglycerol kinase from Escherichia coli. Eur. J. Biochem. 171 (1988) 335–342. [PMID: 2828054]
6.	Walsh, J.P. and Bell, R.M. Diacylglycerol kinase from Escherichia coli. Methods Enzymol. 209 (1992) 153–162. [DOI] [PMID: 1323028]
7.	Wissing, J.B. and Wagner, K.G. Diacylglycerol kinase from suspension cultured plant cells : characterization and subcellular localization. Plant Physiol. 98 (1992) 1148–1153. [PMID: 16668739]

[EC 2.7.1.107 created 1984, modified 2013]

*EC

2.7.1.174

Accepted name:

diacylglycerol kinase (CTP)

Reaction:

CTP + 1,2-diacyl-sn-glycerol = CDP + 1,2-diacyl-sn-glycerol 3-phosphate

Glossary:

1,2-diacyl-sn-glycerol 3-phosphate = phosphatidate

Other name(s):

DAG kinase; CTP-dependent diacylglycerol kinase; diglyceride kinase (ambiguous); DGK1 (gene name); diacylglycerol kinase (CTP dependent)

Systematic name:

CTP:1,2-diacyl-sn-glycerol 3-phosphotransferase

Comments:

Requires Ca²⁺ or Mg²⁺ for activity. Involved in synthesis of membrane phospholipids and the neutral lipid triacylglycerol. Unlike the diacylglycerol kinases from bacteria, plants, and animals [cf. EC 2.7.1.107, diacylglycerol kinase (ATP)], the enzyme from Saccharomyces cerevisiae utilizes CTP. The enzyme can also use dCTP, but not ATP, GTP or UTP.

Links to other databases:

References:

1.	Han, G.S., O'Hara, L., Carman, G.M. and Siniossoglou, S. An unconventional diacylglycerol kinase that regulates phospholipid synthesis and nuclear membrane growth. J. Biol. Chem. 283 (2008) 20433–20442. [DOI] [PMID: 18458075]
2.	Han, G.S., O'Hara, L., Siniossoglou, S. and Carman, G.M. Characterization of the yeast DGK1-encoded CTP-dependent diacylglycerol kinase. J. Biol. Chem. 283 (2008) 20443–20453. [DOI] [PMID: 18458076]
3.	Fakas, S., Konstantinou, C. and Carman, G.M. DGK1-encoded diacylglycerol kinase activity is required for phospholipid synthesis during growth resumption from stationary phase in Saccharomyces cerevisiae. J. Biol. Chem. 286 (2011) 1464–1474. [DOI] [PMID: 21071438]

[EC 2.7.1.174 created 2012, modified 2013]

2.7.1.180

Accepted name:

FAD:protein FMN transferase

Reaction:

FAD + [protein]-L-threonine = [protein]-FMN-L-threonine + AMP

Other name(s):

flavin transferase; apbE (gene name)

Systematic name:

FAD:protein riboflavin-5′-phosphate transferase

Comments:

The enzyme catalyses the transfer of the FMN portion of FAD and its covalent binding to the hydroxyl group of an L-threonine residue in a target flavin-binding protein such as the B and C subunits of EC 7.2.1.1, NADH:ubiquinone reductase (Na⁺-transporting). Requires Mg²⁺.

Links to other databases:

References:

Bertsova, Y.V., Fadeeva, M.S., Kostyrko, V.A., Serebryakova, M.V., Baykov, A.A. and Bogachev, A.V. Alternative pyrimidine biosynthesis protein ApbE is a flavin transferase catalyzing covalent attachment of FMN to a threonine residue in bacterial flavoproteins. J. Biol. Chem. 288 (2013) 14276–14286. [PMID: 23558683]

[EC 2.7.1.180 created 2013, modified 2018]

2.7.1.181

Accepted name:

polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol kinase

Reaction:

ATP + α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol = ADP + 3-O-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol

Other name(s):

WbdD; ATP:α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-α-D-Man-(1→3)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase

Systematic name:

ATP:α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phosphotransferase

Comments:

The enzyme is involved in the biosynthesis of the polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. O-Polysaccharide structures vary extensively because of differences in the number and type of sugars in the repeat unit. The dual kinase/methylase WbdD also catalyses the methylation of 3-phospho-α-D-Man-(1→2)-α-D-Man-(1→2)-[α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-GlcNAc-diphospho-ditrans,octacis-undecaprenol (cf. EC 2.1.1.294, 3-O-phospho-polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 3-phospho-methyltransferase).

Links to other databases:

References:

1.	Clarke, B.R., Cuthbertson, L. and Whitfield, C. Nonreducing terminal modifications determine the chain length of polymannose O antigens of Escherichia coli and couple chain termination to polymer export via an ATP-binding cassette transporter. J. Biol. Chem. 279 (2004) 35709–35718. [DOI] [PMID: 15184370]
2.	Clarke, B.R., Greenfield, L.K., Bouwman, C. and Whitfield, C. Coordination of polymerization, chain termination, and export in assembly of the Escherichia coli lipopolysaccharide O9a antigen in an ATP-binding cassette transporter-dependent pathway. J. Biol. Chem. 284 (2009) 30662–30672. [DOI] [PMID: 19734145]
3.	Clarke, B.R., Richards, M.R., Greenfield, L.K., Hou, D., Lowary, T.L. and Whitfield, C. In vitro reconstruction of the chain termination reaction in biosynthesis of the Escherichia coli O9a O-polysaccharide: the chain-length regulator, WbdD, catalyzes the addition of methyl phosphate to the non-reducing terminus of the growing glycan. J. Biol. Chem. 286 (2011) 41391–41401. [DOI] [PMID: 21990359]
4.	Liston, S.D., Clarke, B.R., Greenfield, L.K., Richards, M.R., Lowary, T.L. and Whitfield, C. Domain interactions control complex formation and polymerase specificity in the biosynthesis of the Escherichia coli O9a antigen. J. Biol. Chem. 290 (2015) 1075–1085. [DOI] [PMID: 25422321]

[EC 2.7.1.181 created 2014, modified 2017]

2.7.1.182

Accepted name:

phytol kinase

Reaction:

CTP + phytol = CDP + phytyl phosphate

Other name(s):

VTE5 (gene name)

Systematic name:

CTP:phytol O-phosphotransferase

Comments:

The enzyme is found in plants and photosynthetic algae [2] and is involved in phytol salvage [1]. It can use UTP as an alternative phosphate donor with lower activity [2].

Links to other databases:

References:

1.	Ischebeck, T., Zbierzak, A.M., Kanwischer, M. and Dormann, P. A salvage pathway for phytol metabolism in Arabidopsis. J. Biol. Chem. 281 (2006) 2470–2477. [DOI] [PMID: 16306049]
2.	Valentin, H.E., Lincoln, K., Moshiri, F., Jensen, P.K., Qi, Q., Venkatesh, T.V., Karunanandaa, B., Baszis, S.R., Norris, S.R., Savidge, B., Gruys, K.J. and Last, R.L. The Arabidopsis vitamin E pathway gene5-1 mutant reveals a critical role for phytol kinase in seed tocopherol biosynthesis. Plant Cell 18 (2006) 212–224. [DOI] [PMID: 16361393]

[EC 2.7.1.182 created 2014]

*EC

2.7.4.21

Accepted name:

inositol-hexakisphosphate 5-kinase

Reaction:

(1) ATP + 1D-myo-inositol hexakisphosphate = ADP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate
(2) ATP + 1D-myo-inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate

Other name(s):

ATP:1D-myo-inositol-hexakisphosphate phosphotransferase; IP6K; inositol-hexakisphosphate kinase (ambiguous)

Systematic name:

ATP:1D-myo-inositol-hexakisphosphate 5-phosphotransferase

Comments:

Three mammalian isoforms are known to exist.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 176898-37-6

References:

1.	Saiardi, A., Erdjument-Bromage, H., Snowman, A.M., Tempst, P. and Snyder, S.H. Synthesis of diphosphoinositol pentakisphosphate by a newly identified family of higher inositol polyphosphate kinases. Curr. Biol. 9 (1999) 1323–1326. [DOI] [PMID: 10574768]
2.	Schell, M.J., Letcher, A.J., Brearley, C.A., Biber, J., Murer, H. and Irvine, R.F. PiUS (P_i uptake stimulator) is an inositol hexakisphosphate kinase. FEBS Lett. 461 (1999) 169–172. [DOI] [PMID: 10567691]
3.	Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553–560. [DOI] [PMID: 9359429]
4.	Lin, H., Fridy, P.C., Ribeiro, A.A., Choi, J.H., Barma, D.K., Vogel, G., Falck, J.R., Shears, S.B., York, J.D. and Mayr, G.W. Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases. J. Biol. Chem. 284 (2009) 1863–1872. [DOI] [PMID: 18981179]
5.	Wang, H., Falck, J.R., Hall, T.M. and Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat. Chem. Biol. 8 (2012) 111–116. [DOI] [PMID: 22119861]

[EC 2.7.4.21 created 2002 as EC 2.7.1.152, transferred 2003 to EC 2.7.4.21, modified 2013, modified 2022]

*EC

2.7.4.24

Accepted name:

diphosphoinositol-pentakisphosphate 1-kinase

Reaction:

(1) ATP + 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate = ADP + 1D-myo-inositol 1,5-bis(diphosphate) 2,3,4,6-tetrakisphosphate
(2) ATP + 1D-myo-inositol hexakisphosphate = ADP + 1D-myo-inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate

Other name(s):

PP-IP₅ kinase; diphosphoinositol pentakisphosphate kinase; ATP:5-diphospho-1D-myo-inositol-pentakisphosphate phosphotransferase; PP-InsP₅ kinase; PPIP5K; PPIP5K1; PPIP5K2; VIP1; VIP2; diphosphoinositol-pentakisphosphate 1/3-kinase (incorrect); diphosphoinositol-pentakisphosphate kinase (ambiguous)

Systematic name:

ATP:1D-myo-inositol-5-diphosphate-pentakisphosphate 1-phosphotransferase

Comments:

This enzyme is activated by osmotic shock [4]. Ins(1,3,4,5,6)P₅, 1D-myo-inositol diphosphate tetrakisphosphate and 1D-myo-inositol bisdiphosphate triphosphate are not substrates [4]. The enzyme specifically phosphorylates the 1-position of the substrates [6].

Links to other databases:

References:

1.	Shears, S.B., Ali, N., Craxton, A. and Bembenek, M.E. Synthesis and metabolism of bis-diphosphoinositol tetrakisphosphate in vitro and in vivo. J. Biol. Chem. 270 (1995) 10489–10497. [DOI] [PMID: 7737983]
2.	Albert, C., Safrany, S.T., Bembenek, M.E., Reddy, K.M., Reddy, K.K., Falck, J.-R., Bröcker, M., Shears, S.B. and Mayr, G.W. Biological variability in the structures of diphosphoinositol polyphosphates in Dictyostelium discoideum and mammalian cells. Biochem. J. 327 (1997) 553–560. [DOI] [PMID: 9359429]
3.	Fridy, P.C., Otto, J.C., Dollins, D.E. and York, J.D. Cloning and characterization of two human VIP1-like inositol hexakisphosphate and diphosphoinositol pentakisphosphate kinases. J. Biol. Chem. 282 (2007) 30754–30762. [DOI] [PMID: 17690096]
4.	Choi, J.H., Williams, J., Cho, J., Falck, J.R. and Shears, S.B. Purification, sequencing, and molecular identification of a mammalian PP-InsP₅ kinase that Is activated when cells are exposed to hyperosmotic stress. J. Biol. Chem. 282 (2007) 30763–30775. [DOI] [PMID: 17702752]
5.	Lin, H., Fridy, P.C., Ribeiro, A.A., Choi, J.H., Barma, D.K., Vogel, G., Falck, J.R., Shears, S.B., York, J.D. and Mayr, G.W. Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases. J. Biol. Chem. 284 (2009) 1863–1872. [DOI] [PMID: 18981179]
6.	Wang, H., Falck, J.R., Hall, T.M. and Shears, S.B. Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding. Nat. Chem. Biol. 8 (2012) 111–116. [DOI] [PMID: 22119861]

[EC 2.7.4.24 created 2003 as EC 2.7.1.155, transferred 2007 to EC 2.7.4.24, modified 2014, modified 2022]

2.8.2.36

Accepted name:

desulfo-A47934 sulfotransferase

Reaction:

3′-phosphoadenylyl sulfate + desulfo-A47934 = adenosine 3′,5′-bisphosphate + A47934

Glossary:

desulfo-A47934 = LY 154989 = 7-demethyl-64-O-demethyl-19-deoxy-22,31,45-trichloro-11-sulfo-ristomycin A aglycone

Other name(s):

StaL; 3′-phosphoadenylyl-sulfate:desulfo-A47934 sulfotransferase

Systematic name:

3′-phosphoadenylyl-sulfate:desulfo-A47934 sulfonotransferase

Comments:

The enzyme from the bacterium Streptomyces toyocaensis catalyses the final step in the biosynthesis of the glycopeptide antibiotic A47934, a naturally occuring antibiotic of the vancomycin group.

Links to other databases:

References:

1.	Lamb, S.S., Patel, T., Koteva, K.P. and Wright, G.D. Biosynthesis of sulfated glycopeptide antibiotics by using the sulfotransferase StaL. Chem. Biol. 13 (2006) 171–181. [DOI] [PMID: 16492565]
2.	Shi, R., Lamb, S.S., Bhat, S., Sulea, T., Wright, G.D., Matte, A. and Cygler, M. Crystal structure of StaL, a glycopeptide antibiotic sulfotransferase from Streptomyces toyocaensis. J. Biol. Chem. 282 (2007) 13073–13086. [DOI] [PMID: 17329243]

[EC 2.8.2.36 created 2014]

2.8.3.7

Deleted entry:

succinate—citramalate CoA-transferase. The activity has now been shown to be due to two separate enzymes described by EC 2.8.3.22, succinyl-CoA—L-malate CoA-transferase, and EC 2.8.3.20, succinyl-CoA—D-citramalate CoA-transferase

[EC 2.8.3.7 created 1972, deleted 2014]

2.8.3.19

Accepted name:

CoA:oxalate CoA-transferase

Reaction:

acetyl-CoA + oxalate = acetate + oxalyl-CoA

Other name(s):

acetyl-coenzyme A transferase; acetyl-CoA oxalate CoA-transferase; ACOCT; YfdE; UctC

Systematic name:

acetyl-CoA:oxalate CoA-transferase

Comments:

The enzymes characterized from the bacteria Escherichia coli and Acetobacter aceti can also use formyl-CoA and oxalate (EC 2.8.3.16, formyl-CoA transferase) or formyl-CoA and acetate, with significantly reduced specific activities.

Links to other databases:

References:

1.	Mullins, E.A., Sullivan, K.L. and Kappock, T.J. Function and X-Ray crystal structure of Escherichia coli YfdE. PLoS One 8 (2013) e67901. [DOI] [PMID: 23935849]

[EC 2.8.3.19 created 2013]

2.8.3.20

Accepted name:

succinyl-CoA—D-citramalate CoA-transferase

Reaction:

(1) succinyl-CoA + (R)-citramalate = succinate + (R)-citramalyl-CoA
(2) succinyl-CoA + (R)-malate = succinate + (R)-malyl-CoA

Glossary:

(R)-citramalate = (2R)-2-hydroxy-2-methylbutanedioate
(R)-malate = (2R)-2-hydroxybutanedioate
(R)-malyl-CoA = (3R)-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s):

Sct

Systematic name:

succinyl-CoA:(R)-citramalate CoA-transferase

Comments:

The enzyme, purified from the bacterium Clostridium tetanomorphum, can also accept itaconate as acceptor, with lower efficiency.

Links to other databases:

References:

1.	Friedmann, S., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:D-citramalate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 6460–6468. [DOI] [PMID: 16952935]

[EC 2.8.3.20 created 2014]

2.8.3.21

Accepted name:

L-carnitine CoA-transferase

Reaction:

(1) (E)-4-(trimethylammonio)but-2-enoyl-CoA + L-carnitine = (E)-4-(trimethylammonio)but-2-enoate + L-carnitinyl-CoA
(2) 4-trimethylammoniobutanoyl-CoA + L-carnitine = 4-trimethylammoniobutanoate + L-carnitinyl-CoA

Glossary:

L-carnitine = (3R)-3-hydroxy-4-(trimethylammonio)butanoate
(E)-4-(trimethylammonio)but-2-enoate = crotonobetaine
4-trimethylammoniobutanoate = γ-butyrobetaine

Other name(s):

CaiB; crotonobetainyl/γ-butyrobetainyl-CoA:carnitine CoA-transferase

Systematic name:

(E)-4-(trimethylammonio)but-2-enoyl-CoA:L-carnitine CoA-transferase

Comments:

The enzyme is found in gammaproteobacteria such as Proteus sp. and Escherichia coli. It has similar activity with both substrates.

Links to other databases:

References:

1.	Engemann, C., Elssner, T. and Kleber, H.P. Biotransformation of crotonobetaine to L-(–)-carnitine in Proteus sp. Arch. Microbiol. 175 (2001) 353–359. [PMID: 11409545]
2.	Elssner, T., Engemann, C., Baumgart, K. and Kleber, H.P. Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli. Biochemistry 40 (2001) 11140–11148. [DOI] [PMID: 11551212]
3.	Stenmark, P., Gurmu, D. and Nordlund, P. Crystal structure of CaiB, a type-III CoA transferase in carnitine metabolism. Biochemistry 43 (2004) 13996–14003. [DOI] [PMID: 15518548]
4.	Engemann, C., Elssner, T., Pfeifer, S., Krumbholz, C., Maier, T. and Kleber, H.P. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183 (2005) 176–189. [DOI] [PMID: 15731894]
5.	Rangarajan, E.S., Li, Y., Iannuzzi, P., Cygler, M. and Matte, A. Crystal structure of Escherichia coli crotonobetainyl-CoA: carnitine CoA-transferase (CaiB) and its complexes with CoA and carnitinyl-CoA. Biochemistry 44 (2005) 5728–5738. [DOI] [PMID: 15823031]

[EC 2.8.3.21 created 2014]

2.8.3.22

Accepted name:

succinyl-CoA—L-malate CoA-transferase

Reaction:

(1) succinyl-CoA + (S)-malate = succinate + (S)-malyl-CoA
(2) succinyl-CoA + (S)-citramalate = succinate + (S)-citramalyl-CoA

For diagram of the 3-hydroxypropanoate cycle, click here

Glossary:

(S)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
(S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s):

SmtAB

Systematic name:

succinyl-CoA:(S)-malate CoA-transferase

Comments:

The enzyme, purified from the bacterium Chloroflexus aurantiacus, can also accept itaconate as acceptor, with lower efficiency. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.

Links to other databases:

References:

1.	Friedmann, S., Steindorf, A., Alber, B.E. and Fuchs, G. Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 188 (2006) 2646–2655. [DOI] [PMID: 16547052]

[EC 2.8.3.22 created 2014]

2.8.4.3

Accepted name:

tRNA-2-methylthio-N⁶-dimethylallyladenosine synthase

Reaction:

N⁶-(3-methylbut-2-en-1-yl)-adenine³⁷ in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = N⁶-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenine³⁷ in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5′-deoxyadenine + electron acceptor (overall reaction)
(1a) N⁶-(3-methylbut-2-en-1-yl)-adenine³⁷ in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = N⁶-(3-methylbut-2-en-1-yl)-2-thioadenine³⁷ in tRNA + (sulfur carrier) + L-methionine + 5′-deoxyadenine + electron acceptor
(1b) S-adenosyl-L-methionine + N⁶-(3-methylbut-2-en-1-yl)-2-thioadenine³⁷ in tRNA = S-adenosyl-L-homocysteine + N⁶-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenine³⁷ in tRNA

For diagram of N⁶-(dimethylallyl)adenosine³⁷ modified tRNA biosynthesis, click here

Glossary:

N⁶-(3-methylbut-2-en-1-yl)-adenine³⁷ in tRNA = N⁶-dimethylallyladenine³⁷ in tRNA

Other name(s):

MiaB; 2-methylthio-N-6-isopentenyl adenosine synthase; tRNA-i6A37 methylthiotransferase; tRNA (N⁶-dimethylallyladenosine³⁷):sulfur-(sulfur carrier),S-adenosyl-L-methionine C²-methylthiotransferase

Systematic name:

tRNA N⁶-(3-methylbut-2-en-1-yl)-adenine³⁷:sulfur-(sulfur carrier),S-adenosyl-L-methionine C²-(methylsulfanyl)transferase

Comments:

This bacterial enzyme binds two [4Fe-4S] clusters as well as the transferred sulfur [3]. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. The sulfur donor is believed to be one of the [4Fe-4S] clusters, which is sacrificed in the process, so that in vitro the reaction is a single turnover. The identity of the electron donor is not known.

Links to other databases:

References:

1.	Pierrel, F., Bjork, G.R., Fontecave, M. and Atta, M. Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. J. Biol. Chem. 277 (2002) 13367–13370. [DOI] [PMID: 11882645]
2.	Pierrel, F., Hernandez, H.L., Johnson, M.K., Fontecave, M. and Atta, M. MiaB protein from Thermotoga maritima. Characterization of an extremely thermophilic tRNA-methylthiotransferase. J. Biol. Chem. 278 (2003) 29515–29524. [DOI] [PMID: 12766153]
3.	Pierrel, F., Douki, T., Fontecave, M. and Atta, M. MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme involved in thiolation and methylation of tRNA. J. Biol. Chem. 279 (2004) 47555–47563. [DOI] [PMID: 15339930]
4.	Hernandez, H.L., Pierrel, F., Elleingand, E., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Fontecave, M. and Atta, M. MiaB, a bifunctional radical-S-adenosylmethionine enzyme involved in the thiolation and methylation of tRNA, contains two essential [4Fe-4S] clusters. Biochemistry 46 (2007) 5140–5147. [DOI] [PMID: 17407324]
5.	Landgraf, B.J., Arcinas, A.J., Lee, K.H. and Booker, S.J. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. J. Am. Chem. Soc. 135 (2013) 15404–15416. [DOI] [PMID: 23991893]

[EC 2.8.4.3 created 2014, modified 2015]

2.8.4.4

Accepted name:

[ribosomal protein uS12] (aspartate⁸⁹-C³)-methylthiotransferase

Reaction:

L-aspartate⁸⁹-[ribosomal protein uS12] + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced acceptor = 3-(methylsulfanyl)-L-aspartate⁸⁹-[ribosomal protein uS12] + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5′-deoxyadenosine + oxidized acceptor (overall reaction)
(1a) S-adenosyl-L-methionine + L-aspartate⁸⁹-[ribosomal protein uS12] + sulfur-(sulfur carrier) = S-adenosyl-L-homocysteine + L-aspartate⁸⁹-[ribosomal protein uS12]-methanethiol + (sulfur carrier)
(1b) L-aspartate⁸⁹-[ribosomal protein uS12]-methanethiol + S-adenosyl-L-methionine + reduced acceptor = 3-(methylsulfanyl)-L-aspartate⁸⁹-[ribosomal protein uS12] + L-methionine + 5′-deoxyadenosine + oxidized acceptor

Other name(s):

RimO; [ribosomal protein S12]-Asp⁸⁹:sulfur-(sulfur carrier),S-adenosyl-L-methionine C³-methylthiotransferase; [ribosomal protein S12]-L-aspartate⁸⁹:sulfur-(sulfur carrier),S-adenosyl-L-methionine C³-methylthiotransferase

Systematic name:

[ribosomal protein uS12]-L-aspartate⁸⁹:sulfur-(sulfur carrier),S-adenosyl-L-methionine C³-(methylsulfanyl)transferase

Comments:

This bacterial enzyme binds two [4Fe-4S] clusters [2,3]. A bridge of five sulfur atoms is formed between the free Fe atoms of the two [4Fe-4S] clusters [6]. In the first reaction the enzyme transfers a methyl group from AdoMet to the external sulfur ion of the sulfur bridge. In the second reaction the enzyme catalyses the reductive fragmentation of a second molecule of AdoMet, yielding a 5′-deoxyadenosine radical, which then attacks the methylated sulfur atom of the polysulfide bridge, resulting in the transfer of a methylsulfanyl group to aspartate⁸⁹ [5,6]. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes.

Links to other databases:

References:

1.	Anton, B.P., Saleh, L., Benner, J.S., Raleigh, E.A., Kasif, S. and Roberts, R.J. RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp⁸⁸ residue of ribosomal protein S12 in Escherichia coli. Proc. Natl. Acad. Sci. USA 105 (2008) 1826–1831. [DOI] [PMID: 18252828]
2.	Lee, K.H., Saleh, L., Anton, B.P., Madinger, C.L., Benner, J.S., Iwig, D.F., Roberts, R.J., Krebs, C. and Booker, S.J. Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry 48 (2009) 10162–10174. [DOI] [PMID: 19736993]
3.	Arragain, S., Garcia-Serres, R., Blondin, G., Douki, T., Clemancey, M., Latour, J.M., Forouhar, F., Neely, H., Montelione, G.T., Hunt, J.F., Mulliez, E., Fontecave, M. and Atta, M. Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. J. Biol. Chem. 285 (2010) 5792–5801. [DOI] [PMID: 20007320]
4.	Strader, M.B., Costantino, N., Elkins, C.A., Chen, C.Y., Patel, I., Makusky, A.J., Choy, J.S., Court, D.L., Markey, S.P. and Kowalak, J.A. A proteomic and transcriptomic approach reveals new insight into β-methylthiolation of Escherichia coli ribosomal protein S12. Mol. Cell. Proteomics 10:M110.005199 (2011). [DOI] [PMID: 21169565]
5.	Landgraf, B.J., Arcinas, A.J., Lee, K.H. and Booker, S.J. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. J. Am. Chem. Soc. 135 (2013) 15404–15416. [DOI] [PMID: 23991893]
6.	Forouhar, F., Arragain, S., Atta, M., Gambarelli, S., Mouesca, J.M., Hussain, M., Xiao, R., Kieffer-Jaquinod, S., Seetharaman, J., Acton, T.B., Montelione, G.T., Mulliez, E., Hunt, J.F. and Fontecave, M. Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases. Nat. Chem. Biol. 9 (2013) 333–338. [DOI] [PMID: 23542644]

[EC 2.8.4.4 created 2014, modified 2014, modified 2023]

2.8.4.5

Accepted name:

tRNA (N⁶-L-threonylcarbamoyladenosine³⁷-C²)-methylthiotransferase

Reaction:

N⁶-L-threonylcarbamoyladenine³⁷ in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = 2-(methylsulfanyl)-N⁶-L-threonylcarbamoyladenine³⁷ in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5′-deoxyadenosine + electron acceptor (overall reaction)
(1a) N⁶-L-threonylcarbamoyladenine³⁷ in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = 2-sulfanyl-N⁶-L-threonylcarbamoyladenine³⁷ in tRNA + (sulfur carrier) + L-methionine + 5′-deoxyadenosine + electron acceptor
(1b) S-adenosyl-L-methionine + 2-sulfanyl-N⁶-L-threonylcarbamoyladenine³⁷ in tRNA = S-adenosyl-L-homocysteine + 2-(methylsulfanyl)-N⁶-L-threonylcarbamoyladenine³⁷ in tRNA

For diagram of N⁶-L-Threonylcarbamoyladenosine³⁷ modified tRNA biosynthesis, click here

Glossary:

N⁶-L-threonylcarbamoyladenine³⁷ = t6A37
2-sulfanyl-N⁶-L-threonylcarbamoyladenine³⁷ = ms2t6A37

Other name(s):

MtaB; methylthio-threonylcarbamoyl-adenosine transferase B; CDKAL1 (gene name); tRNA (N⁶-L-threonylcarbamoyladenosine³⁷):sulfur-(sulfur carrier),S-adenosyl-L-methionine C²-methylthiotransferase

Systematic name:

tRNA (N⁶-L-threonylcarbamoyladenosine³⁷):sulfur-(sulfur carrier),S-adenosyl-L-methionine C²-(methylsulfanyl)transferase

Comments:

The enzyme, which is a member of the S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes superfamily, binds two [4Fe-4S] clusters as well as the transferred sulfur. The sulfur donor is believed to be one of the [4Fe-4S] clusters, which is sacrificed in the process, so that in vitro the reaction is a single turnover. The identity of the electron donor is not known.

Links to other databases:

References:

Arragain, S., Handelman, S.K., Forouhar, F., Wei, F.Y., Tomizawa, K., Hunt, J.F., Douki, T., Fontecave, M., Mulliez, E. and Atta, M. Identification of eukaryotic and prokaryotic methylthiotransferase for biosynthesis of 2-methylthio-N⁶-threonylcarbamoyladenosine in tRNA. J. Biol. Chem. 285 (2010) 28425–28433. [DOI] [PMID: 20584901]

[EC 2.8.4.5 created 2014, modified 2015]

3.1.2.30

Accepted name:

(3S)-malyl-CoA thioesterase

Reaction:

(S)-malyl-CoA + H₂O = (S)-malate + CoA

Glossary:

(S)-malate = (2S)-2-hydroxybutanedioate
(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s):

mcl2 (gene name)

Systematic name:

(S)-malyl-CoA hydrolase

Comments:

Stimulated by Mg²⁺ or Mn²⁺. The enzyme has no activity with (2R,3S)-2-methylmalyl-CoA (cf. EC 4.1.3.24, malyl-CoA lyase) or other CoA esters.

Links to other databases:

References:

Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249–1258. [DOI] [PMID: 20047909]

[EC 3.1.2.30 created 2014]

*EC

3.1.3.16

Accepted name:

protein-serine/threonine phosphatase

Reaction:

[a protein]-serine/threonine phosphate + H₂O = [a protein]-serine/threonine + phosphate

Other name(s):

phosphoprotein phosphatase (ambiguous); protein phosphatase-1; protein phosphatase-2A; protein phosphatase-2B; protein phosphatase-2C; protein D phosphatase; phosphospectrin phosphatase; casein phosphatase; Aspergillus awamori acid protein phosphatase; calcineurin; phosphatase 2A; phosphatase 2B; phosphatase II; phosphatase IB; phosphatase C-II; polycation modulated (PCM-) phosphatase; phosphopyruvate dehydrogenase phosphatase; phosphatase SP; branched-chain α-keto acid dehydrogenase phosphatase; BCKDH phosphatase; 3-hydroxy 3-methylglutaryl coenzymeA reductase phosphatase; HMG-CoA reductase phosphatase; phosphatase H-II; phosphatase III; phosphatase I; protein phosphatase; phosphatase IV; phosphoprotein phosphohydrolase

Systematic name:

protein-serine/threonine-phosphate phosphohydrolase

Comments:

A group of enzymes removing the serine- or threonine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes that have been phosphorylated under the action of a kinase (cf. EC 3.1.3.48 protein-tyrosine-phosphatase). The spleen enzyme also acts on phenolic phosphates and phosphamides (cf. EC 3.9.1.1, phosphoamidase).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9025-75-6

References:

1.	Deutscher, J., Kessler, U. and Hengstenberg, W. Streptococcal phosphoenolpyruvate: sugar phosphotransferase system: purification and characterization of a phosphoprotein phosphatase which hydrolyzes the phosphoryl bond in seryl-phosphorylated histidine-containing protein. J. Bacteriol. 163 (1985) 1203–1209. [PMID: 2993239]
2.	Ingebritsen, T.S. and Cohen, P. The protein phosphatases involved in cellular regulation. 1. Classification and substrate specificities. Eur. J. Biochem. 132 (1983) 255–261. [DOI] [PMID: 6301824]
3.	Sundarajan, T.A. and Sarma, P.S. Substrate specificity of phosphoprotein phosphatase from spleen. Biochem. J. 71 (1959) 537–544. [PMID: 13638262]
4.	Tonks, N.K. and Cohen, P. The protein phosphatases involved in cellular regulation. Identification of the inhibitor-2 phosphatases in rabbit skeletal muscle. Eur. J. Biochem. 145 (1984) 65–70. [DOI] [PMID: 6092084]

[EC 3.1.3.16 created 1961, modified 1989, modified 2013]

3.1.3.93

Accepted name:

L-galactose 1-phosphate phosphatase

Reaction:

β-L-galactose 1-phosphate + H₂O = L-galactose + phosphate

Other name(s):

VTC4 (gene name) (ambiguous); IMPL2 (gene name) (ambiguous)

Systematic name:

β-L-galactose-1-phosphate phosphohydrolase

Comments:

The enzyme from plants also has the activity of EC 3.1.3.25, inositol-phosphate phosphatase. The enzymes have very low activity with D-galactose 1-phosphate (cf. EC 3.1.3.94, D-galactose 1-phosphate phosphatase).

Links to other databases:

References:

1.	Laing, W.A., Bulley, S., Wright, M., Cooney, J., Jensen, D., Barraclough, D. and MacRae, E. A highly specific L-galactose-1-phosphate phosphatase on the path to ascorbate biosynthesis. Proc. Natl. Acad. Sci. USA 101 (2004) 16976–16981. [DOI] [PMID: 15550539]
2.	Torabinejad, J., Donahue, J.L., Gunesekera, B.N., Allen-Daniels, M.J. and Gillaspy, G.E. VTC4 is a bifunctional enzyme that affects myoinositol and ascorbate biosynthesis in plants. Plant Physiol. 150 (2009) 951–961. [DOI] [PMID: 19339506]
3.	Petersen, L.N., Marineo, S., Mandala, S., Davids, F., Sewell, B.T. and Ingle, R.A. The missing link in plant histidine biosynthesis: Arabidopsis myoinositol monophosphatase-like2 encodes a functional histidinol-phosphate phosphatase. Plant Physiol. 152 (2010) 1186–1196. [DOI] [PMID: 20023146]

[EC 3.1.3.93 created 2014]

3.1.3.94

Accepted name:

D-galactose 1-phosphate phosphatase

Reaction:

α-D-galactose 1-phosphate + H₂O = D-galactose + phosphate

Systematic name:

α-D-galactose-1-phosphate phosphohydrolase

Comments:

The human enzyme also has the activity of EC 3.1.3.25, inositol-phosphate phosphatase. The enzyme has very low activity with L-galactose 1-phosphate (cf. EC 3.1.3.93, L-galactose 1-phosphate phosphatase).

Links to other databases:

References:

1.	Parthasarathy, R., Parthasarathy, L. and Vadnal, R. Brain inositol monophosphatase identified as a galactose 1-phosphatase. Brain Res. 778 (1997) 99–106. [DOI] [PMID: 9462881]

[EC 3.1.3.94 created 2014]

3.1.3.95

Accepted name:

phosphatidylinositol-3,5-bisphosphate 3-phosphatase

Reaction:

1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H₂O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate

Glossary:

1-phosphatidyl-1D-myo-inositol 5-phosphate = PtdIns5P
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate = PtdIns(3,5)P₂

Other name(s):

MTMR; PtdIns-3,5-P₂ 3-Ptase

Systematic name:

1-phosphatidyl-1D-myo-inositol-3,5-bisphosphate 3-phosphohydrolase

Comments:

The enzyme is found in both plants and animals. It also has the activity of EC 3.1.3.64 (phosphatidylinositol-3-phosphatase).

Links to other databases:

References:

1.	Walker, D.M., Urbe, S., Dove, S.K., Tenza, D., Raposo, G. and Clague, M.J. Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity. Curr. Biol. 11 (2001) 1600–1605. [DOI] [PMID: 11676921]
2.	Berger, P., Bonneick, S., Willi, S., Wymann, M. and Suter, U. Loss of phosphatase activity in myotubularin-related protein 2 is associated with Charcot-Marie-Tooth disease type 4B1. Hum. Mol. Genet. 11 (2002) 1569–1579. [DOI] [PMID: 12045210]
3.	Ding, Y., Lapko, H., Ndamukong, I., Xia, Y., Al-Abdallat, A., Lalithambika, S., Sadder, M., Saleh, A., Fromm, M., Riethoven, J.J., Lu, G. and Avramova, Z. The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought. Plant Signal. Behav. 4 (2009) 1049–1058. [PMID: 19901554]

[EC 3.1.3.95 created 2014]

*EC

3.1.21.2

Accepted name:

deoxyribonuclease IV

Reaction:

Endonucleolytic cleavage of ssDNA at apurinic/apyrimidinic sites to 5′-phosphooligonucleotide end-products

Other name(s):

deoxyribonuclease IV (phage-T₄-induced) (misleading); endodeoxyribonuclease IV (phage T₄-induced) (misleading); E. coli endonuclease IV; endodeoxyribonuclease (misleading); redoxyendonuclease; deoxriboendonuclease (misleading); endonuclease II; endonuclease IV; DNA-adenine-transferase; nfo (gene name)

Comments:

The enzyme is an apurinic/apyrimidinic (AP) site endonuclease that primes DNA repair synthesis at AP sites. It specifically cleaves the DNA backbone at AP sites and also removes 3′ DNA-blocking groups such as 3′ phosphates, 3′ phosphoglycolates, and 3′ α,β-unsaturated aldehydes that arise from oxidative base damage and the activity of combined glycosylase/lyase enzymes. It is also the only known repair enzyme that is able to cleave the DNA backbone 5′ of the oxidative lesion α-deoxyadenosine. The enzyme has a strong preference for single-stranded DNA.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 63363-78-0

References:

1.	Friedberg, E.C. and Goldthwait, D.A. Endonuclease II of E. coli. I. Isolation and purification. Proc. Natl. Acad. Sci. USA 62 (1969) 934–940. [DOI] [PMID: 4895219]
2.	Friedberg, E.C., Hadi, S.-M. and Goldthwait, D.A. Endonuclease II of Escherichia coli. II. Enzyme properties and studies on the degradation of alkylated and native deoxyribonucleic acid. J. Biol. Chem. 244 (1969) 5879–5889. [PMID: 4981786]
3.	Hadi, S.M. and Goldthwait, D.A. Endonuclease II of Escherichia coli. Degradation of partially depurinated deoxyribonucleic acid. Biochemistry 10 (1971) 4986–4993. [PMID: 4944066]
4.	Cunningham, R.P., Saporito, S.M., Spitzer, S.G. and Weiss, B. Endonuclease IV (nfo) mutant of Escherichia coli. J. Bacteriol. 168 (1986) 1120–1127. [DOI] [PMID: 2430946]
5.	Ide, H., Tedzuka, K., Shimzu, H., Kimura, Y., Purmal, A.A., Wallace, S.S. and Kow, Y.W. Alpha-deoxyadenosine, a major anoxic radiolysis product of adenine in DNA, is a substrate for Escherichia coli endonuclease IV. Biochemistry 33 (1994) 7842–7847. [PMID: 7516707]
6.	Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P. and Tainer, J.A. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98 (1999) 397–408. [DOI] [PMID: 10458614]

[EC 3.1.21.2 created 1972 as EC 3.1.4.30, transferred 1978 to EC 3.1.21.2, modified 2014]

3.1.21.8

Accepted name:

T₄ deoxyribonuclease II

Reaction:

Endonucleolytic nicking and cleavage of cytosine-containing double-stranded DNA.

Other name(s):

T₄ endonuclease II; EndoII (ambiguous); denA (gene name)

Comments:

Requires Mg²⁺. This phage T₄ enzyme is involved in degradation of host DNA. The enzyme primarily catalyses nicking of the bottom strand of double stranded DNA between the first and second base pair to the right of a top-strand CCGC motif. Double-stranded breaks are produced 5- to 10-fold less frequently [3]. It does not cleave the T4 native DNA, which contains 5-hydroxymethylcytosine instead of cytosine.

Links to other databases:

References:

1.	Carlson, K., Krabbe, M., Nystrom, A.C. and Kosturko, L.D. DNA determinants of restriction. Bacteriophage T₄ endonuclease II-dependent cleavage of plasmid DNA in vivo. J. Biol. Chem. 268 (1993) 8908–8918. [PMID: 8386173]
2.	Carlson, K. and Kosturko, L.D. Endonuclease II of coliphage T₄: a recombinase disguised as a restriction endonuclease. Mol. Microbiol. 27 (1998) 671–676. [DOI] [PMID: 9515694]
3.	Carlson, K., Kosturko, L.D. and Nystrom, A.C. Sequence-specific cleavage by bacteriophage T₄ endonuclease II in vitro. Mol. Microbiol. 31 (1999) 1395–1405. [DOI] [PMID: 10200960]
4.	Andersson, C.E., Lagerback, P. and Carlson, K. Structure of bacteriophage T₄ endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. J. Mol. Biol. 397 (2010) 1003–1016. [DOI] [PMID: 20156453]

[EC 3.1.21.8 created 2014]

3.1.21.9

Accepted name:

T₄ deoxyribonuclease IV

Reaction:

Endonucleolytic cleavage of the 5′ phosphodiester bond of deoxycytidine in single-stranded DNA.

Other name(s):

T₄ endonuclease IV; EndoIV (ambiguous); denB (gene name)

Comments:

This phage T₄ enzyme is involved in degradation of host DNA. The enzyme does not cleave double-stranded DNA or native T4 DNA, which contains 5-hydroxymethylcytosine instead of cytosine.

Links to other databases:

References:

1.	Sadowski, P.D. and Hurwitz, J. Enzymatic breakage of deoxyribonucleic acid. II. Purification and properties of endonuclease IV from T4 phage-infected Escherichia coli. J. Biol. Chem. 244 (1969) 6192–6198. [PMID: 4900512]
2.	Ling, V. Partial digestion of ³²P-fd DNA with T⁴ endonuclease IV. FEBS Lett. 19 (1971) 50–54. [DOI] [PMID: 11946172]
3.	Sadowski, P.D. and Bakyta, I. T₄ endonuclease IV. Improved purification procedure and resolution from T₄ endonuclease 3. J. Biol. Chem. 247 (1972) 405–412. [PMID: 4550601]
4.	Bernardi, A., Maat, J., de Waard, A. and Bernardi, G. Preparation and specificity of endonuclease IV induced by bacteriophage T₄. Eur. J. Biochem. 66 (1976) 175–179. [DOI] [PMID: 782881]
5.	Hirano, N., Ohshima, H. and Takahashi, H. Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T₄, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis. Nucleic Acids Res. 34 (2006) 4743–4751. [DOI] [PMID: 16971463]
6.	Ohshima, H., Hirano, N. and Takahashi, H. A hexanucleotide sequence (dC1-dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T₄. Nucleic Acids Res. 35 (2007) 6681–6689. [DOI] [PMID: 17940096]

[EC 3.1.21.9 created 2014]

3.1.27.9

Transferred entry:

tRNA-intron endonuclease. Now EC 4.6.1.16, tRNA-intron lyase

[EC 3.1.27.9 created 1992, deleted 2014]

3.2.1.187

Accepted name:

(Ara-f)₃-Hyp β-L-arabinobiosidase

Reaction:

4-O-(β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H₂O = 4-O-(β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranose

Glossary:

4-O-(β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline = (Ara-f)₃-Hyp

Other name(s):

hypBA2 (gene name); β-L-arabinobiosidase

Systematic name:

4-O-(β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline β-L-arabinofuranosyl-(1→2)-β-L-arabinofuranose hydrolase

Comments:

The enzyme, which was identified in the bacterium Bifidobacterium longum JCM1217, is specific for (Ara-f)₃-Hyp, a sugar chain found in hydroxyproline-rich glyoproteins such as extensin and lectin. The enzyme was not able to accept (Ara-f)₂-Hyp or (Ara-f)₄-Hyp as substrates. In the presence of 1-alkanols, the enzyme demonstrates transglycosylation activity, retaining the anomeric configuration of the arabinofuranose residue.

Links to other databases:

References:

1.	Fujita, K., Sakamoto, S., Ono, Y., Wakao, M., Suda, Y., Kitahara, K. and Suganuma, T. Molecular cloning and characterization of a β-L-Arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family. J. Biol. Chem. 286 (2011) 5143–5150. [DOI] [PMID: 21149454]

[EC 3.2.1.187 created 2013]

3.2.1.188

Accepted name:

avenacosidase

Reaction:

avenacoside B + H₂O = 26-desgluco-avenacoside B + D-glucose

Glossary:

avenacoside B = (22S,25S)-3β-{β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-[α-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyloxy}-26-(β-D-glucopyranosyloxy)-22,25-epoxyfurost-5-ene
26-desgluco-avenacoside B = (22S,25S)-3β-{β-D-glucopyranosyl-(1→3)-β-D-glucopyranosyl-(1→4)-[α-L-rhamnopyranosyl-(1→2)]-β-D-glucopyranosyloxy}-22,25-epoxyfurost-5-en-26-ol

Other name(s):

As-P60

Systematic name:

avenacoside B 26-β-D-glucohydrolase

Comments:

Isolated from oat (Avena sativa) seedlings. The product acts as a defense system against fungal infection. Also acts on avenacoside A.

Links to other databases:

References:

1.	Gus-Mayer, S., Brunner, H., Schneider-Poetsch, H.A. and Rudiger, W. Avenacosidase from oat: purification, sequence analysis and biochemical characterization of a new member of the BGA family of β-glucosidases. Plant Mol. Biol. 26 (1994) 909–921. [PMID: 8000004]
2.	Gus-Mayer, S., Brunner, H., Schneider-Poetsch, H.A., Lottspeich, F., Eckerskorn, C., Grimm, R. and Rudiger, W. The amino acid sequence previously attributed to a protein kinase or a TCP1-related molecular chaperone and co-purified with phytochrome is a β-glucosidase. FEBS Lett. 347 (1994) 51–54. [DOI] [PMID: 8013661]

[EC 3.2.1.188 created 2013]

3.2.1.189

Accepted name:

dioscin glycosidase (diosgenin-forming)

Reaction:

3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin + 3 H₂O = D-glucose + 2 L-rhamnose + diosgenin

For diagram of diosgenin catabolism, click here

Glossary:

3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin = (3β,25R)-spirost-5-en-3-yl 6-deoxy-α-L-mannopyranosyl-(1→2)-[6-deoxy-α-L-mannopyranosyl-(1→4)]-β-D-glucopyranoside = dioscin
diosgenin = (3β,25R)-spirost-5-en-3-ol

Other name(s):

dioscin glycosidase (aglycone-forming)

Systematic name:

3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin hydrolase (diosgenin-forming)

Comments:

The enzyme is involved in degradation of the steroid saponin dioscin by some fungi of the Absidia genus. The enzyme can also hydrolyse 3-O-[α-L-Ara-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin into diosgenin and free sugars as the final products. cf. EC 3.2.1.190, dioscin glycosidase (3-O-β-D-Glc-diosgenin-forming).

Links to other databases:

References:

1.	Fu, Y., Yu, H., Tang, S.H., Hu, X., Wang, Y., Liu, B., Yu, C. and Jin, F. New dioscin-glycosidase hydrolyzing multi-glycosides of dioscin from Absidia strain. J. Microbiol. Biotechnol. 20 (2010) 1011–1017. [PMID: 20622501]

[EC 3.2.1.189 created 2013]

3.2.1.190

Accepted name:

dioscin glycosidase (3-O-β-D-Glc-diosgenin-forming)

Reaction:

3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin + 2 H₂O = 2 L-rhamnopyranose + diosgenin 3-O-β-D-glucopyranoside

For diagram of diosgenin catabolism, click here

Glossary:

Other name(s):

dioscin-α-L-rhamnosidase

Systematic name:

3-O-[α-L-Rha-(1→4)-[α-L-Rha-(1→2)]-β-D-Glc]diosgenin (3-O-β-D-Glc-diosgenin-forming)

Comments:

The enzyme is involved in the hydrolysis of the steroid saponin dioscin by the digestive system of Sus scrofa (pig). cf. EC 3.2.1.189, dioscin glycosidase (diosgenin-forming).

Links to other databases:

References:

1.	Qian, S., Yu, H., Zhang, C., Lu, M., Wang, H. and Jin, F. Purification and characterization of dioscin-α-L-rhamnosidase from pig liver. Chem Pharm Bull (Tokyo) 53 (2005) 911–914. [PMID: 16079518]

[EC 3.2.1.190 created 2013]

3.2.1.191

Accepted name:

ginsenosidase type III

Reaction:

a protopanaxadiol-type ginsenoside with two glucosyl residues at position 3 + 2 H₂O = a protopanaxadiol-type ginsenoside with no glycosidic modification at position 3 + 2 D-glucopyranose (overall reaction)
(1a) a protopanaxadiol-type ginsenoside with two glucosyl residues at position 3 + H₂O = a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + D-glucopyranose
(1b) a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + H₂O = a protopanaxadiol-type ginsenoside with no glycosidic modification at position 3 + D-glucopyranose

For diagram of protopanaxadiol ginsenosides ginsenosidases, click here

Glossary:

ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
gypenoside XVII = 3β-(β-D-glucopyranosyloxy)-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
gypenoside LXXV = 20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-ene-3β,12β-diol

Systematic name:

protopanaxadiol-type ginsenoside 3-β-D-hydrolase

Comments:

Ginsenosidase type III catalyses the sequential hydrolysis of the 3-O-β-D-(1→2)-glucopyranosyl bond followed by hydrolysis of the 3-O-β-D-glucopyranosyl bond of protopanaxadiol ginsenosides. When acting for example on ginsenoside Rb1 the enzyme first generates ginsenoside XVII, and subsequently ginsenoside LXXV.

Links to other databases:

References:

1.	Jin, X.F., Yu, H.S., Wang, D.M., Liu, T.Q., Liu, C.Y., An, D.S., Im, W.T., Kim, S.G. and Jin, F.X. Kinetics of a cloned special ginsenosidase hydrolyzing 3-O-glucoside of multi-protopanaxadiol-type ginsenosides, named ginsenosidase type III. J. Microbiol. Biotechnol. 22 (2012) 343–351. [PMID: 22450790]
2.	An, D.S., Cui, C.H., Lee, H.G., Wang, L., Kim, S.C., Lee, S.T., Jin, F., Yu, H., Chin, Y.W., Lee, H.K., Im, W.T. and Kim, S.G. Identification and characterization of a novel Terrabacter ginsenosidimutans sp. nov. β-glucosidase that transforms ginsenoside Rb1 into the rare gypenosides XVII and LXXV. Appl. Environ. Microbiol. 76 (2010) 5827–5836. [DOI] [PMID: 20622122]
3.	Hong, H., Cui, C.H., Kim, J.K., Jin, F.X., Kim, S.C. and Im, W.T. Enzymatic Biotransformation of Ginsenoside Rb1 and Gypenoside XVII into Ginsenosides Rd and F2 by Recombinant β-glucosidase from Flavobacterium johnsoniae. J Ginseng Res 36 (2012) 418–424. [DOI] [PMID: 23717145]

[EC 3.2.1.191 created 2014]

3.2.1.192

Accepted name:

ginsenoside Rb1 β-glucosidase

Reaction:

ginsenoside Rb1 + 2 H₂O = ginsenoside Rg3 + 2 D-glucopyranose (overall reaction)
(1a) ginsenoside Rb1 + H₂O = ginsenoside Rd + D-glucopyranose
(1b) ginsenoside Rd + H₂O = ginsenoside Rg3 + D-glucopyranose

For diagram of protopanaxadiol ginsenosides ginsenosidases, click here

Glossary:

ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rd = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside F2 = 3β,20-bis(β-D-glucopyranosyloxy)dammar-24-en-12β-ol

Systematic name:

ginsenoside Rb1 glucohydrolase

Comments:

Ginsenosidases catalyse the hydrolysis of glycosyl moieties attached to the C-3, C-6 or C-20 position of ginsenosides. They are specific with respect to the nature of the glycosidic linkage, the position and the order in which the linkages are cleaved. Ginsenoside Rb1 β-glucosidase specifically and sequentially hydrolyses the 20-[β-D-glucopyranosyl-(1→6)-β-D glucopyranosyloxy] residues attached to position 20 by first hydrolysing the (1→6)-glucosidic bond to generate ginsenoside Rd as an intermediate, followed by hydrolysis of the remaining 20-O-β-D-glucosidic bond.

Links to other databases:

References:

1.	Yan, Q., Zhou, W., Li, X., Feng, M. and Zhou, P. Purification method improvement and characterization of a novel ginsenoside-hydrolyzing β-glucosidase from Paecilomyces Bainier sp. 229. Biosci. Biotechnol. Biochem. 72 (2008) 352–359. [DOI] [PMID: 18256474]

[EC 3.2.1.192 created 2014]

3.2.1.193

Accepted name:

ginsenosidase type I

Reaction:

(1) a protopanaxadiol-type ginsenoside with two glucosyl residues at position 3 + H₂O = a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + D-glucopyranose
(2) a protopanaxadiol-type ginsenoside with one glucosyl residue at position 3 + H₂O = a protopanaxadiol-type ginsenoside with no glycosidic modifications at position 3 + D-glucopyranose
(3) a protopanaxadiol-type ginsenoside with two glycosyl residues at position 20 + H₂O = a protopanaxadiol-type ginsenoside with a single glucosyl residue at position 20 + a monosaccharide

For diagram of protopanaxadiol ginsenosides ginsenosidases, click here

Glossary:

ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb2 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb3 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[β-D-xylopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rc = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinofuranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rd = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside F2 = 3β,20-bis(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside C-K = 20β-(β-D-glucopyranosyloxy)dammar-24-ene-3β,12β-diol
ginsenoside Rh2 = 3β-(β-D-glucopyranosyloxy)dammar-24-ene-12β,20-diol

Systematic name:

ginsenoside glucohydrolase

Comments:

Ginsenosidase type I is slightly activated by Mg²⁺ or Ca²⁺ [1]. The enzyme hydrolyses the 3-O-β-D-(1→2)-glucosidic bond, the 3-O-β-D-glucopyranosyl bond and the 20-O-β-D-(1→6)-glycosidic bond of protopanaxadiol-type ginsenosides. It usually leaves a single glucosyl residue attached at position 20 and one or no glucosyl residues at position 3. Starting with a ginsenoside that is glycosylated at both positions (e.g. ginsenoside Rb1, Rb2, Rb3, Rc or Rd), the most common products are ginsenoside F2 and ginsenoside C-K, with low amounts of ginsenoside Rh2.

Links to other databases:

References:

1.	Yu, H., Zhang, C., Lu, M., Sun, F., Fu, Y. and Jin, F. Purification and characterization of new special ginsenosidase hydrolyzing multi-glycisides of protopanaxadiol ginsenosides, ginsenosidase type I. Chem Pharm Bull (Tokyo) 55 (2007) 231–235. [PMID: 17268094]

[EC 3.2.1.193 created 2014]

3.2.1.194

Accepted name:

ginsenosidase type IV

Reaction:

a protopanaxatriol-type ginsenoside with two glycosyl residues at position 6 + 2 H₂O = a protopanaxatriol-type ginsenoside with no glycosidic modification at position 6 + D-glucopyranose + a monosaccharide (overall reaction)
(1a) a protopanaxatriol-type ginsenoside with two glycosyl residues at position 6 + H₂O = a protopanaxatriol-type ginsenoside with a single glucosyl at position 6 + a monosaccharide
(1b) a protopanaxatriol-type ginsenoside with a single glucosyl at position 6 + H₂O = a protopanaxatriol-type ginsenoside with no glycosidic modification at position 6 + D-glucopyranose

For diagram of protopanaxatriol ginsenosides ginsenosidases, click here

Glossary:

ginsenoside Re = 20-(β-D-glucopyranosyl)oxy-6α-[α-L-rhamnopyranosyl-(1→2)-β-D-glucopyranosyloxy]dammar-24-en-3β,12β-diol
ginsenoside Rg1 = 6α,20-bis(β-D-glucopyranosyl)oxy-dammar-24-en-3β,12β-diol
ginsenoside F1 = 20-(β-D-glucopyranosyloxy)dammar-24-en-3β,6α,12β-triol

Systematic name:

protopanaxatriol-type ginsenoside 6-β-D-glucohydrolase

Comments:

Ginsenosidase type IV catalyses the sequential hydrolysis of the 6-O-β-D-(1→2)-glycosidic bond or the 6-O-α-D-(1→2)-glycosidic bond in protopanaxatriol-type ginsenosides with a disacchride attached to the C₆ position, followed by the hydrolysis of the remaining 6-O-β-D-glycosidic bond (e.g. ginsenoside Re → ginsenoside Rg1 → ginsenoside F1).

Links to other databases:

References:

1.	Wang, D.M., Yu, H.S., Song, J.G., Xu, Y.F., Liu, C.Y. and Jin, F.X. A novel ginsenosidase from an Aspergillus strain hydrolyzing 6-O-multi-glycosides of protopanaxatriol-type ginsenosides, named ginsenosidase type IV. J. Microbiol. Biotechnol. 21 (2011) 1057–1063. [PMID: 22031031]
2.	Wang, D, Yu, H., Song, J., Xu, Y., Jin, F. Enzyme kinetics of ginsenosidase type IV hydrolyzing 6-O-multi-glycosides of protopanaxatriol type ginsenosides. Process Biochem. 47 (2012) 133–138.

[EC 3.2.1.194 created 2014]

3.2.1.195

Accepted name:

20-O-multi-glycoside ginsenosidase

Reaction:

a protopanaxadiol-type ginsenoside with two glycosyl residues at position 20 + H₂O = a protopanaxadiol-type ginsenoside with a single glucosyl residue at position 20 + a monosaccharide

For diagram of protopanaxadiol ginsenosides ginsenosidases, click here

Glossary:

ginsenoside Rb1 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-[β-D-glucopyranosyl-(1→6)-β-D-glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb2 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rb3 = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[β-D-xylopyranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rc = 3β-[β-D-glucopyranosyl-(1→2)-β-D glucopyranosyloxy]-20-[α-L-arabinofuranosyl-(1→6)-β-D glucopyranosyloxy]dammar-24-en-12β-ol
ginsenoside Rd = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-en-12β-ol
ginsenoside Rg3 = 3β-[β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyloxy]-20-(β-D-glucopyranosyloxy)dammar-24-ene-12β,20-diol

Other name(s):

ginsenosidase type II (erroneous)

Systematic name:

protopanaxadiol-type ginsenoside 20-β-D-glucohydrolase

Comments:

The 20-O-multi-glycoside ginsenosidase catalyses the hydrolysis of the 20-O-α-(1→6)-glycosidic bond and the 20-O-β-(1→6)-glycosidic bond of protopanaxadiol-type ginsenosides. The enzyme usually leaves a single glucosyl residue attached at position 20, although it can cleave the remaining glucosyl residue with a lower efficiency. Starting with a ginsenoside that is glycosylated at positions 3 and 20, such as ginsenosides Rb1, Rb2, Rb3 and Rc, the most common product is ginsenoside Rd, with a low amount of ginsenoside Rg3 also formed.

Links to other databases:

References:

1.	Yu, H., Liu, Q., Zhang, C., Lu, M., Fu, Y., Im, W.-T., Lee, S.-T. and Jin, F. A new ginsenosidase from Aspergillus strain hydrolyzing 20-O-multi-glycoside of PPD ginsenoside. Process Biochem. 44 (2009) 772–775.

[EC 3.2.1.195 created 2014]

*EC

3.2.2.5

Accepted name:

NAD⁺ glycohydrolase

Reaction:

NAD⁺ + H₂O = ADP-D-ribose + nicotinamide

Glossary:

ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)

Other name(s):

NAD glycohydrolase; nicotinamide adenine dinucleotide glycohydrolase; β-NAD⁺ glycohydrolase; DPNase (ambiguous); NAD hydrolase (ambiguous); diphosphopyridine nucleosidase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD nucleosidase (ambiguous); DPN hydrolase (ambiguous); NADase (ambiguous); nga (gene name); NAD⁺ nucleosidase

Systematic name:

NAD⁺ glycohydrolase

Comments:

This enzyme catalyses the hydrolysis of NAD⁺, without associated ADP-ribosyl cyclase activity (unlike the metazoan enzyme EC 3.2.2.6, bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase). The enzyme from Group A streptococci has been implicated in the pathogenesis of diseases such as streptococcal toxic shock-like syndrome (STSS) and necrotizing fasciitis. The enzyme from the venom of the snake Agkistrodon acutus also catalyses EC 3.6.1.5, apyrase [3].

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9025-46-1

References:

1.	Fehrenbach, F.J. Reinigung und Kristallisation der NAD-Glykohydrolase aus C-Streptokokken. Eur. J. Biochem. 18 (1971) 94–102. [DOI] [PMID: 4322210]
2.	Grushoff, P.S., Shany, S. and Bernheimer, A.W. Purification and properties of streptococcal nicotinamide adenine dinucleotide glycohydrolase. J. Bacteriol. 122 (1975) 599–605. [PMID: 236282]
3.	Zhang, L., Xu, X., Luo, Z., Shen, D. and Wu, H. Identification of an unusual AT(D)Pase-like activity in multifunctional NAD glycohydrolase from the venom of Agkistrodon acutus. Biochimie 91 (2009) 240–251. [DOI] [PMID: 18952139]
4.	Ghosh, J., Anderson, P.J., Chandrasekaran, S. and Caparon, M.G. Characterization of Streptococcus pyogenes β-NAD⁺ glycohydrolase: re-evaluation of enzymatic properties associated with pathogenesis. J. Biol. Chem. 285 (2010) 5683–5694. [DOI] [PMID: 20018886]
5.	Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T. Structural basis of Streptococcus pyogenes immunity to its NAD⁺ glycohydrolase toxin. Structure 19 (2011) 192–202. [DOI] [PMID: 21300288]

[EC 3.2.2.5 created 1961, modified 2013]

*EC

3.2.2.6

Accepted name:

ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

Reaction:

NAD⁺ + H₂O = ADP-D-ribose + nicotinamide (overall reaction)
(1a) NAD⁺ = cyclic ADP-ribose + nicotinamide
(1b) cyclic ADP-ribose + H₂O = ADP-D-ribose

For diagram of cyclic ADP-ribose biosynthesis, click here

Glossary:

ADP-D-ribose = adenosine 5′-(5-deoxy-D-ribofuranos-5-yl diphosphate)
cyclic ADP-ribose = N¹-(β-D-ribosyl)adenosine 5′(P1),5′′(P2)-cyclic diphosphate

Other name(s):

NAD⁺ nucleosidase; NADase (ambiguous); DPNase (ambiguous); DPN hydrolase (ambiguous); NAD hydrolase (ambiguous); nicotinamide adenine dinucleotide nucleosidase (ambiguous); NAD glycohydrolase (misleading); NAD nucleosidase (ambiguous); nicotinamide adenine dinucleotide glycohydrolase (misleading); CD38 (gene name); BST1 (gene name)

Systematic name:

NAD⁺ glycohydrolase (cyclic ADP-ribose-forming)

Comments:

This multiunctional enzyme acts on NAD⁺, catalysing both the synthesis and hydrolysis of cyclic ADP-ribose, a calcium messenger that can mobilize intracellular Ca²⁺ stores and activate Ca²⁺ influx to regulate a wide range of physiological processes. In addition, the enzyme also catalyses EC 2.4.99.20, 2′-phospho-ADP-ribosyl cyclase/2′-phospho-cyclic-ADP-ribose transferase. It is also able to act on β-nicotinamide D-ribonucleotide. cf. EC 3.2.2.5, NAD⁺ glycohydrolase.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9032-65-9

References:

1.	Imai, T. Purification and characterization of a pyridine nucleotide glycohydrolase from rabbit spleen. J. Biochem. 106 (1989) 928–937. [PMID: 2613697]
2.	Howard, M., Grimaldi, J.C., Bazan, J.F., Lund, F.E., Santos-Argumedo, L., Parkhouse, R.M., Walseth, T.F. and Lee, H.C. Formation and hydrolysis of cyclic ADP-ribose catalyzed by lymphocyte antigen CD38. Science 262 (1993) 1056–1059. [DOI] [PMID: 8235624]
3.	Takasawa, S., Tohgo, A., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Yonekura, H. and Okamoto, H. Synthesis and hydrolysis of cyclic ADP-ribose by human leukocyte antigen CD38 and inhibition of the hydrolysis by ATP. J. Biol. Chem. 268 (1993) 26052–26054. [PMID: 8253715]
4.	Tohgo, A., Takasawa, S., Noguchi, N., Koguma, T., Nata, K., Sugimoto, T., Furuya, Y., Yonekura, H. and Okamoto, H. Essential cysteine residues for cyclic ADP-ribose synthesis and hydrolysis by CD38. J. Biol. Chem. 269 (1994) 28555–28557. [PMID: 7961800]
5.	Fryxell, K.B., O'Donoghue, K., Graeff, R.M., Lee, H.C. and Branton, W.D. Functional expression of soluble forms of human CD38 in Escherichia coli and Pichia pastoris. Protein Expr. Purif. 6 (1995) 329–336. [DOI] [PMID: 7663169]
6.	Yamamoto-Katayama, S., Ariyoshi, M., Ishihara, K., Hirano, T., Jingami, H. and Morikawa, K. Crystallographic studies on human BST-1/CD157 with ADP-ribosyl cyclase and NAD glycohydrolase activities. J. Mol. Biol. 316 (2002) 711–723. [DOI] [PMID: 11866528]
7.	Liu, Q., Kriksunov, I.A., Graeff, R., Munshi, C., Lee, H.C. and Hao, Q. Crystal structure of human CD38 extracellular domain. Structure 13 (2005) 1331–1339. [DOI] [PMID: 16154090]

[EC 3.2.2.6 created 1961, modified 2004, modified 2014, modified 2018]

3.2.2.30

Accepted name:

aminodeoxyfutalosine nucleosidase

Reaction:

6-amino-6-deoxyfutalosine + H₂O = dehypoxanthine futalosine + adenine

For diagram of the futalosine pathway, click here

Glossary:

6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
dehypoxanthine futalosine = 3-{3-[(2R,3S,4R)-3,4,5-trihydroxytetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s):

AFL nucleosidase; aminofutalosine nucleosidase; methylthioadenosine nucleosidase; MqnB (ambiguous)

Systematic name:

6-amino-6-deoxyfutalosine ribohydrolase

Comments:

The enzyme, found in several bacterial species, catalyses a step in a modified futalosine pathway for menaquinone biosynthesis. While the enzyme from some organisms also has the activity of EC 3.2.2.9, adenosylhomocysteine nucleosidase, the enzyme from Chlamydia trachomatis is specific for 6-amino-6-deoxyfutalosine [7].

Links to other databases:

References:

1.	Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H. and Dairi, T. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321 (2008) 1670–1673. [DOI] [PMID: 18801996]
2.	Li, X., Apel, D., Gaynor, E.C. and Tanner, M.E. 5′-methylthioadenosine nucleosidase is implicated in playing a key role in a modified futalosine pathway for menaquinone biosynthesis in Campylobacter jejuni. J. Biol. Chem. 286 (2011) 19392–19398. [DOI] [PMID: 21489995]
3.	Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913–916. [DOI] [PMID: 21098241]
4.	Wang, S., Haapalainen, A.M., Yan, F., Du, Q., Tyler, P.C., Evans, G.B., Rinaldo-Matthis, A., Brown, R.L., Norris, G.E., Almo, S.C. and Schramm, V.L. A picomolar transition state analogue inhibitor of MTAN as a specific antibiotic for Helicobacter pylori. Biochemistry 51 (2012) 6892–6894. [DOI] [PMID: 22891633]
5.	Mishra, V. and Ronning, D.R. Crystal structures of the Helicobacter pylori MTAN enzyme reveal specific interactions between S-adenosylhomocysteine and the 5′-alkylthio binding subsite. Biochemistry 51 (2012) 9763–9772. [DOI] [PMID: 23148563]
6.	Kim, R.Q., Offen, W.A., Davies, G.J. and Stubbs, K.A. Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 177–185. [DOI] [PMID: 24419390]
7.	Barta, M.L., Thomas, K., Yuan, H., Lovell, S., Battaile, K.P., Schramm, V.L. and Hefty, P.S. Structural and biochemical characterization of Chlamydia trachomatis hypothetical protein CT263 supports that menaquinone synthesis occurs through the futalosine pathway. J. Biol. Chem. 289 (2014) 32214–32229. [DOI] [PMID: 25253688]

[EC 3.2.2.30 created 2014]

3.3.2.13

Accepted name:

chorismatase

Reaction:

chorismate + H₂O = (4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate

For diagram of shikimate and chorismate biosynthesis, click here

Glossary:

chorismate = (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylate

Other name(s):

chorismate/3,4-dihydroxycyclohexa-1,5-dienoate synthase; fkbO (gene name); rapK (gene name)

Systematic name:

chorismate pyruvate-hydrolase

Comments:

The enzyme found in several bacterial species is involved in the biosynthesis of macrocyclic polyketides.

Links to other databases:

References:

Andexer, J.N., Kendrew, S.G., Nur-e-Alam, M., Lazos, O., Foster, T.A., Zimmermann, A.S., Warneck, T.D., Suthar, D., Coates, N.J., Koehn, F.E., Skotnicki, J.S., Carter, G.T., Gregory, M.A., Martin, C.J., Moss, S.J., Leadlay, P.F. and Wilkinson, B. Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate. Proc. Natl. Acad. Sci. USA 108 (2011) 4776–4781. [DOI] [PMID: 21383123]

Juneja, P., Hubrich, F., Diederichs, K., Welte, W. and Andexer, J.N. Mechanistic implications for the chorismatase FkbO based on the crystal structure. J. Mol. Biol. 426 (2014) 105–115. [DOI] [PMID: 24036425]

[EC 3.3.2.13 created 2013]

3.4.21.121

Accepted name:

Lys-Lys/Arg-Xaa endopeptidase

Reaction:

Cleavage of -Lys-Lys┼ and -Lys-Arg┼ bonds.

Other name(s):

ASP (Aeromonas sobria)-type peptidase; Aeromonas extracellular serine protease

Comments:

The enzyme is a serine peptidase, which has been shown to cleave prothrombin and prekallikrein. It hydrolyses the complement component C5 releasing complement component C5a.

Links to other databases:

References:

1.	Kobayashi, H., Utsunomiya, H., Yamanaka, H., Sei, Y., Katunuma, N., Okamoto, K. and Tsuge, H. Structural basis for the kexin-like serine protease from Aeromonas sobria as sepsis-causing factor. J. Biol. Chem. 284 (2009) 27655–27663. [DOI] [PMID: 19654332]
2.	Nitta, H., Kobayashi, H., Irie, A., Baba, H., Okamoto, K. and Imamura, T. Activation of prothrombin by ASP, a serine protease released from Aeromonas sobria. FEBS Lett. 581 (2007) 5935–5939. [DOI] [PMID: 18067862]
3.	Kobayashi, H., Takahashi, E., Oguma, K., Fujii, Y., Yamanaka, H., Negishi, T., Arimoto-Kobayashi, S., Tsuji, T. and Okamoto, K. Cleavage specificity of the serine protease of Aeromonas sobria, a member of the kexin family of subtilases. FEMS Microbiol. Lett. 256 (2006) 165–170. [DOI] [PMID: 16487335]
4.	Imamura, T., Nitta, H., Wada, Y., Kobayashi, H. and Okamoto, K. Impaired plasma clottability induction through fibrinogen degradation by ASP, a serine protease released from Aeromonas sobria. FEMS Microbiol. Lett. 284 (2008) 35–42. [DOI] [PMID: 18462393]
5.	Nitta, H., Imamura, T., Wada, Y., Irie, A., Kobayashi, H., Okamoto, K. and Baba, H. Production of C5a by ASP, a serine protease released from Aeromonas sobria. J. Immunol. 181 (2008) 3602–3608. [DOI] [PMID: 18714034]

[EC 3.4.21.121 created 2013]

*EC

3.5.1.14

Accepted name:

N-acyl-aliphatic-L-amino acid amidohydrolase

Reaction:

(1) an N-acyl-aliphatic-L-amino acid + H₂O = an aliphatic L-amino acid + a carboxylate
(2) an N-acetyl-L-cysteine-S-conjugate + H₂O = an L-cysteine-S-conjugate + acetate

Glossary:

N-acetyl-L-cysteine-S-conjugate = mercapturic acid

Other name(s):

aminoacylase 1; aminoacylase I; dehydropeptidase II; histozyme; hippuricase; benzamidase; acylase I; hippurase; amido acid deacylase; L-aminoacylase; acylase; aminoacylase; L-amino-acid acylase; α-N-acylaminoacid hydrolase; long acyl amidoacylase; short acyl amidoacylase; ACY1 (gene name); N-acyl-L-amino-acid amidohydrolase

Systematic name:

N-acyl-aliphatic-L-amino acid amidohydrolase (carboxylate-forming)

Comments:

Contains Zn²⁺. The enzyme is found in animals and is involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate). It acts on mercapturic acids (S-conjugates of N-acetyl-L-cysteine) and neutral aliphatic N-acyl-α-amino acids. Some bacterial aminoacylases demonstrate substrate specificity of both EC 3.5.1.14 and EC 3.5.1.114. cf. EC 3.5.1.15, aspartoacylase and EC 3.5.1.114, N-acyl-aromatic-L-amino acid amidohydrolase.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9012-37-7

References:

1.	Birnbaum, S.M., Levintow, L., Kingsley, R.B. and Greenstein, J.P. Specificity of amino acid acylases. J. Biol. Chem. 194 (1952) 455–470. [PMID: 14927637]
2.	Fones, W.S. and Lee, M. Hydrolysis of N-acyl derivatives of alanine and phenylalanine by acylase I and carboxypeptidase. J. Biol. Chem. 201 (1953) 847–856. [PMID: 13061423]
3.	Henseling, J. and Rohm, K.H. Aminoacylase I from hog kidney: anion effects and the pH dependence of kinetic parameters. Biochim. Biophys. Acta 959 (1988) 370–377. [DOI] [PMID: 3355856]
4.	Heese, D., Berger, S. and Rohm, K.H. Nuclear magnetic relaxation studies of the role of the metal ion in Mn²⁺-substituted aminoacylase I. Eur. J. Biochem. 188 (1990) 175–180. [DOI] [PMID: 2318199]
5.	Palm, G.J. and Rohm, K.H. Aminoacylase I from porcine kidney: identification and characterization of two major protein domains. J. Protein Chem. 14 (1995) 233–240. [PMID: 7662111]
6.	Uttamsingh, V., Keller, D.A. and Anders, M.W. Acylase I-catalyzed deacetylation of N-acetyl-L-cysteine and S-alkyl-N-acetyl-L-cysteines. Chem. Res. Toxicol. 11 (1998) 800–809. [DOI] [PMID: 9671543]
7.	Lindner, H., Hopfner, S., Tafler-Naumann, M., Miko, M., Konrad, L. and Rohm, K.H. The distribution of aminoacylase I among mammalian species and localization of the enzyme in porcine kidney. Biochimie 82 (2000) 129–137. [DOI] [PMID: 10727768]

[EC 3.5.1.14 created 1965, modified 2013]

3.5.1.114

Accepted name:

N-acyl-aromatic-L-amino acid amidohydrolase

Reaction:

(1) an N-acyl-aromatic-L-amino acid + H₂O = an aromatic-L-amino acid + a carboxylate
(2) an N-acetyl-L-cysteine-S-conjugate + H₂O = an L-cysteine-S-conjugate + acetate

Glossary:

N-acetyl-L-cysteine-S-conjugate = mercapturic acid

Other name(s):

aminoacylase 3; aminoacylase III; ACY3 (gene name)

Systematic name:

N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)

Comments:

This enzyme is found in animals and is involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate). It preferentially deacetylates N^α-acetylated aromatic amino acids and mercapturic acids (S-conjugates of N-acetyl-L-cysteine) that are usually not deacetylated by EC 3.5.1.14, N-acyl-aliphatic-L-amino acid amidohydrolase. The enzyme is significantly activated by Co²⁺ and Ni²⁺ [3]. Some bacterial aminoacylases demonstrate substrate specificity for both EC 3.5.1.14 and EC 3.5.1.114. cf. EC 3.5.1.14, N-acyl-aliphatic-L-amino acid amidohydrolase and EC 3.5.1.15, aspartoacylase.

Links to other databases:

References:

1.	Pushkin, A., Carpenito, G., Abuladze, N., Newman, D., Tsuprun, V., Ryazantsev, S., Motemoturu, S., Sassani, P., Solovieva, N., Dukkipati, R. and Kurtz, I. Structural characterization, tissue distribution, and functional expression of murine aminoacylase III. Am. J. Physiol. Cell Physiol. 286 (2004) C848–C856. [DOI] [PMID: 14656720]
2.	Newman, D., Abuladze, N., Scholz, K., Dekant, W., Tsuprun, V., Ryazantsev, S., Bondar, G., Sassani, P., Kurtz, I. and Pushkin, A. Specificity of aminoacylase III-mediated deacetylation of mercapturic acids. Drug Metab. Dispos. 35 (2007) 43–50. [DOI] [PMID: 17012540]
3.	Tsirulnikov, K., Abuladze, N., Newman, D., Ryazantsev, S., Wolak, T., Magilnick, N., Koag, M.C., Kurtz, I. and Pushkin, A. Mouse aminoacylase 3: a metalloenzyme activated by cobalt and nickel. Biochim. Biophys. Acta 1794 (2009) 1049–1057. [DOI] [PMID: 19362172]
4.	Hsieh, J.M., Tsirulnikov, K., Sawaya, M.R., Magilnick, N., Abuladze, N., Kurtz, I., Abramson, J. and Pushkin, A. Structures of aminoacylase 3 in complex with acetylated substrates. Proc. Natl. Acad. Sci. USA 107 (2010) 17962–17967. [DOI] [PMID: 20921362]
5.	Tsirulnikov, K., Abuladze, N., Bragin, A., Faull, K., Cascio, D., Damoiseaux, R., Schibler, M.J. and Pushkin, A. Inhibition of aminoacylase 3 protects rat brain cortex neuronal cells from the toxicity of 4-hydroxy-2-nonenal mercapturate and 4-hydroxy-2-nonenal. Toxicol. Appl. Pharmacol. 263 (2012) 303–314. [DOI] [PMID: 22819785]

[EC 3.5.1.114 created 2013]

3.5.1.115

Accepted name:

mycothiol S-conjugate amidase

Reaction:

a mycothiol S-conjugate + H₂O = an N-acetyl L-cysteine-S-conjugate + 1-O-(2-amino-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol

Glossary:

mycothiol = 1-O-[2-(N²-acetyl-L-cysteinamido)-2-deoxy-α-D-glucopyranosyl]-1D-myo-inositol
N-acetyl L-cysteine-S-conjugate = mercapturic acid

Other name(s):

MCA

Systematic name:

mycothiol S-conjugate 1D-myo-inositol 2-amino-2-deoxy-α-D-glucopyranosyl-hydrolase

Comments:

The enzyme that is found in actinomycetes is involved in the detoxification of oxidizing agents and electrophilic antibiotics. The enzyme has low activity with 1-O-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-1D-myo-inositol as substrate (cf. EC 3.5.1.103, N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-α-D-glucopyranoside deacetylase) [2].

Links to other databases:

References:

1.	Newton, G.L., Av-Gay, Y. and Fahey, R.C. A novel mycothiol-dependent detoxification pathway in mycobacteria involving mycothiol S-conjugate amidase. Biochemistry 39 (2000) 10739–10746. [DOI] [PMID: 10978158]
2.	Steffek, M., Newton, G.L., Av-Gay, Y. and Fahey, R.C. Characterization of Mycobacterium tuberculosis mycothiol S-conjugate amidase. Biochemistry 42 (2003) 12067–12076. [DOI] [PMID: 14556638]

[EC 3.5.1.115 created 2013]

3.5.1.116

Accepted name:

ureidoglycolate amidohydrolase

Reaction:

(S)-ureidoglycolate + H₂O = glyoxylate + 2 NH₃ + CO₂

For diagram of AMP catabolism, click here

Other name(s):

ureidoglycolate hydrolase; UAH (gene name)

Systematic name:

(S)-ureidoglycolate amidohydrolase (decarboxylating)

Comments:

This plant enzyme is involved in the degradation of ureidoglycolate, an intermediate of purine degradation. Not to be confused with EC 4.3.2.3, ureidoglycolate lyase, which releases urea rather than ammonia.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 115629-07-7

References:

1.	Winkler, R.G., Blevins, D.G. and Randall, D.D. Ureide catabolism in soybeans. III. Ureidoglycolate amidohydrolase and allantoate amidohydrolase are activities of an allantoate degrading enzyme complex. Plant Physiol. 86 (1988) 1084–1088. [PMID: 16666035]
2.	Wells, X.E. and Lees, E.M. Ureidoglycolate amidohydrolase from developing French bean fruits (Phaseolus vulgaris [L.].). Arch. Biochem. Biophys. 287 (1991) 151–159. [DOI] [PMID: 1910298]
3.	Werner, A.K., Romeis, T. and Witte, C.P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 (2010) 19–21. [DOI] [PMID: 19935661]

[EC 3.5.1.116 created 1992 as EC 3.5.3.19, transferred 2014 to EC 3.5.1.116]

3.5.3.19

Transferred entry:

ureidoglycolate hydrolase. Now EC 3.5.1.116, ureidoglycolate amidohydrolase

[EC 3.5.3.19 created 1992, deleted 2014]

3.5.3.26

Accepted name:

(S)-ureidoglycine aminohydrolase

Reaction:

(S)-2-ureidoglycine + H₂O = (S)-ureidoglycolate + NH₃

Other name(s):

UGlyAH; UGHY; ylbA (gene name)

Systematic name:

(S)-ureidoglycine aminohydrolase

Comments:

Binds Mn²⁺. This enzyme, found in plants and bacteria, is part of the ureide pathway, which enables the recycling of the nitrogen in purine compounds. In plants it is localized in the endoplasmic reticulum.

Links to other databases:

References:

1.	Serventi, F., Ramazzina, I., Lamberto, I., Puggioni, V., Gatti, R. and Percudani, R. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. ACS Chem. Biol. 5 (2010) 203–214. [DOI] [PMID: 20038185]
2.	Werner, A.K., Romeis, T. and Witte, C.P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 (2010) 19–21. [DOI] [PMID: 19935661]
3.	Shin, I., Percudani, R. and Rhee, S. Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J. Biol. Chem. 287 (2012) 18796–18805. [DOI] [PMID: 22493446]

[EC 3.5.3.26 created 2013]

3.5.4.40

Accepted name:

aminodeoxyfutalosine deaminase

Reaction:

6-amino-6-deoxyfutalosine + H₂O = futalosine + NH₃

For diagram of the futalosine pathway, click here

Glossary:

6-amino-6-deoxyfutalosine = 3-{3-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]propanoyl}benzoate
futalosine = 3-{3-[(3S,4R)-3,4-dihydroxy-5-(6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]propanoyl}benzoate

Other name(s):

AFL deaminase; aminofutalosine deaminase; mqnX (gene name)

Systematic name:

6-amino-6-deoxyfutalosine deaminase

Comments:

The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

Links to other databases:

References:

1.	Arakawa, C., Kuratsu, M., Furihata, K., Hiratsuka, T., Itoh, N., Seto, H. and Dairi, T. Diversity of the early step of the futalosine pathway. Antimicrob. Agents Chemother. 55 (2011) 913–916. [DOI] [PMID: 21098241]
2.	Goble, A.M., Toro, R., Li, X., Ornelas, A., Fan, H., Eswaramoorthy, S., Patskovsky, Y., Hillerich, B., Seidel, R., Sali, A., Shoichet, B.K., Almo, S.C., Swaminathan, S., Tanner, M.E. and Raushel, F.M. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry 52 (2013) 6525–6536. [DOI] [PMID: 23972005]

[EC 3.5.4.40 created 2014]

3.5.99.10

Accepted name:

2-iminobutanoate/2-iminopropanoate deaminase

Reaction:

(1) 2-iminobutanoate + H₂O = 2-oxobutanoate + NH₃
(2) 2-iminopropanoate + H₂O = pyruvate + NH₃

Other name(s):

yjgF (gene name); ridA (gene name); enamine/imine deaminase (ambiguous)

Systematic name:

2-iminobutanoate aminohydrolase

Comments:

This enzyme, which has been found in all species and tissues examined, catalyses the hydrolytic deamination of imine intermediates formed by several types of pyridoxal-5′-phosphate-dependent dehydratases, such as EC 4.3.1.19, threonine ammonia-lyase and EC 4.3.1.17, L-serine ammonia-lyase. The reactions, which can occur spontaneously, are accelerated to minimize the cellular damage that could be caused by these reactive intermediates.

Links to other databases:

References:

1.	Lambrecht, J.A., Flynn, J.M. and Downs, D.M. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5′-phosphate (PLP)-dependent enzyme reactions. J. Biol. Chem. 287 (2012) 3454–3461. [DOI] [PMID: 22094463]

[EC 3.5.99.10 created 2014]

3.6.1.66

Accepted name:

XTP/dITP diphosphatase

Reaction:

(1) XTP + H₂O = XMP + diphosphate
(2) dITP + H₂O = dIMP + diphosphate
(3) ITP + H₂O = IMP + diphosphate

Other name(s):

hypoxanthine/xanthine dNTP pyrophosphatase; rdgB (gene name)

Systematic name:

XTP/dITP diphosphohydrolase (diphosphate-forming)

Comments:

The enzymes from the bacterium Escherichia coli and the archaea Methanococcus jannaschii and Archaeoglobus fulgidus are highly specific for XTP, dITP and ITP. The activity is dependent on divalent cations, Mg²⁺ is preferred.

Links to other databases:

References:

1.	Hwang, K.Y., Chung, J.H., Kim, S.H., Han, Y.S. and Cho, Y. Structure-based identification of a novel NTPase from Methanococcus jannaschii. Nat. Struct. Biol. 6 (1999) 691–696. [DOI] [PMID: 10404228]
2.	Chung, J.H., Back, J.H., Park, Y.I. and Han, Y.S. Biochemical characterization of a novel hypoxanthine/xanthine dNTP pyrophosphatase from Methanococcus jannaschii. Nucleic Acids Res. 29 (2001) 3099–3107. [DOI] [PMID: 11452035]
3.	Chung, J.H., Park, H.Y., Lee, J.H. and Jang, Y. Identification of the dITP- and XTP-hydrolyzing protein from Escherichia coli. J. Biochem. Mol. Biol. 35 (2002) 403–408. [PMID: 12297000]
4.	Savchenko, A., Proudfoot, M., Skarina, T., Singer, A., Litvinova, O., Sanishvili, R., Brown, G., Chirgadze, N. and Yakunin, A.F. Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli. J. Mol. Biol. 374 (2007) 1091–1103. [DOI] [PMID: 17976651]

[EC 3.6.1.66 created 2013]

3.7.1.21

Accepted name:

6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase

Reaction:

6-oxocyclohex-1-ene-1-carbonyl-CoA + 2 H₂O = 3-hydroxypimeloyl-CoA (overall reaction)
(1a) 6-oxocyclohex-1-ene-1-carbonyl-CoA + H₂O = 2-hydroxy-6-oxocyclohexane-1-carbonyl-CoA
(1b) 2-hydroxy-6-oxocyclohexane-1-carbonyl-CoA + H₂O = 3-hydroxypimeloyl-CoA

For diagram of Benzoyl-CoA catabolism, click here

Glossary:

3-hydroxypimeloyl-CoA = 3-hydroxy-6-carboxyhexanoyl-CoA

Other name(s):

6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (decyclizing)

Systematic name:

6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (ring-opening)

Comments:

The enzyme, which participates in the anaerobic benzoyl-CoA degradation pathway in certain organisms, catalyses the addition of one molecule of water to the double bound of 6-oxocyclohex-1-ene-1-carbonyl-CoA followed by the hydrolytic C-C cleavage of the alicyclic ring.

Links to other databases:

References:

1.	Laempe, D., Jahn, M. and Fuchs, G. 6-Hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, enzymes of the benzoyl-CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 263 (1999) 420–429. [DOI] [PMID: 10406950]
2.	Kuntze, K., Shinoda, Y., Moutakki, H., McInerney, M.J., Vogt, C., Richnow, H.H. and Boll, M. 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environ. Microbiol. 10 (2008) 1547–1556. [DOI] [PMID: 18312395]

[EC 3.7.1.21 created 2014]

3.7.1.22

Accepted name:

3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (ring-opening)

Reaction:

3D-3,5/4-trihydroxycyclohexa-1,2-dione + H₂O = 5-deoxy-D-glucuronate

For diagram of inositol catabolism, click here

Glossary:

3D-3,5/4-trihydroxycyclohexa-1,2-dione = (3R,4S,5R)-3,4,5-trihydroxycyclohexane-1,2-dione

Other name(s):

IolD; THcHDO hydrolase; 3D-3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (decyclizing); 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)

Systematic name:

3D-3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (ring-opening)

Comments:

The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol degradation pathway leading to acetyl-CoA.

Links to other databases:

References:

1.	Yoshida, K., Yamaguchi, M., Morinaga, T., Kinehara, M., Ikeuchi, M., Ashida, H. and Fujita, Y. myo-Inositol catabolism in Bacillus subtilis. J. Biol. Chem. 283 (2008) 10415–10424. [DOI] [PMID: 18310071]

[EC 3.7.1.22 created 2014, modified 2014]

4.1.1.97

Accepted name:

2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase

Reaction:

5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO₂

For diagram of AMP catabolism, click here

Glossary:

5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline

Other name(s):

OHCU decarboxylase; hpxQ (gene name); PRHOXNB (gene name)

Systematic name:

5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate carboxy-lyase [(S)-allantoin-forming]

Comments:

This enzyme is part of the pathway from urate to (S)-allantoin, which is present in bacteria, plants and animals (but not in humans).

Links to other databases:

References:

1.	Ramazzina, I., Folli, C., Secchi, A., Berni, R. and Percudani, R. Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Nat. Chem. Biol. 2 (2006) 144–148. [DOI] [PMID: 16462750]
2.	Cendron, L., Berni, R., Folli, C., Ramazzina, I., Percudani, R. and Zanotti, G. The structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase provides insights into the mechanism of uric acid degradation. J. Biol. Chem. 282 (2007) 18182–18189. [DOI] [PMID: 17428786]
3.	Kim, K., Park, J. and Rhee, S. Structural and functional basis for (S)-allantoin formation in the ureide pathway. J. Biol. Chem. 282 (2007) 23457–23464. [DOI] [PMID: 17567580]
4.	French, J.B. and Ealick, S.E. Structural and mechanistic studies on Klebsiella pneumoniae 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase. J. Biol. Chem. 285 (2010) 35446–35454. [DOI] [PMID: 20826786]

[EC 4.1.1.97 created 2014]

*EC

4.1.2.14

Accepted name:

2-dehydro-3-deoxy-phosphogluconate aldolase

Reaction:

2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate

For diagram of the Entner-Doudoroff pathway, click here

Other name(s):

phospho-2-keto-3-deoxygluconate aldolase; KDPG aldolase; phospho-2-keto-3-deoxygluconic aldolase; 2-keto-3-deoxy-6-phosphogluconic aldolase; 2-keto-3-deoxy-6-phosphogluconate aldolase; 6-phospho-2-keto-3-deoxygluconate aldolase; ODPG aldolase; 2-oxo-3-deoxy-6-phosphogluconate aldolase; 2-keto-3-deoxygluconate-6-P-aldolase; 2-keto-3-deoxygluconate-6-phosphate aldolase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Systematic name:

2-dehydro-3-deoxy-6-phospho-D-gluconate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Comments:

The enzyme shows no activity with 2-dehydro-3-deoxy-6-phosphate-D-galactonate. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase [2]. Also acts on 2-oxobutanoate [1].

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9024-53-7

References:

1.	Meloche, H.P. and Wood, W.A. Crystallization and characteristics of 2-keto-3-deoxy-6-phosphogluconic aldolase. J. Biol. Chem. 239 (1964) 3515–3518. [PMID: 14245411]
2.	Barran, L.R. and Wood, W.A. The mechanism of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Nature of the inactivation by fluorodinitrobenzene. J. Biol. Chem. 246 (1971) 4028–4035. [PMID: 5561473]

[EC 4.1.2.14 created 1965, modified 1976, modified 2014]

*EC

4.1.2.21

Accepted name:

2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Reaction:

2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate

For diagram of the Entner-Doudoroff pathway, click here

Other name(s):

6-phospho-2-keto-3-deoxygalactonate aldolase; phospho-2-keto-3-deoxygalactonate aldolase; 2-keto-3-deoxy-6-phosphogalactonic aldolase; phospho-2-keto-3-deoxygalactonic aldolase; 2-keto-3-deoxy-6-phosphogalactonic acid aldolase; (KDPGal)aldolase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Systematic name:

2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phospho-lyase (pyruvate-forming)

Comments:

The enzyme catalyses the last reaction in a D-galactose degradation pathway. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9030-99-3

References:

1.	Shuster, C.W. 2-Keto-3-deoxy-6-phosphogalactonic acid aldolase. Methods Enzymol. 9 (1966) 524–528.

[EC 4.1.2.21 created 1972, modified 2014]

4.1.2.55

Accepted name:

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Reaction:

(1) 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
(2) 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate

For diagram of the Entner-Doudoroff pathway, click here

Other name(s):

2-keto-3-deoxygluconate aldolase (ambiguous); KDGA (ambiguous)

Systematic name:

2-dehydro-3-deoxy-6-phospho-D-gluconate/2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)

Comments:

In the archaeon Sulfolobus solfataricus the enzyme is involved in glucose and galactose catabolism via the branched variant of the Entner-Doudoroff pathway. It utilizes 2-dehydro-3-deoxy-6-phosphate-D-gluconate and 2-dehydro-3-deoxy-6-phosphate-D-galactonate with similar catalytic efficiency. In vitro the enzyme can also catalyse the cleavage of the non-phosphorylated forms 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate with much lower catalytic efficiency. cf. EC 4.1.2.21, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, and EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.

Links to other databases:

References:

1.	Buchanan, C.L., Connaris, H., Danson, M.J., Reeve, C.D. and Hough, D.W. An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates. Biochem. J. 343 (1999) 563–570. [PMID: 10527934]
2.	Lamble, H.J., Theodossis, A., Milburn, C.C., Taylor, G.L., Bull, S.D., Hough, D.W. and Danson, M.J. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett. 579 (2005) 6865–6869. [DOI] [PMID: 16330030]
3.	Wolterink-van Loo, S., van Eerde, A., Siemerink, M.A., Akerboom, J., Dijkstra, B.W. and van der Oost, J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem. J. 403 (2007) 421–430. [DOI] [PMID: 17176250]

[EC 4.1.2.55 created 2014]

4.1.2.56

Accepted name:

2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate synthase

Reaction:

2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = glycerone phosphate + L-aspartate 4-semialdehyde

For diagram of 3-amino-4-hydroxybenzoate biosynthesis, click here

Other name(s):

griI (gene name)

Systematic name:

2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate L-aspartate 4-semialdehyde-lyase (glycerone phosphate-forming)

Comments:

Part of the pathway for the biosynthesis of grixazone, a mixture of yellow pigments produced by the bacterium Streptomyces griseus.

Links to other databases:

References:

1.	Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C₃ and C₄ primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944–36951. [DOI] [PMID: 17003031]

[EC 4.1.2.56 created 2014]

*EC

4.1.3.24

Accepted name:

malyl-CoA lyase

Reaction:

(1) (S)-malyl-CoA = acetyl-CoA + glyoxylate
(2) (2R,3S)-2-methylmalyl-CoA = propanoyl-CoA + glyoxylate

For diagram of the 3-hydroxypropanoate cycle, click here

Glossary:

(S)-malyl-CoA = (3S)-3-carboxy-3-hydroxypropanoyl-CoA
(2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA

Other name(s):

malyl-coenzyme A lyase; (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase; mclA (gene name); mcl1 (gene name); (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming); L-malyl-CoA lyase

Systematic name:

(S)-malyl-CoA glyoxylate-lyase (acetyl-CoA-forming)

Comments:

The enzymes from Rhodobacter species catalyse a step in the ethylmalonyl-CoA pathway for acetate assimilation [3,5]. The enzyme from halophilic bacteria participate in the methylaspartate cycle and catalyse the reaction in the direction of malyl-CoA formation [6]. The enzyme from the bacterium Chloroflexus aurantiacus, which participates in the 3-hydroxypropanoate cycle for carbon assimilation, also has the activity of EC 4.1.3.25, (3S)-citramalyl-CoA lyase [2,4].

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 37290-67-8

References:

1.	Tuboi, S. and Kikuchi, G. Enzymic cleavage of malyl-Coenzyme A into acetyl-Coenzyme A and glyoxylic acid. Biochim. Biophys. Acta 96 (1965) 148–153. [DOI] [PMID: 14285256]
2.	Herter, S., Busch, A. and Fuchs, G. L-Malyl-coenzyme A lyase/β-methylmalyl-coenzyme A lyase from Chloroflexus aurantiacus, a bifunctional enzyme involved in autotrophic CO₂ fixation. J. Bacteriol. 184 (2002) 5999–6006. [DOI] [PMID: 12374834]
3.	Meister, M., Saum, S., Alber, B.E. and Fuchs, G. L-Malyl-coenzyme A/β-methylmalyl-coenzyme A lyase is involved in acetate assimilation of the isocitrate lyase-negative bacterium Rhodobacter capsulatus. J. Bacteriol. 187 (2005) 1415–1425. [DOI] [PMID: 15687206]
4.	Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [DOI] [PMID: 17259315]
5.	Erb, T.J., Frerichs-Revermann, L., Fuchs, G. and Alber, B.E. The apparent malate synthase activity of Rhodobacter sphaeroides is due to two paralogous enzymes, (3S)-malyl-coenzyme A (CoA)/β-methylmalyl-CoA lyase and (3S)-malyl-CoA thioesterase. J. Bacteriol. 192 (2010) 1249–1258. [DOI] [PMID: 20047909]
6.	Borjian, F., Han, J., Hou, J., Xiang, H., Zarzycki, J. and Berg, I.A. Malate Synthase and β-Methylmalyl Coenzyme A Lyase Reactions in the Methylaspartate Cycle in Haloarcula hispanica. J. Bacteriol. 199 (2017) . [DOI] [PMID: 27920298]

[EC 4.1.3.24 created 1972, modified 2014]

*EC

4.1.3.25

Accepted name:

(S)-citramalyl-CoA lyase

Reaction:

(3S)-citramalyl-CoA = acetyl-CoA + pyruvate

For diagram of the 3-hydroxypropanoate cycle, click here

Other name(s):

citramalyl coenzyme A lyase (ambiguous); (+)-CMA-CoA lyase; (3S)-citramalyl-CoA pyruvate-lyase; Mcl (ambiguous); citramalyl-CoA lyase (ambiguous)

Systematic name:

(3S)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)

Comments:

Requires Mg²⁺ ions for activity [3]. The enzyme from the bacterium Clostridium tetanomorphum is a component of EC 4.1.3.22, citramalate lyase [2]. It also acts on (3S)-citramalyl thioacyl-carrier protein [2]. The enzyme from the bacterium Chloroflexus aurantiacus also has the activity of EC 4.1.3.24, malyl-CoA lyase [3]. It has no activity with (3R)-citramalyl-CoA (cf. EC 4.1.3.46, (R)-citramalyl-CoA lyase) [3].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37290-68-9

References:

1.	Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82–91. [PMID: 4284209]
2.	Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469–477. [DOI] [PMID: 923590]
3.	Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [DOI] [PMID: 17259315]

[EC 4.1.3.25 created 1972, modified 2014]

4.1.3.45

Accepted name:

3-hydroxybenzoate synthase

Reaction:

chorismate = 3-hydroxybenzoate + pyruvate

For diagram of shikimate and chorismate biosynthesis, click here

Glossary:

chorismate = (3R,4R)-3-[(1-carboxyethenyl)oxy]-4-hydroxycyclohexa-1,5-diene-1-carboxylate

Other name(s):

chorismatase/3-hydroxybenzoate synthase; hyg5 (gene name); bra8 (gene name); XanB2

Systematic name:

chorismate pyruvate-lyase (3-hydroxybenzoate-forming)

Comments:

The enzyme, found in several bacterial species is involved in biosynthesis of secondary products. The enzyme from the bacterium Xanthomonas campestris pv. campestris also has the activity of EC 4.1.3.40, chorismate lyase [3].

Links to other databases:

References:

1.	Andexer, J.N., Kendrew, S.G., Nur-e-Alam, M., Lazos, O., Foster, T.A., Zimmermann, A.S., Warneck, T.D., Suthar, D., Coates, N.J., Koehn, F.E., Skotnicki, J.S., Carter, G.T., Gregory, M.A., Martin, C.J., Moss, S.J., Leadlay, P.F. and Wilkinson, B. Biosynthesis of the immunosuppressants FK506, FK520, and rapamycin involves a previously undescribed family of enzymes acting on chorismate. Proc. Natl. Acad. Sci. USA 108 (2011) 4776–4781. [DOI] [PMID: 21383123]
2.	Jiang, Y., Wang, H., Lu, C., Ding, Y., Li, Y. and Shen, Y. Identification and characterization of the cuevaene A biosynthetic gene cluster in Streptomyces sp. LZ35. ChemBioChem 14 (2013) 1468–1475. [DOI] [PMID: 23824670]
3.	Zhou, L., Wang, J.Y., Wang, J., Poplawsky, A., Lin, S., Zhu, B., Chang, C., Zhou, T., Zhang, L.H. and He, Y.W. The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways. Mol. Microbiol. 87 (2013) 80–93. [DOI] [PMID: 23113660]

[EC 4.1.3.45 created 2013]

4.1.3.46

Accepted name:

(R)-citramalyl-CoA lyase

Reaction:

(3R)-citramalyl-CoA = acetyl-CoA + pyruvate

Other name(s):

Ccl

Systematic name:

(3R)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)

Comments:

Requires Mn²⁺ ions for activity. The enzyme, purified from the bacterium Chloroflexus aurantiacus, has no activity with (3S)-citramalyl-CoA (cf. EC 4.1.3.25, (S)-citramalyl-CoA lyase).

Links to other databases:

References:

1.	Friedmann, S., Alber, B.E. and Fuchs, G. Properties of R-citramalyl-coenzyme A lyase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus. J. Bacteriol. 189 (2007) 2906–2914. [DOI] [PMID: 17259315]

[EC 4.1.3.46 created 2014]

4.2.1.89

Deleted entry:

carnitine dehydratase. The activity has now been shown to be due to EC 2.8.3.21, L-carnitine CoA-transferase and EC 4.2.1.149, crotonobetainyl-CoA hydratase.

[EC 4.2.1.89 created 1989, deleted 2014]

4.2.1.147

Accepted name:

5,6,7,8-tetrahydromethanopterin hydro-lyase

Reaction:

5,6,7,8-tetrahydromethanopterin + formaldehyde = 5,10-methylenetetrahydromethanopterin + H₂O

Other name(s):

formaldehyde-activating enzyme

Systematic name:

5,6,7,8-tetrahydromethanopterin hydro-lyase (formaldehyde-adding, tetrahydromethanopterin-forming)

Comments:

Found in methylotrophic bacteria and methanogenic archaea.

Links to other databases:

References:

1.	Vorholt, J.A., Marx, C.J., Lidstrom, M.E. and Thauer, R.K. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182 (2000) 6645–6650. [DOI] [PMID: 11073907]
2.	Acharya, P., Goenrich, M., Hagemeier, C.H., Demmer, U., Vorholt, J.A., Thauer, R.K. and Ermler, U. How an enzyme binds the C₁ carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J. Biol. Chem. 280 (2005) 13712–13719. [DOI] [PMID: 15632161]

[EC 4.2.1.147 created 2014]

4.2.1.148

Accepted name:

2-methylfumaryl-CoA hydratase

Reaction:

(2R,3S)-2-methylmalyl-CoA = 2-methylfumaryl-CoA + H₂O

For diagram of the 3-hydroxypropanoate cycle, click here

Glossary:

(2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA

Other name(s):

Mcd; erythro-β-methylmalonyl-CoA hydrolyase; mesaconyl-coenzyme A hydratase (ambiguous); mesaconyl-C₁-CoA hydratase

Systematic name:

(2R,3S)-2-methylmalyl-CoA hydro-lyase (2-methylfumaryl-CoA-forming)

Comments:

The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.

Links to other databases:

References:

1.	Zarzycki, J., Schlichting, A., Strychalsky, N., Muller, M., Alber, B.E. and Fuchs, G. Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J. Bacteriol. 190 (2008) 1366–1374. [DOI] [PMID: 18065535]

[EC 4.2.1.148 created 2014]

4.2.1.149

Accepted name:

crotonobetainyl-CoA hydratase

Reaction:

L-carnitinyl-CoA = (E)-4-(trimethylammonio)but-2-enoyl-CoA + H₂O

Glossary:

L-carnitinyl-CoA = (3R)-3-hydroxy-4-(trimethylammonio)butanoyl-CoA
(E)-4-(trimethylammonio)but-2-enoyl-CoA = crotonobetainyl-CoA

Other name(s):

CaiD; L-carnityl-CoA dehydratase

Systematic name:

L-carnitinyl-CoA hydro-lyase [(E)-4-(trimethylammonio)but-2-enoyl-CoA-forming]

Comments:

The enzyme is also able to use crotonyl-CoA as substrate, with low efficiency [2].

Links to other databases:

References:

1.	Engemann, C., Elssner, T. and Kleber, H.P. Biotransformation of crotonobetaine to L-(–)-carnitine in Proteus sp. Arch. Microbiol. 175 (2001) 353–359. [PMID: 11409545]
2.	Elssner, T., Engemann, C., Baumgart, K. and Kleber, H.P. Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli. Biochemistry 40 (2001) 11140–11148. [DOI] [PMID: 11551212]
3.	Engemann, C., Elssner, T., Pfeifer, S., Krumbholz, C., Maier, T. and Kleber, H.P. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183 (2005) 176–189. [DOI] [PMID: 15731894]

[EC 4.2.1.149 created 2014]

4.2.1.150

Accepted name:

short-chain-enoyl-CoA hydratase

Reaction:

a short-chain (3S)-3-hydroxyacyl-CoA = a short-chain trans-2-enoyl-CoA + H₂O

Other name(s):

3-hydroxybutyryl-CoA dehydratase; crotonase; crt (gene name)

Systematic name:

short-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase

Comments:

The enzyme from the bacterium Clostridium acetobutylicum is part of the central fermentation pathway and plays a key role in the production of both acids and solvents. It is specific for short, C₄-C₆, chain length substrates and exhibits an extremely high turnover number for crotonyl-CoA. cf. EC 4.2.1.17, enoyl-CoA hydratase and EC 4.2.1.74, long-chain-enoyl-CoA hydratase.

Links to other databases:

References:

1.	Waterson, R.M., Castellino, F.J., Hass, G.M. and Hill, R.L. Purification and characterization of crotonase from Clostridium acetobutylicum. J. Biol. Chem. 247 (1972) 5266–5271. [PMID: 5057466]
2.	Waterson, R.M. and Conway, R.S. Enoyl-CoA hydratases from Clostridium acetobutylicum and Escherichia coli. Methods Enzymol. 71 Pt C (1981) 421–430. [PMID: 7024731]
3.	Boynton, Z.L., Bennet, G.N. and Rudolph, F.B. Cloning, sequencing, and expression of clustered genes encoding β-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178 (1996) 3015–3024. [DOI] [PMID: 8655474]

[EC 4.2.1.150 created 2014]

4.2.1.151

Accepted name:

chorismate dehydratase

Reaction:

chorismate = 3-[(1-carboxyvinyl)oxy]benzoate + H₂O

For diagram of the futalosine pathway, click here

Other name(s):

MqnA

Systematic name:

chorismate hydro-lyase (3-[(1-carboxyvinyl)oxy]benzoate-forming)

Comments:

The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

Links to other databases:

References:

1.	Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318–15321. [DOI] [PMID: 24083939]

[EC 4.2.1.151 created 2014]

*EC

4.3.1.17

Accepted name:

L-serine ammonia-lyase

Reaction:

L-serine = pyruvate + NH₃ (overall reaction)
(1a) L-serine = 2-aminoprop-2-enoate + H₂O
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H₂O = pyruvate + NH₃ (spontaneous)

Other name(s):

serine deaminase; L-hydroxyaminoacid dehydratase; L-serine deaminase; L-serine dehydratase; L-serine hydro-lyase (deaminating)

Systematic name:

L-serine ammonia-lyase (pyruvate-forming)

Comments:

Most enzymes that catalyse this reaction are pyridoxal-phosphate-dependent, although some enzymes contain an iron-sulfur cluster instead [6]. The reaction catalysed by both types of enzymes involves the initial elimination of water to form an enamine intermediate (hence the enzyme’s original classification as EC 4.2.1.13, L-serine dehydratase), followed by tautomerization to an imine form and hydrolysis of the C-N bond. The latter reaction, which can occur spontaneously, is also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase. This reaction is also carried out by EC 4.3.1.19, threonine ammonia-lyase, from a number of sources.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9014-27-1

References:

1.	Ramos, F. and Wiame, J.-M. Occurrence of a catabolic L-serine (L-threonine) deaminase in Saccharomyces cerevisiae. Eur. J. Biochem. 123 (1982) 571–576. [DOI] [PMID: 7042346]
2.	Simon, D., Hoshino, J. and Kröger, H. L-Serine dehydratase from rat liver. Purification and some properties. Biochim. Biophys. Acta 321 (1973) 361–368. [DOI] [PMID: 4750769]
3.	Suda, M. and Nakagawa, H. L-Serine dehydratase (rat liver). Methods Enzymol. 17B (1971) 346–351.
4.	Sagers, R.D. and Carter, J. E. L-Serine dehydratase (Clostridium acidiurica). Methods Enzymol. 17B (1971) 351–356.
5.	Robinson, W.G. and Labow, R. L-Serine dehydratase (Escherichia coli). Methods Enzymol. 17B (1971) 356–360.
6.	Grabowski, R., Hofmeister, A.E. and Buckel, W. Bacterial L-serine dehydratases: a new family of enzymes containing iron-sulfur clusters. Trends Biochem. Sci. 18 (1993) 297–300. [DOI] [PMID: 8236444]
7.	Yamada, T., Komoto, J., Takata, Y., Ogawa, H., Pitot, H.C. and Takusagawa, F. Crystal structure of serine dehydratase from rat liver. Biochemistry 42 (2003) 12854–12865. [DOI] [PMID: 14596599]

[EC 4.3.1.17 created 1961 as EC 4.2.1.13, transferred 2001 to EC 4.3.1.17, modified 2014]

*EC

4.3.1.19

Accepted name:

threonine ammonia-lyase

Reaction:

L-threonine = 2-oxobutanoate + NH₃ (overall reaction)
(1a) L-threonine = 2-aminobut-2-enoate + H₂O
(1b) 2-aminobut-2-enoate = 2-iminobutanoate (spontaneous)
(1c) 2-iminobutanoate + H₂O = 2-oxobutanoate + NH₃ (spontaneous)

For diagram of isoleucine and valine biosynthesis, click here

Other name(s):

threonine deaminase; L-serine dehydratase; serine deaminase; L-threonine dehydratase; threonine dehydrase; L-threonine deaminase; threonine dehydratase; L-threonine hydro-lyase (deaminating); L-threonine ammonia-lyase

Systematic name:

L-threonine ammonia-lyase (2-oxobutanoate-forming)

Comments:

Most enzymes that catalyse this reaction are pyridoxal-phosphate-dependent, although some enzymes contain an iron-sulfur cluster instead. The reaction catalysed by both types of enzymes involves the initial elimination of water to form an enamine intermediate (hence the enzyme’s original classification as EC 4.2.1.16, threonine dehydratase), followed by tautomerization to an imine form and hydrolysis of the C-N bond [3,5]. The latter reaction, which can occur spontaneously, is also be catalysed by EC 3.5.99.10, 2-iminobutanoate/2-iminopropanoate deaminase [5]. The enzymes from a number of sources also act on L-serine, cf. EC 4.3.1.17, L-serine ammonia-lyase.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 774231-81-1

References:

1.	Cohn, M.S. and Phillips, A.T. Purification and characterization of a B6-independent threonine dehydratase from Pseudomonas putida. Biochemistry 13 (1974) 1208–1214. [PMID: 4814721]
2.	Nishimura, J.S. and Greenberg, D.M. Purification and properties of L-threonine dehydrase of sheep liver. J. Biol. Chem. 236 (1961) 2684–2691. [PMID: 14479973]
3.	Phillips, A.T. and Wood, W.A. The mechanism of action of 5′-adenylic acid-activated threonine dehydrase. J. Biol. Chem. 240 (1965) 4703–4709. [PMID: 5321308]
4.	Shizuta, Y., Nakazawa, A., Tokushige, M. and Hayaishi, O. Studies on the interaction between regulatory enzymes and effectors. 3. Crystallization and characterization of adenosine 5′-monophosphate-dependent threonine deaminase from Escherichia coli. J. Biol. Chem. 244 (1969) 1883–1889. [PMID: 4889010]
5.	Lambrecht, J.A., Flynn, J.M. and Downs, D.M. Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5′-phosphate (PLP)-dependent enzyme reactions. J. Biol. Chem. 287 (2012) 3454–3461. [DOI] [PMID: 22094463]

[EC 4.3.1.19 created 1961 as EC 4.2.1.16, transferred 2001 to EC 4.3.1.19, modified 2014]

4.3.1.29

Accepted name:

D-glucosaminate-6-phosphate ammonia-lyase

Reaction:

2-amino-2-deoxy-D-gluconate 6-phosphate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + NH₃

Other name(s):

DgaE; 6-phospho-D-glucosaminate ammonia-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming)

Systematic name:

2-amino-2-deoxy-D-gluconate 6-phosphate ammonia-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming)

Comments:

The enzyme, from the bacterium Salmonella typhimurium, is involved in the degradation pathway of 2-amino-2-deoxy-D-gluconate.

Links to other databases:

References:

1.	Miller, K.A., Phillips, R.S., Mrazek, J. and Hoover, T.R. Salmonella utilizes D-glucosaminate via a mannose family phosphotransferase system permease and associated enzymes. J. Bacteriol. 195 (2013) 4057–4066. [DOI] [PMID: 23836865]

[EC 4.3.1.29 created 2013]

4.3.1.30

Accepted name:

dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase

Reaction:

dTDP-4-amino-4,6-dideoxy-α-D-glucopyranose + S-adenosyl-L-methionine + reduced acceptor = dTDP-3-dehydro-4,6-dideoxy-α-D-glucopyranose + NH₃ + L-methionine + 5′-deoxyadenosine + acceptor

For diagram of dTDP-D-desosamine biosynthesis, click here

Other name(s):

desII (gene name); eryCV (gene name); MegCV

Systematic name:

dTDP-4-amino-4,6-dideoxy-α-D-glucopyranose ammonia lyase (dTDP-3-dehydro-4,6-dideoxy-α-D-glucopyranose-forming)

Comments:

The enzyme, which is a member of the ’AdoMet radical’ (radical SAM) family, is involved in biosynthesis of TDP-α-D-desosamine. The reaction starts by the transfer of an electron from the reduced form of the enzyme’s [4Fe-4S] cluster to S-adenosyl-L-methionine, spliting it into methionine and the radical 5-deoxyadenosin-5′-yl, which attacks the sugar substrate.

Links to other databases:

References:

1.	Szu, P.H., Ruszczycky, M.W., Choi, S.H., Yan, F. and Liu, H.W. Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-methionine enzyme involved in the biosynthesis of TDP-D-desosamine. J. Am. Chem. Soc. 131 (2009) 14030–14042. [DOI] [PMID: 19746907]
2.	Ruszczycky, M.W., Choi, S.H. and Liu, H.W. Stoichiometry of the redox neutral deamination and oxidative dehydrogenation reactions catalyzed by the radical SAM enzyme DesII. J. Am. Chem. Soc. 132 (2010) 2359–2369. [DOI] [PMID: 20121093]
3.	Ruszczycky, M.W., Choi, S.H., Mansoorabadi, S.O. and Liu, H.W. Mechanistic studies of the radical S-adenosyl-L-methionine enzyme DesII: EPR characterization of a radical intermediate generated during its catalyzed dehydrogenation of TDP-D-quinovose. J. Am. Chem. Soc. 133 (2011) 7292–7295. [DOI] [PMID: 21513273]

[EC 4.3.1.30 created 2011]

*EC

4.3.2.3

Accepted name:

ureidoglycolate lyase

Reaction:

(S)-ureidoglycolate = glyoxylate + urea

For diagram of AMP catabolism, click here

Other name(s):

ureidoglycolatase (ambiguous); ureidoglycolase (ambiguous); ureidoglycolate hydrolase (misleading); (S)-ureidoglycolate urea-lyase

Systematic name:

(S)-ureidoglycolate urea-lyase (glyoxylate-forming)

Comments:

This microbial enzyme is involved in the degradation of ureidoglycolate, an intermediate of purine degradation. Not to be confused with EC 3.5.1.116, ureidoglycolate amidohydrolase, which releases ammonia rather than urea.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9014-57-7

References:

1.	Trijbels, F. and Vogels, G.D. Allantoate and ureidoglycolate degradation by Pseudomonas aeruginosa. Biochim. Biophys. Acta 132 (1967) 115–126. [DOI] [PMID: 6030341]
2.	Werner, A.K., Romeis, T. and Witte, C.P. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 (2010) 19–21. [DOI] [PMID: 19935661]

[EC 4.3.2.3 created 1972, modified 2014]

4.6.1.16

Accepted name:

tRNA-intron lyase

Reaction:

pretRNA = a 3′-half-tRNA molecule with a 5′-OH end + a 5′-half-tRNA molecule with a 2′,3′-cyclic phosphate end + an intron with a 2′,3′-cyclic phosphate and a 5′-hydroxyl terminus

Other name(s):

transfer ribonucleate intron endoribonuclease; tRNA splicing endonuclease; splicing endonuclease; tRNATRPintron endonuclease; transfer splicing endonuclease

Systematic name:

pretRNA lyase (intron-removing; cyclic-2′,3′-phosphate-forming)

Comments:

The enzyme catalyses the final stage in the maturation of tRNA molecules.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 117444-13-0

References:

1.	Attardi, D.G., Margarit, I. and Tocchini-Valentini, G.P. Structural alterations in mutant precursors of the yeast tRNA^Leu³ gene which behave as defective substrates for a highly purified splicing endoribonuclease. EMBO J. 4 (1985) 3289–3297. [PMID: 3937725]
2.	Peebles, C.L., Gegenheimer, P. and Abelson, J. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell 32 (1983) 525–536. [DOI] [PMID: 6186398]
3.	Thompson, L.D., Brandon, L.D., Nieuwlandt, D.T. and Daniels, C.J. Transfer RNA intron processing in the halophilic archaebacteria. Can. J. Microbiol. 35 (1989) 36–42. [PMID: 2470486]
4.	Thompson, L.D. and Daniels, C.J. A tRNA(Trp) intron endonuclease from Halobacterium volcanii. Unique substrate recognition properties. J. Biol. Chem. 263 (1988) 17951–17959. [PMID: 3192521]

[EC 4.6.1.16 created 1992 as EC 3.1.27.9, transferred 2014 to EC 4.6.1.16]

5.1.3.27

Accepted name:

dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase

Reaction:

dTDP-4-dehydro-6-deoxy-α-D-glucose = dTDP-4-dehydro-6-deoxy-α-D-gulose

For diagram of dTDP-6-deoxy-α-D-allose biosynthesis, click here and for diagram of dTDP-6-deoxyhexose biosynthesis, click here

Glossary:

dTDP-4-dehydro-6-deoxy-α-D-gulose = dTDP-4-dehydro-6-deoxy-α-D-allose

Other name(s):

dTDP-deoxyglucose 3-epimerase; dTDP-4-keto-6-deoxy-D-glucose 3-epimerase; dTDP-4-keto-6-deoxyglucose 3-epimerase; gerF (gene name); tylJ (gene name); chmJ (gene name); mydH (gene name)

Systematic name:

dTDP-4-dehydro-6-deoxy-α-D-glucose 3-epimerase

Comments:

The enzyme is involved in the biosynthetic pathway of dTDP-6-deoxy-α-D-allose, which is converted to mycinose after attachment to the aglycones of several macrolide antibiotics, including tylosin, chalcomycin, dihydrochalcomycin, and mycinamicin II.

Links to other databases:

References:

1.	Sohng, J.K., Kim, H.J., Nam, D.H., Lim, D.O., Han, J.M., Lee, H.J. and Yoo, J.C. Cloning, expression, and biological function of a dTDP-deoxyglucose epimerase (gerF) gene from Streptomyces sp. GERI-155. Biotechnol. Lett. 26 (2004) 185–191. [PMID: 15049360]
2.	Thuy, T.T., Liou, K., Oh, T.J., Kim, D.H., Nam, D.H., Yoo, J.C. and Sohng, J.K. Biosynthesis of dTDP-6-deoxy-β-D-allose, biochemical characterization of dTDP-4-keto-6-deoxyglucose reductase (GerKI) from Streptomyces sp. KCTC 0041BP. Glycobiology 17 (2007) 119–126. [DOI] [PMID: 17053005]
3.	Kubiak, R.L., Phillips, R.K., Zmudka, M.W., Ahn, M.R., Maka, E.M., Pyeatt, G.L., Roggensack, S.J. and Holden, H.M. Structural and functional studies on a 3′-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose. Biochemistry 51 (2012) 9375–9383. [DOI] [PMID: 23116432]

[EC 5.1.3.27 created 2013]

5.1.3.28

Accepted name:

UDP-N-acetyl-L-fucosamine synthase

Reaction:

UDP-2-acetamido-2,6-dideoxy-β-L-talose = UDP-N-acetyl-β-L-fucosamine

For diagram of UDP-N-acetyl-β-L-fucosamine biosynthesis, click here

Glossary:

UDP-2-acetamido-2,6-dideoxy-β-L-talose = UDP-N-acetyl-β-L-pneumosamine

Other name(s):

WbjD; Cap5G

Systematic name:

UDP-2-acetamido-2,6-dideoxy-β-L-talose 2-epimerase

Comments:

Isolated from the bacteria Pseudomonas aeruginosa and Staphylococcus aureus. Involved in bacterial polysaccharide biosynthesis.

Links to other databases:

References:

Kneidinger, B., O'Riordan, K., Li, J., Brisson, J.R., Lee, J.C. and Lam, J.S. Three highly conserved proteins catalyze the conversion of UDP-N-acetyl-D-glucosamine to precursors for the biosynthesis of O antigen in Pseudomonas aeruginosa O11 and capsule in Staphylococcus aureus type 5. Implications for the UDP-N-acetyl-L-fucosamine biosynthetic pathway. J. Biol. Chem. 278 (2003) 3615–3627. [DOI] [PMID: 12464616]

Mulrooney, E.F., Poon, K.K., McNally, D.J., Brisson, J.R. and Lam, J.S. Biosynthesis of UDP-N-acetyl-L-fucosamine, a precursor to the biosynthesis of lipopolysaccharide in Pseudomonas aeruginosa serotype O11. J. Biol. Chem. 280 (2005) 19535–19542. [DOI] [PMID: 15778500]

[EC 5.1.3.28 created 2014]

*EC

5.3.1.3

Accepted name:

D-arabinose isomerase

Reaction:

D-arabinose = D-ribulose

For diagram of D-arabinose catabolism, click here

Other name(s):

D-arabinose(L-fucose) isomerase; L-fucose isomerase; D-arabinose ketol-isomerase; arabinose isomerase (misleading)

Systematic name:

D-arabinose aldose-ketose-isomerase

Comments:

Requires a divalent metal ion (the enzyme from the bacterium Escherichia coli prefers Mn²⁺). The enzyme binds the closed form of the sugar and catalyses ring opening to generate a form of open-chain conformation that facilitates the isomerization reaction, which proceeds via an ene-diol mechanism [3]. The enzyme catalyses the aldose-ketose isomerization of several sugars. Most enzymes also catalyse the reaction of EC 5.3.1.25, L-fucose isomerase [3]. The enzyme from the bacterium Falsibacillus pallidus also converts D-altrose to D-psicose [4]. cf. EC 5.3.1.4, L-arabinose isomerase.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9023-81-8

References:

1.	Cohen, S.S. Studies on D-ribulose and its enzymatic conversion to D-arabinose. J. Biol. Chem. 201 (1953) 71–84. [PMID: 13044776]
2.	Green, M. and Cohen, S.S. Enzymatic conversion of L-fucose to L-fuculose. J. Biol. Chem. 219 (1956) 557–568. [PMID: 13319278]
3.	Seemann, J.E. and Schulz, G.E. Structure and mechanism of L-fucose isomerase from Escherichia coli. J. Mol. Biol. 273 (1997) 256–268. [DOI] [PMID: 9367760]
4.	Takeda, K., Yoshida, H., Izumori, K. and Kamitori, S. X-ray structures of Bacillus pallidus D-arabinose isomerase and its complex with L-fucitol. Biochim. Biophys. Acta 1804 (2010) 1359–1368. [DOI] [PMID: 20123133]

[EC 5.3.1.3 created 1961, modified 2013]

5.3.1.30

Accepted name:

5-deoxy-glucuronate isomerase

Reaction:

5-deoxy-D-glucuronate = 5-dehydro-2-deoxy-D-gluconate

For diagram of inositol catabolism, click here

Glossary:

5-dehydro-2-deoxy-D-gluconate = 2-deoxy-D-threo-hex-5-ulosonic acid
5-deoxy-D-glucuronate = 5-deoxy-D-xylo-hexuronic acid

Other name(s):

5DG isomerase; IolB

Systematic name:

5-deoxy-D-glucuronate aldose-ketose-isomerase

Comments:

The enzyme, found in the bacterium Bacillus subtilis, is part of a myo-inositol degradation pathway leading to acetyl-CoA.

Links to other databases:

References:

1.	Yoshida, K., Yamaguchi, M., Morinaga, T., Kinehara, M., Ikeuchi, M., Ashida, H. and Fujita, Y. myo-Inositol catabolism in Bacillus subtilis. J. Biol. Chem. 283 (2008) 10415–10424. [DOI] [PMID: 18310071]

[EC 5.3.1.30 created 2014]

5.3.99.11

Accepted name:

2-keto-myo-inositol isomerase

Reaction:

2,4,6/3,5-pentahydroxycyclohexanone = 2D-2,3,5/4,6-pentahydroxycyclohexanone

For diagram of inositol catabolism, click here

Glossary:

2,4,6/3,5-pentahydroxycyclohexanone = (2R,3S,4s,5R,6S)-2,3,4,5,6-pentahydroxycyclohexanone = scyllo-inosose

Other name(s):

IolI; inosose isomerase; 2KMI isomerase.

Systematic name:

2,4,6/3,5-pentahydroxycyclohexanone 2-isomerase

Comments:

Requires a divalent metal ion for activity. Mn²⁺, Fe²⁺ and Co²⁺ can be used. The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol/D-chiro-inositol degradation pathway leading to acetyl-CoA.

Links to other databases:

References:

1.	Zhang, R.G., Dementieva, I., Duke, N., Collart, F., Quaite-Randall, E., Alkire, R., Dieckman, L., Maltsev, N., Korolev, O. and Joachimiak, A. Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding. Proteins 48 (2002) 423–426. [DOI] [PMID: 12112707]
2.	Yoshida, K., Yamaguchi, M., Morinaga, T., Ikeuchi, M., Kinehara, M. and Ashida, H. Genetic modification of Bacillus subtilis for production of D-chiro-inositol, an investigational drug candidate for treatment of type 2 diabetes and polycystic ovary syndrome. Appl. Environ. Microbiol. 72 (2006) 1310–1315. [DOI] [PMID: 16461681]

[EC 5.3.99.11 created 2014]

5.4.1.2

Transferred entry:

precorrin-8X methylmutase. Now EC 5.4.99.61, precorrin-8X methylmutase

[EC 5.4.1.2 created 1999, deleted 2014]

5.4.1.3

Accepted name:

2-methylfumaryl-CoA isomerase

Reaction:

2-methylfumaryl-CoA = 3-methylfumaryl-CoA

For diagram of the 3-hydroxypropanoate cycle, click here

Glossary:

2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
3-methylfumaryl-CoA = (E)-3-carboxybut-2-enoyl-CoA

Other name(s):

mesaconyl-CoA C₁-C₄ CoA transferase; Mct

Systematic name:

2-methylfumaryl-CoA 1,4-CoA-mutase

Comments:

The enzyme, purified from the bacterium Chloroflexus aurantiacus, acts as an intramolecular CoA transferase and does not transfer CoA to free mesaconate. It is part of the 3-hydroxypropanoate cycle for carbon assimilation.

Links to other databases:

References:

1.	Zarzycki, J., Brecht, V., Muller, M. and Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO₂ fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. USA 106 (2009) 21317–21322. [DOI] [PMID: 19955419]

[EC 5.4.1.3 created 2014]

5.4.99.60

Accepted name:

cobalt-precorrin-8 methylmutase

Reaction:

cobalt-precorrin-8 = cobyrinate

For diagram of anaerobic corrin biosynthesis (part 2), click here

Other name(s):

cbiC (gene name)

Systematic name:

precorrin-8 11,12-methylmutase

Comments:

The enzyme, which participates in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway, catalyses the conversion of cobalt-precorrin-8 to cobyrinate by methyl rearrangement. The equivalent enzyme in the aerobic pathway is EC 5.4.99.61, precorrin-8X methylmutase.

Links to other databases:

References:

1.	Roessner, C.A., Warren, M.J., Santander, P.J., Atshaves, B.P., Ozaki, S., Stolowich, N.J., Iida, K., Scott, A.I. Expression of Salmonella typhimurium enzymes for cobinamide synthesis. Identification of the 11-methyl and 20-methyl transferases of corrin biosynthesis. FEBS Lett. 301 (1992) 73–78. [DOI] [PMID: 1451790]
2.	Roth, J.R., Lawrence, J.G., Rubenfield, M., Kieffer-Higgins, S., Church, G.M. Characterization of the cobalamin (vitamin B₁₂) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175 (1993) 3303–3316. [DOI] [PMID: 8501034]
3.	Xue, Y., Wei, Z., Li, X. and Gong, W. The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis. J. Struct. Biol. 153 (2006) 307–311. [DOI] [PMID: 16427313]
4.	Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B₁₂). Proc. Natl. Acad. Sci. USA 110 (2013) 14906–14911. [DOI] [PMID: 23922391]

[EC 5.4.99.60 created 2014]

5.4.99.61

Accepted name:

precorrin-8X methylmutase

Reaction:

precorrin-8X = hydrogenobyrinate

For diagram of corrin biosynthesis (part 4), click here

Other name(s):

precorrin isomerase; hydrogenobyrinic acid-binding protein; cobH (gene name)

Systematic name:

precorrin-8X 11,12-methylmutase

Comments:

The enzyme, which participates in the aerobic (late cobalt insertion) adenosylcobalamin biosynthesis pathway, catalyses the conversion of precorrin-8X to hydrogenobyrinate by methyl rearrangement. The equivalent enzyme in the anaerobic pathway is EC 5.4.99.60, cobalt-precorrin-8 methylmutase.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 138238-71-8

References:

1.	Thibaut, D., Couder, M., Famechon, A., Debussche, L., Cameron, B., Crouzet, J., Blanche, F. The final step in the biosynthesis of hydrogenobyrinic acid is catalyzed by the cobH gene product with precorrin-8X as the substrate. J. Bacteriol. 174 (1992) 1043–1049. [DOI] [PMID: 1732194]
2.	Crouzet, J., Cameron, B., Cauchois, L., Rigault, S., Rouyez, M.C., Blanche, F. , Thibaut D., Debussche, L. Genetic and sequence analysis of an 8.7-kilobase Pseudomonas denitrificans fragment carrying eight genes involved in transformation of precorrin-2 to cobyrinic acid. J. Bacteriol. 172 (1990) 5980–5990. [DOI] [PMID: 2211521]
3.	Shipman, L.W., Li, D., Roessner, C.A., Scott, A.I. and Sacchettini, J.C. Crystal structure of precorrin-8x methyl mutase. Structure 9 (2001) 587–596. [DOI] [PMID: 11470433]

[EC 5.4.99.61 created 1999 as EC 5.4.1.2, transferred 2014 to EC 5.4.99.61]

5.5.1.24

Accepted name:

tocopherol cyclase

Reaction:

(1) δ-tocopherol = 2-methyl-6-phytylbenzene-1,4-diol
(2) γ-tocopherol = 2,3-dimethyl-6-phytylbenzene-1,4-diol
(3) δ-tocotrienol = 6-geranylgeranyl-2-methylbenzene-1,4-diol
(4) γ-tocotrienol = 6-geranylgeranyl-2,3-dimethylbenzene-1,4-diol

For diagram of tocopherol biosynthesis, click here and for diagram of tocotrienol biosynthesis, click here

Other name(s):

VTE1 (gene name); SXD1 (gene name); δ/γ-tocopherol lyase (decyclizing)

Systematic name:

δ/γ-tocopherol lyase (ring-opening)

Comments:

The enzyme has been described from plants and cyanobacteria. It has similar activity with all four listed benzoquinol substrates. Involved in the biosynthesis of vitamin E (tocopherols and tocotrienols).

Links to other databases:

References:

1.	Porfirova, S., Bergmuller, E., Tropf, S., Lemke, R. and Dormann, P. Isolation of an Arabidopsis mutant lacking vitamin E and identification of a cyclase essential for all tocopherol biosynthesis. Proc. Natl. Acad. Sci. USA 99 (2002) 12495–12500. [DOI] [PMID: 12213958]
2.	Sattler, S.E., Cahoon, E.B., Coughlan, S.J. and DellaPenna, D. Characterization of tocopherol cyclases from higher plants and cyanobacteria. Evolutionary implications for tocopherol synthesis and function. Plant Physiol. 132 (2003) 2184–2195. [DOI] [PMID: 12913173]

[EC 5.5.1.24 created 2013]

6.2.1.40

Accepted name:

4-hydroxybutyrate—CoA ligase (AMP-forming)

Reaction:

ATP + 4-hydroxybutanoate + CoA = AMP + diphosphate + 4-hydroxybutanoyl-CoA

For diagram of the 3-hydroxypropanoate/4-hydroxybutanoate cycle and dicarboxylate/4-hydroxybutanoate cycle in archaea, click here

Other name(s):

4-hydroxybutyrate-CoA synthetase (ambiguous); 4-hydroxybutyrate:CoA ligase (ambiguous); hbs (gene name); 4-hydroxybutyrate—CoA ligase

Systematic name:

4-hydroxybutanoate:CoA ligase (AMP-forming)

Comments:

Isolated from the archaeon Metallosphaera sedula. Involved in the 3-hydroxypropanoate/4-hydroxybutanoate cycle. cf. EC 6.2.1.56, 4-hydroxybutyrate—CoA ligase (ADP-forming).

Links to other databases:

References:

1.	Ramos-Vera, W.H., Weiss, M., Strittmatter, E., Kockelkorn, D. and Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. J. Bacteriol. 193 (2011) 1201–1211. [DOI] [PMID: 21169482]
2.	Hawkins, A.S., Han, Y., Bennett, R.K., Adams, M.W. and Kelly, R.M. Role of 4-hydroxybutyrate-CoA synthetase in the CO₂ fixation cycle in thermoacidophilic archaea. J. Biol. Chem. 288 (2013) 4012–4022. [DOI] [PMID: 23258541]

[EC 6.2.1.40 created 2014, modified 2019]

6.3.1.17

Accepted name:

β-citrylglutamate synthase

Reaction:

ATP + citrate + L-glutamate = ADP + phosphate + β-citryl-L-glutamate

Other name(s):

NAAG synthetase I; NAAGS-I; RIMKLB (gene name) (ambiguous)

Systematic name:

citrate:L-glutamate ligase (ADP-forming)

Comments:

The enzyme, found in animals, also has the activity of EC 6.3.2.41, N-acetylaspartylglutamate synthase.

Links to other databases:

References:

Collard, F., Stroobant, V., Lamosa, P., Kapanda, C.N., Lambert, D.M., Muccioli, G.G., Poupaert, J.H., Opperdoes, F. and Van Schaftingen, E. Molecular identification of N-acetylaspartylglutamate synthase and β-citrylglutamate synthase. J. Biol. Chem. 285 (2010) 29826–29833. [DOI] [PMID: 20657015]

[EC 6.3.1.17 created 2014]

6.3.2.41

Accepted name:

N-acetylaspartylglutamate synthase

Reaction:

ATP + N-acetyl-L-aspartate + L-glutamate = ADP + phosphate + N-acetyl-L-aspartyl-L-glutamate

Other name(s):

N-acetylaspartylglutamate synthetase; NAAG synthetase; NAAGS; RIMKLA (gene name) (ambiguous); RIMKLB (gene name) (ambiguous)

Systematic name:

N-acetyl-L-aspartate:L-glutamate ligase (ADP, N-acetyl-L-aspartyl-L-glutamate-forming)

Comments:

The enzyme, found in animals, produces the neurotransmitter N-acetyl-L-aspartyl-L-glutamate. One isoform also has the activity of EC 6.3.1.17, β-citrylglutamate synthase [2], while another isoform has the activity of EC 6.3.2.42, N-acetylaspartylglutamylglutamate synthase [3].

Links to other databases:

References:

1.	Becker, I., Lodder, J., Gieselmann, V. and Eckhardt, M. Molecular characterization of N-acetylaspartylglutamate synthetase. J. Biol. Chem. 285 (2010) 29156–29164. [DOI] [PMID: 20643647]
2.	Collard, F., Stroobant, V., Lamosa, P., Kapanda, C.N., Lambert, D.M., Muccioli, G.G., Poupaert, J.H., Opperdoes, F. and Van Schaftingen, E. Molecular identification of N-acetylaspartylglutamate synthase and β-citrylglutamate synthase. J. Biol. Chem. 285 (2010) 29826–29833. [DOI] [PMID: 20657015]
3.	Lodder-Gadaczek, J., Becker, I., Gieselmann, V., Wang-Eckhardt, L. and Eckhardt, M. N-acetylaspartylglutamate synthetase II synthesizes N-acetylaspartylglutamylglutamate. J. Biol. Chem. 286 (2011) 16693–16706. [DOI] [PMID: 21454531]

[EC 6.3.2.41 created 2014]

6.3.2.42

Accepted name:

N-acetylaspartylglutamylglutamate synthase

Reaction:

2 ATP + N-acetyl-L-aspartate + 2 L-glutamate = 2 ADP + 2 phosphate + N-acetyl-L-aspartyl-L-glutamyl-L-glutamate

Other name(s):

N-acetylaspartylglutamylglutamate synthetase; NAAG(2) synthase; NAAG synthetase II; NAAGS-II; RIMKLA (gene name) (ambiguous)

Systematic name:

N-acetyl-L-aspartate:L-glutamate ligase (ADP, N-acetyl-L-aspartyl-L-glutamyl-L-glutamate-forming)

Comments:

The enzyme, found in mammals, also has the activity of EC 6.3.2.41, N-acetylaspartylglutamate synthase.

Links to other databases: