Proposed Changes to the Enzyme List

References:

Carter, M.S., Zhang, X., Huang, H., Bouvier, J.T., Francisco, B.S., Vetting, M.W., Al-Obaidi, N., Bonanno, J.B., Ghosh, A., Zallot, R.G., Andersen, H.M., Almo, S.C. and Gerlt, J.A. Functional assignment of multiple catabolic pathways for D-apiose. Nat. Chem. Biol. 14 (2018) 696–705. [DOI] [PMID: 29867142]

[EC 1.1.1.420 created 2019]

1.1.1.421

Accepted name:

D-apionate oxidoisomerase

Reaction:

D-apionate + NAD⁺ = 3-oxoisoapionate + NADH + H⁺

Glossary:

3-oxoisoapionate = 2,4-dihydroxy-2-(hydroxymethyl)-3-oxobutanoate

Other name(s):

apnO (gene name)

Systematic name:

D-apionate:NAD⁺ oxidoreductase (isomerizing)

Comments:

The enzyme, characterized from several bacterial species, participates in the degradation of D-apionate. The reaction involves migration of a hydroxymethyl group from position 3 to position 2 and oxidation of the 3-hydroxyl group. Stereospecificity of the product, 3-oxoisoapionate, has not been determined.

Links to other databases:

References:

[EC 1.1.1.421 created 2019]

1.1.1.422

Accepted name:

pseudoephedrine dehydrogenase

Reaction:

(+)-(1S,2S)-pseudoephedrine + NAD⁺ = (S)-2-(methylamino)-1-phenylpropan-1-one + NADH + H⁺

Glossary:

(+)-(1S,2S)-pseudoephedrine = (1S,2S)-2-(methylamino)-1-phenylpropan-1-ol
(S)-2-(methylamino)-1-phenylpropan-1-one = (S)-methcathinone

Other name(s):

PseDH

Systematic name:

(+)-(1S,2S)-pseudoephedrine:NAD⁺ 1-oxidoreductase

Comments:

The enzyme, characterized from the bacterium Arthrobacter sp. TS-15, acts on a broad range of different aryl-alkyl ketones, such as haloketones, ketoamines, diketones, and ketoesters. It accepts various types of aryl groups including phenyl-, pyridyl-, thienyl-, and furyl-rings, but the presence of an aromatic ring is essential for the activity. In addition, the presence of a functional group on the alkyl chain, such as an amine, a halogen, or a ketone, is also crucial. The enzyme exhibits a strict anti-Prelog enantioselectivity. When acting on diketones, it catalyses the reduction of only the keto group closest to the ring, with no further reduction to the diol. cf. EC 1.1.1.423, ephedrine dehydrogenase.

Links to other databases:

References:

1.	Shanati, T., Lockie, C., Beloti, L., Grogan, G. and Ansorge-Schumacher, M.B. Two enantiocomplementary ephedrine dehydrogenases from Arthrobacter sp. TS-15 with broad substrate specificity. ACS Catal. 9 (2019) 6202–6211.
2.	Shanati, T., Ansorge-Schumacher, M. Enzymes and methods for the stereoselective reduction of carbonyl compounds, oxidation and stereoselective reductive amination - for the enantioselective preparation of alcohol amine compounds. (2019) Patent WO2019002459.
3.	Shanati, T. and Ansorge-Schumacher, M.B. Biodegradation of ephedrine isomers by Arthrobacter sp. strain TS-15: discovery of novel ephedrine and pseudoephedrine dehydrogenases. Appl. Environ. Microbiol. 86(6):e02487-19 (2020). [DOI] [PMID: 31900306]

[EC 1.1.1.422 created 2020]

1.1.1.423

Accepted name:

(1R,2S)-ephedrine 1-dehydrogenase

Reaction:

(–)-(1R,2S)-ephedrine + NAD⁺ = (S)-2-(methylamino)-1-phenylpropan-1-one + NADH + H⁺

Glossary:

(–)-(1R,2S)-ephedrine = (1R,2S)-2-(methylamino)-1-phenylpropan-1-ol
(S)-2-(methylamino)-1-phenylpropan-1-one = (S)-methcathinone

Other name(s):

EDH; ephedrine dehydrogenase

Systematic name:

(–)-(1R,2S)-ephedrine:NAD⁺ 1-oxidoreductase

Comments:

The enzyme, characterized from the bacterium Arthrobacter sp. TS-15, acts on a broad range of different aryl-alkyl ketones, such as haloketones, ketoamines, diketones, and ketoesters. It exhibits a strict enantioselectivity and accepts various types of aryl groups including phenyl-, pyridyl-, thienyl-, and furyl-rings, but the presence of an aromatic ring is essential for the activity. In addition, the presence of a functional group on the alkyl chain, such as an amine, a halogen, or a ketone, is also crucial. When acting on diketones, it catalyses the reduction of only the keto group closest to the ring, with no further reduction to the diol. cf. EC 1.1.1.422, pseudoephedrine dehydrogenase and EC 1.5.1.18, ephedrine dehydrogenase.

Links to other databases:

References:

1.	Shanati, T., Lockie, C., Beloti, L., Grogan, G. and Ansorge-Schumacher, M.B. Two enantiocomplementary ephedrine dehydrogenases from Arthrobacter sp. TS-15 with broad substrate specificity. ACS Catal. 9 (2019) 6202–6211.
2.	Shanati, T., Ansorge-Schumacher, M. Enzymes and methods for the stereoselective reduction of carbonyl compounds, oxidation and stereoselective reductive amination - for the enantioselective preparation of alcohol amine compounds. (2019) Patent WO2019002459.

[EC 1.1.1.423 created 2020, modified 2020]

1.1.2.10

Accepted name:

lanthanide-dependent methanol dehydrogenase

Reaction:

methanol + 2 oxidized cytochrome c_L = formaldehyde + 2 reduced cytochrome c_L

Other name(s):

XoxF; XoxF-MDH; Ce-MDH; La³⁺-dependent MDH; Ce³⁺-induced methanol dehydrogenase; cerium dependent MDH

Systematic name:

methanol:cytochrome c_L oxidoreductase

Comments:

Isolated from the bacterium Methylacidiphilum fumariolicum and many Methylobacterium species. Requires La³⁺, Ce³⁺, Pr³⁺ or Nd³⁺. The higher lanthanides show decreasing activity with Sm³⁺, Eu³⁺ and Gd³⁺. The lanthanide is coordinated by the enzyme and pyrroloquinoline quinone. Shows little activity with Ca²⁺, the required cofactor of EC 1.1.2.7, methanol dehydrogenase (cytochrome c).

Links to other databases:

References:

1.	Hibi, Y., Asai, K., Arafuka, H., Hamajima, M., Iwama, T. and Kawai, K. Molecular structure of La³⁺-induced methanol dehydrogenase-like protein in Methylobacterium radiotolerans. J. Biosci. Bioeng. 111 (2011) 547–549. [PMID: 21256798]
2.	Nakagawa, T., Mitsui, R., Tani, A., Sasa, K., Tashiro, S., Iwama, T., Hayakawa, T. and Kawai, K. A catalytic role of XoxF1 as La³⁺-dependent methanol dehydrogenase in Methylobacterium extorquens strain AM1. PLoS One 7:e50480 (2012). [PMID: 23209751]
3.	Pol, A., Barends, T.R., Dietl, A., Khadem, A.F., Eygensteyn, J., Jetten, M.S. and Op den Camp, H.J. Rare earth metals are essential for methanotrophic life in volcanic mudpots. Environ. Microbiol. 16 (2014) 255–264. [PMID: 24034209]
4.	Bogart, J.A., Lewis, A.J. and Schelter, E.J. DFT study of the active site of the XoxF-type natural, cerium-dependent methanol dehydrogenase enzyme. Chemistry Eur. J. 21 (2015) 1743–1748. [PMID: 25421364]
5.	Prejano, M., Marino, T. and Russo, N. How can methanol dehydrogenase from Methylacidiphilum fumariolicum work with the alien Ce(III) ion in the active center? A theoretical study. Chemistry 23 (2017) 8652–8657. [PMID: 28488399]
6.	Masuda, S., Suzuki, Y., Fujitani, Y., Mitsui, R., Nakagawa, T., Shintani, M. and Tani, A. Lanthanide-dependent regulation of methylotrophy in Methylobacterium aquaticum strain 22A. mSphere 3 (2018) e00462. [PMID: 29404411]

[EC 1.1.2.10 created 2019]

1.1.98.7

Accepted name:

serine-type anaerobic sulfatase-maturating enzyme

Reaction:

S-adenosyl-L-methionine + a [sulfatase]-L-serine = a [sulfatase]-3-oxo-L-alanine + 5′-deoxyadenosine + L-methionine

Glossary:

3-oxo-L-alanine = (S)-formylglycine = (S)-Cα-formylglycine = FGly

Other name(s):

atsB (gene name)

Systematic name:

[sulfatase]-L-serine:S-adenosyl-L-methionine oxidoreductase (3-oxo-L-alanine-forming)

Comments:

A bacterial radical S-adenosyl-L-methionine (AdoMet) enzyme that contains three [4Fe-4S] clusters. The enzyme, found in some bacteria, activates a type I sulfatase enzyme (EC 3.1.6.1) by converting a conserved L-serine residue in the active site to a unique 3-oxo-L-alanine residue that is essential for the sulfatase activity. While the enzyme from Klebsiella pneumoniae is specific for L-serine, the enzyme from Clostridium perfringens can also act on L-cysteine, see EC 1.8.98.7, cysteine-type anaerobic sulfatase-maturating enzyme.

Links to other databases:

References:

1.	Szameit, C., Miech, C., Balleininger, M., Schmidt, B., von Figura, K. and Dierks, T. The iron sulfur protein AtsB is required for posttranslational formation of formylglycine in the Klebsiella sulfatase. J. Biol. Chem. 274 (1999) 15375–15381. [PMID: 10336424]
2.	Fang, Q., Peng, J. and Dierks, T. Post-translational formylglycine modification of bacterial sulfatases by the radical S-adenosylmethionine protein AtsB. J. Biol. Chem. 279 (2004) 14570–14578. [PMID: 14749327]
3.	Grove, T.L., Lee, K.H., St Clair, J., Krebs, C. and Booker, S.J. In vitro characterization of AtsB, a radical SAM formylglycine-generating enzyme that contains three [4Fe-4S] clusters. Biochemistry 47 (2008) 7523–7538. [PMID: 18558715]

[EC 1.1.98.7 created 2020]

*EC

1.2.1.25

Accepted name:

branched-chain α-keto acid dehydrogenase system

Reaction:

3-methyl-2-oxobutanoate + CoA + NAD⁺ = 2-methylpropanoyl-CoA + CO₂ + NADH

Other name(s):

branched-chain α-keto acid dehydrogenase complex; 2-oxoisovalerate dehydrogenase; α-ketoisovalerate dehydrogenase; 2-oxoisovalerate dehydrogenase (acylating)

Systematic name:

3-methyl-2-oxobutanoate:NAD⁺ 2-oxidoreductase (CoA-methylpropanoylating)

Comments:

This enzyme system catalyses the oxidative decarboxylation of branched-chain α-keto acids derived from L-leucine, L-isoleucine, and L-valine to branched-chain acyl-CoAs. It belongs to the 2-oxoacid dehydrogenase system family, which also includes EC 1.2.1.104, pyruvate dehydrogenase system, EC 1.2.1.105, 2-oxoglutarate dehydrogenase system, EC 1.4.1.27, glycine cleavage system, and EC 2.3.1.190, acetoin dehydrogenase system. With the exception of the glycine cleavage system, which contains 4 components, the 2-oxoacid dehydrogenase systems share a common structure, consisting of three main components, namely a 2-oxoacid dehydrogenase (E1), a dihydrolipoamide acyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The reaction catalysed by this system is the sum of three activities: EC 1.2.4.4, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring), EC 2.3.1.168, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase, and EC 1.8.1.4, dihydrolipoyl dehydrogenase. The system also acts on (S)-3-methyl-2-oxopentanoate and 4-methyl-2-oxopentanoate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 37211-61-3

References:

1.	Namba, Y., Yoshizawa, K., Ejima, A., Hayashi, T. and Kaneda, T. Coenzyme A- and nicotinamide adenine dinucleotide-dependent branched chain α-keto acid dehydrogenase. I. Purification and properties of the enzyme from Bacillus subtilis. J. Biol. Chem. 244 (1969) 4437–4447. [PMID: 4308861]
2.	Pettit, F.H., Yeaman, S.J. and Reed, L.J. Purification and characterization of branched chain α-keto acid dehydrogenase complex of bovine kidney. Proc. Natl. Acad. Sci. USA 75 (1978) 4881–4885. [DOI] [PMID: 283398]
3.	Harris, R.A., Hawes, J.W., Popov, K.M., Zhao, Y., Shimomura, Y., Sato, J., Jaskiewicz, J. and Hurley, T.D. Studies on the regulation of the mitochondrial α-ketoacid dehydrogenase complexes and their kinases. Adv. Enzyme Regul. 37 (1997) 271–293. [DOI] [PMID: 9381974]
4.	Evarsson, A., Chuang, J.L., Wynn, R.M., Turley, S., Chuang, D.T. and Hol, W.G. Crystal structure of human branched-chain α-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease. Structure 8 (2000) 277–291. [PMID: 10745006]
5.	Reed, L.J. A trail of research from lipoic acid to α-keto acid dehydrogenase complexes. J. Biol. Chem. 276 (2001) 38329–38336. [DOI] [PMID: 11477096]

[EC 1.2.1.25 created 1972, modified 2019, modified 2020]

1.2.1.103

Accepted name:

[amino-group carrier protein]-6-phospho-L-2-aminoadipate reductase

Reaction:

an [amino-group carrier protein]-C-terminal-[N-(1-carboxy-5-oxopentyl)-L-glutamine] + phosphate + NADP⁺ = an [amino-group carrier protein]-C-terminal-[N-(1-carboxy-5-phosphooxy-5-oxopentyl)-L-glutamine] + NADPH + H⁺

Other name(s):

lysY (gene name)

Systematic name:

[amino-group carrier protein]-C-terminal-[N-(1-carboxy-5-oxopentyl)-L-glutamine]:NADP⁺ 5-oxidoreductase (phosphorylating)

Comments:

The enzyme participates in an L-lysine biosynthesis in certain species of archaea and bacteria.

Links to other databases:

References:

1.	Nishida, H., Nishiyama, M., Kobashi, N., Kosuge, T., Hoshino, T. and Yamane, H. A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Genome Res. 9 (1999) 1175–1183. [PMID: 10613839]
2.	Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673–679. [DOI] [PMID: 19620981]
3.	Shimizu, T., Tomita, T., Kuzuyama, T. and Nishiyama, M. Crystal Structure of the LysY.LysW Complex from Thermus thermophilus. J. Biol. Chem. 291 (2016) 9948–9959. [PMID: 26966182]

[EC 1.2.1.103 created 2019]

1.3.1.99

Transferred entry:

iridoid synthase. Now known to be catalyzed by two different enzymes, EC 1.3.1.122, (S)-8-oxocitronellyl enol synthase, and EC 5.5.1.34, (+)-cis,trans-nepetalactol synthase

[EC 1.3.1.99 created 2013, deleted 2019]

1.3.1.121

Accepted name:

4-amino-4-deoxyprephenate dehydrogenase

Reaction:

4-amino-4-deoxyprephenate + NAD⁺ = 3-(4-aminophenyl)pyruvate + CO₂ + NADH + H⁺

Other name(s):

cmlC (gene name); papC (gene name)

Systematic name:

4-amino-4-deoxyprephenate:NAD⁺ oxidoreductase (decarboxylating)

Comments:

The enzyme, characterized from the bacteria Streptomyces venezuelae and Streptomyces pristinaespiralis, participates in the biosynthesis of the antibiotics chloramphenicol and pristinamycin IA, respectively. cf. EC 1.3.1.12, prephenate dehydrogenase.

Links to other databases:

References:

1.	Blanc, V., Gil, P., Bamas-Jacques, N., Lorenzon, S., Zagorec, M., Schleuniger, J., Bisch, D., Blanche, F., Debussche, L., Crouzet, J. and Thibaut, D. Identification and analysis of genes from Streptomyces pristinaespiralis encoding enzymes involved in the biosynthesis of the 4-dimethylamino-L-phenylalanine precursor of pristinamycin I. Mol. Microbiol. 23 (1997) 191–202. [PMID: 9044253]
2.	He, J., Magarvey, N., Piraee, M. and Vining, L.C. The gene cluster for chloramphenicol biosynthesis in Streptomyces venezuelae ISP5230 includes novel shikimate pathway homologues and a monomodular non-ribosomal peptide synthetase gene. Microbiology 147 (2001) 2817–2829. [PMID: 11577160]

[EC 1.3.1.121 created 2019]

1.3.1.122

Accepted name:

(S)-8-oxocitronellyl enol synthase

Reaction:

(S)-8-oxocitronellyl enol + NAD(P)⁺ = (6E)-8-oxogeranial + NAD(P)H + H⁺

For diagram of secologanin biosynthesis, click here

Glossary:

(S)-8-oxocitronellyl enol = (2E,6S,7E)-8-hydroxy-2,6-dimethylocta-2,7-dienal

Other name(s):

CrISY; 8-oxogeranial:NAD(P)⁺ oxidoreductase (cyclizing, cis-trans-nepetalactol forming); iridoid synthase (incorrect)

Systematic name:

(S)-8-oxocitronellyl enol:NAD(P)⁺ oxidoreductase

Comments:

Isolated from the plants Catharanthus roseus, Olea europaea (common olive), and several Nepeta species. The enzyme reduces 8-oxogeranial, generating an unstable product that is subsequently cyclized into several possible products, either non-enzymically or by dedicated cyclases. The products, known as iridoids, are involved in the biosynthesis of many indole alkaloids. cf. EC 1.3.1.123, 7-epi-iridoid synthase.

Links to other databases:

References:

1.	Geu-Flores, F., Sherden, N.H., Courdavault, V., Burlat, V., Glenn, W.S., Wu, C., Nims, E., Cui, Y. and O'Connor, S.E. An alternative route to cyclic terpenes by reductive cyclization in iridoid biosynthesis. Nature 492 (2012) 138–142. [DOI] [PMID: 23172143]
2.	Hu, Y., Liu, W., Malwal, S.R., Zheng, Y., Feng, X., Ko, T.P., Chen, C.C., Xu, Z., Liu, M., Han, X., Gao, J., Oldfield, E. and Guo, R.T. Structures of iridoid synthase from Catharanthus roseus with bound NAD⁺, NADPH, or NAD⁺/10-oxogeranial: Reaction mechanisms. Angew. Chem. Int. Ed. Engl. 54 (2015) 15478–15482. [PMID: 26768532]
3.	Alagna, F., Geu-Flores, F., Kries, H., Panara, F., Baldoni, L., O'Connor, S.E. and Osbourn, A. Identification and characterization of the iridoid synthase involved in oleuropein biosynthesis in olive (Olea europaea) fruits. J. Biol. Chem. 291 (2016) 5542–5554. [PMID: 26709230]
4.	Qin, L., Zhu, Y., Ding, Z., Zhang, X., Ye, S. and Zhang, R. Structure of iridoid synthase in complex with NADP⁺/8-oxogeranial reveals the structural basis of its substrate specificity. J. Struct. Biol. 194 (2016) 224–230. [PMID: 26868105]
5.	Sherden, N.H., Lichman, B., Caputi, L., Zhao, D., Kamileen, M.O., Buell, C.R. and O'Connor, S.E. Identification of iridoid synthases from Nepeta species: Iridoid cyclization does not determine nepetalactone stereochemistry. Phytochemistry 145 (2018) 48–56. [PMID: 29091815]
6.	Lichman, B.R., Kamileen, M.O., Titchiner, G.R., Saalbach, G., Stevenson, C.EM., Lawson, D.M. and O'Connor, S.E. Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis. Nat. Chem. Biol. 15 (2019) 71–79. [PMID: 30531909]
7.	Lichman, B.R., O'Connor, S.E. and Kries, H. Biocatalytic strategies towards [4+2] cycloadditions. Chemistry 25 (2019) 6864–6877. [PMID: 30664302]

[EC 1.3.1.122 created 2013 as EC 1.3.1.99, part transferred 2019 to EC 1.3.1.122]

1.3.1.123

Accepted name:

8-oxogeranial reductase

Reaction:

(R)-8-oxocitronellyl enol + NADP⁺ = (6E)-8-oxogeranial + NADPH + H⁺

Glossary:

(R)-8-oxocitronellyl enol = (2E,6R,7E)-8-hydroxy-2,6-dimethylocta-2,7-dienal

Other name(s):

AmISY

Systematic name:

(R)-8-oxocitronellyl enol:NADP⁺ oxidoreductase

Comments:

The enzyme, characterized from the plant Antirrhinum majus (snapdragon), is involved in biosynthesis of 7-epi-iridoids such as antirrhinoside. The enzyme catalyses the stereospecific reduction of 8-oxogeranial, forming an unstable product that in the absence of additional cylases undergoes spontaneous cyclization to (–)-cis,trans-nepetalactol. cf. EC 1.3.1.122, (S)-8-oxocitronellyl enol synthase.

Links to other databases:

References:

1.	Kries, H., Kellner, F., Kamileen, M.O. and O'Connor, S.E. Inverted stereocontrol of iridoid synthase in snapdragon. J. Biol. Chem. 292 (2017) 14659–14667. [PMID: 28701463]
2.	Lichman, B.R., O'Connor, S.E. and Kries, H. Biocatalytic strategies towards [4+2] cycloadditions. Chemistry 25 (2019) 6864–6877. [PMID: 30664302]

[EC 1.3.1.123 created 2019]

*EC

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:

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:

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]

1.3.8.15

Accepted name:

3-(aryl)acrylate reductase

Reaction:

(1) phloretate + electron-transfer flavoprotein = 4-coumarate + reduced electron-transfer flavoprotein
(2) 3-phenylpropanoate + electron-transfer flavoprotein = trans-cinnamate + reduced electron-transfer flavoprotein
(3) 3-(1H-indol-3-yl)propanoate + electron-transfer flavoprotein = 3-(indol-3-yl)acrylate + reduced electron-transfer flavoprotein

Glossary:

phloretate = 3-(4-hydroxyphenyl)propanoate
crotonate = (2E)-but-2-enoate

Other name(s):

acdA (gene name)

Systematic name:

3-(phenyl)propanoate:electron-transfer flavoprotein 2,3-oxidoreductase

Comments:

The enzyme, found in some amino acid-fermenting anaerobic bacteria, participates in the fermentation pathways of L-phenylalanine, L-tyrosine, and L-tryptophan. Unlike EC 1.3.1.31, 2-enoate reductase, this enzyme has minimal activity with crotonate.

Links to other databases:

References:

Dodd, D., Spitzer, M.H., Van Treuren, W., Merrill, B.D., Hryckowian, A.J., Higginbottom, S.K., Le, A., Cowan, T.M., Nolan, G.P., Fischbach, M.A. and Sonnenburg, J.L. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551 (2017) 648–652. [PMID: 29168502]

[EC 1.3.8.15 created 2019]

*EC

1.6.5.9

Accepted name:

NADH:quinone reductase (non-electrogenic)

Reaction:

NADH + H⁺ + a quinone = NAD⁺ + a quinol

Other name(s):

type II NAD(P)H:quinone oxidoreductase; NDE2 (gene name); ndh (gene name); NDH-II; NDH-2; NADH dehydrogenase (quinone) (ambiguous); ubiquinone reductase (ambiguous); coenzyme Q reductase (ambiguous); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH-Q6 oxidoreductase (ambiguous); NADH₂ dehydrogenase (ubiquinone) (ambiguous); NADH:ubiquinone oxidoreductase; NADH:ubiquinone reductase (non-electrogenic)

Systematic name:

NADH:quinone oxidoreductase

Comments:

A flavoprotein (FAD or FMN). Occurs in mitochondria of yeast and plants, and in aerobic bacteria. Has low activity with NADPH. Unlike EC 7.1.1.2, NADH:ubiquinone reductase (H⁺-translocating), this enzyme does not pump proteons of sodium ions across the membrane. It is also not sensitive to rotenone.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9028-04-0

References:

1.	Bergsma, J., Strijker, R., Alkema, J.Y., Seijen, H.G. and Konings, W.N. NADH dehydrogenase and NADH oxidation in membrane vesicle from Bacillus subtilis. Eur. J. Biochem. 120 (1981) 599–606. [PMID: 6800784]
2.	Møller, I.M, and Palmer, J.M. Direct evidence for the presence of a rotenone-resistant NADH dehydrogenase on the inner surface of plant mitochondria. Physiol. Plant. 54 (1982) 267–274. [DOI]
3.	de Vries, S. and Grivell, L.A. Purification and characterization of a rotenone-insensitive NADH:Q6 oxidoreductase from mitochondria of Saccharomyces cerevisiae. Eur. J. Biochem. 176 (1988) 377–384. [DOI] [PMID: 3138118]
4.	Kerscher, S.J., Okun, J.G. and Brandt, U. A single external enzyme confers alternative NADH:ubiquinone oxidoreductase activity in Yarrowia lipolytica. J. Cell Sci. 112 ( Pt 14) (1999) 2347–2354. [PMID: 10381390]
5.	Rasmusson, A.G., Soole, K.L. and Elthon, T.E. Alternative NAD(P)H dehydrogenases of plant mitochondria. Annu. Rev. Plant Biol. 55 (2004) 23–39. [DOI] [PMID: 15725055]
6.	Melo, A.M., Bandeiras, T.M. and Teixeira, M. New insights into type II NAD(P)H:quinone oxidoreductases. Microbiol. Mol. Biol. Rev. 68 (2004) 603–616. [PMID: 15590775]

[EC 1.6.5.9 created 2011 (EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, incorporated 2019), modified 2019]

1.6.5.11

Deleted entry:

NADH dehydrogenase (quinone). Identical to EC 1.6.5.9, NADH:quinone reductase (non-electrogenic)

[EC 1.6.5.11 created 1972 as EC 1.6.99.5, transferred 2015 to EC 1.6.5.11, deleted 2019]

1.8.4.15

Accepted name:

protein dithiol oxidoreductase (disulfide-forming)

Reaction:

a [DsbA protein] carrying a disulfide bond + a [protein] with reduced L-cysteine residues = a [DsbA protein] with reduced L-cysteine residues + a [protein] carrying a disulfide bond

Other name(s):

dsbA (gene name)

Systematic name:

protein dithiol:[DsbA protein] oxidoreductase (protein disulfide-forming)

Comments:

DsbA is a periplasmic thiol:disulfide oxidoreductase found in Gram-negative bacteria that promotes protein disulfide bond formation. DsbA contains a redox active disulfide bond that is catalytically transferred via disulfide exchange to a diverse range of newly translocated protein substrates. The protein is restored to the oxidized state by EC 1.8.5.9, protein dithiol:quinone oxidoreductase DsbB.

Links to other databases:

References:

1.	Bardwell, J.C., McGovern, K. and Beckwith, J. Identification of a protein required for disulfide bond formation in vivo. Cell 67 (1991) 581–589. [PMID: 1934062]
2.	Akiyama, Y., Kamitani, S., Kusukawa, N. and Ito, K. In vitro catalysis of oxidative folding of disulfide-bonded proteins by the Escherichia coli dsbA (ppfA) gene product. J. Biol. Chem. 267 (1992) 22440–22445. [PMID: 1429594]
3.	Zapun, A., Bardwell, J.C. and Creighton, T.E. The reactive and destabilizing disulfide bond of DsbA, a protein required for protein disulfide bond formation in vivo. Biochemistry 32 (1993) 5083–5092. [PMID: 8494885]
4.	Bader, M., Muse, W., Zander, T. and Bardwell, J. Reconstitution of a protein disulfide catalytic system. J. Biol. Chem. 273 (1998) 10302–10307. [PMID: 9553083]
5.	Guddat, L.W., Bardwell, J.C. and Martin, J.L. Crystal structures of reduced and oxidized DsbA: investigation of domain motion and thiolate stabilization. Structure 6 (1998) 757–767. [PMID: 9655827]
6.	Kadokura, H., Tian, H., Zander, T., Bardwell, J.C. and Beckwith, J. Snapshots of DsbA in action: detection of proteins in the process of oxidative folding. Science 303 (2004) 534–537. [PMID: 14739460]

[EC 1.8.4.15 created 2019]

1.8.4.16

Accepted name:

thioredoxin:protein disulfide reductase

Reaction:

a [protein] with reduced L-cysteine residues + thioredoxin disulfide = a [protein] carrying a disulfide bond + thioredoxin (overall reaction)
(1a) a [thioredoxin:protein disulfide reductase] with reduced L-cysteine residues + thioredoxin disulfide = a [thioredoxin:protein disulfide reductase] carrying a disulfide bond + thioredoxin
(1b) a [thioredoxin:protein disulfide reductase] carrying a disulfide bond + a [protein] with reduced L-cysteine residues = a [thioredoxin:protein disulfide reductase] with reduced L-cysteine residues + a [protein] carrying a disulfide bond

Other name(s):

dsbD (gene name); dipZ (gene name)

Systematic name:

thioredoxin:protein disulfide oxidoreductase (dithiol-forming)

Comments:

The DsbD protein is found in Gram-negative bacteria and transfers electrons from cytoplasmic thioredoxin to the periplasmic substrate proteins DsbC, DsbG and CcmG, reducing disulfide bonds in the target proteins to dithiols. NrdH redoxins, which are found in Gram-positive bacteria, catalyse a similar reaction.

Links to other databases:

References:

1.	Missiakas, D., Schwager, F. and Raina, S. Identification and characterization of a new disulfide isomerase-like protein (DsbD) in Escherichia coli. EMBO J. 14 (1995) 3415–3424. [DOI] [PMID: 7628442]
2.	Gordon, E.H., Page, M.D., Willis, A.C. and Ferguson, S.J. Escherichia coli DipZ: anatomy of a transmembrane protein disulphide reductase in which three pairs of cysteine residues, one in each of three domains, contribute differentially to function. Mol. Microbiol. 35 (2000) 1360–1374. [DOI] [PMID: 10760137]
3.	Katzen, F. and Beckwith, J. Transmembrane electron transfer by the membrane protein DsbD occurs via a disulfide bond cascade. Cell 103 (2000) 769–779. [DOI] [PMID: 11114333]
4.	Goulding, C.W., Sawaya, M.R., Parseghian, A., Lim, V., Eisenberg, D. and Missiakas, D. Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD. Biochemistry 41 (2002) 6920–6927. [DOI] [PMID: 12033924]
5.	Katzen, F. and Beckwith, J. Role and location of the unusual redox-active cysteines in the hydrophobic domain of the transmembrane electron transporter DsbD. Proc. Natl. Acad. Sci. USA 100 (2003) 10471–10476. [DOI] [PMID: 12925743]
6.	Rozhkova, A. and Glockshuber, R. Thermodynamic aspects of DsbD-mediated electron transport. J. Mol. Biol. 380 (2008) 783–788. [DOI] [PMID: 18571669]
7.	Si, M.R., Zhang, L., Yang, Z.F., Xu, Y.X., Liu, Y.B., Jiang, C.Y., Wang, Y., Shen, X.H. and Liu, S.J. NrdH Redoxin enhances resistance to multiple oxidative stresses by acting as a peroxidase cofactor in Corynebacterium glutamicum. Appl. Environ. Microbiol. 80 (2014) 1750–1762. [DOI] [PMID: 24375145]

[EC 1.8.4.16 created 2019, modified 2023]

1.8.5.9

Accepted name:

protein dithiol:quinone oxidoreductase DsbB

Reaction:

a [DsbA protein] with reduced L-cysteine residues + a quinone = a [DsbA protein] carrying a disulfide bond + a quinol (overall reaction)
(1a) a [DsbA protein] with reduced L-cysteine residues + a [DsbB protein] carrying a disulfide bond = a [DsbA protein] carrying a disulfide bond + a [DsbB protein] with reduced L-cysteine residues
(1b) a [DsbB protein] with reduced L-cysteine residues + a quinone = a [DsbB protein] carrying a disulfide bond + a quinol

Other name(s):

dsbB (gene name)

Systematic name:

protein dithiol:quinone oxidoreductase (disulfide-forming)

Comments:

DsbB is a protein found in Gram-negative bacteria that functions within a pathway for protein disulfide bond formation. The enzyme catalyses the oxidation of the DsbA protein by generating disulfide bonds de novo via the reduction of membrane quinones. cf. EC 1.8.4.15, protein dithiol oxidoreductase (disulfide-forming).

Links to other databases:

References:

1.	Guilhot, C., Jander, G., Martin, N.L. and Beckwith, J. Evidence that the pathway of disulfide bond formation in Escherichia coli involves interactions between the cysteines of DsbB and DsbA. Proc. Natl. Acad. Sci. USA 92 (1995) 9895–9899. [PMID: 7568240]
2.	Kishigami, S., Kanaya, E., Kikuchi, M. and Ito, K. DsbA-DsbB interaction through their active site cysteines. Evidence from an odd cysteine mutant of DsbA. J. Biol. Chem. 270 (1995) 17072–17074. [PMID: 7615498]
3.	Kishigami, S. and Ito, K. Roles of cysteine residues of DsbB in its activity to reoxidize DsbA, the protein disulphide bond catalyst of Escherichia coli. Genes Cells 1 (1996) 201–208. [PMID: 9140064]
4.	Collet, J.F. and Bardwell, J.C. Oxidative protein folding in bacteria. Mol. Microbiol. 44 (2002) 1–8. [PMID: 11967064]
5.	Dutton, R.J., Boyd, D., Berkmen, M. and Beckwith, J. Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. Proc. Natl. Acad. Sci. USA 105 (2008) 11933–11938. [PMID: 18695247]
6.	Inaba, K. Disulfide bond formation system in Escherichia coli. J. Biochem. 146 (2009) 591–597. [PMID: 19567379]

[EC 1.8.5.9 created 2019]

1.8.98.7

Accepted name:

cysteine-type anaerobic sulfatase-maturating enzyme

Reaction:

S-adenosyl-L-methionine + a [sulfatase]-L-cysteine + H₂O = a [sulfatase]-3-oxo-L-alanine + 5′-deoxyadenosine + L-methionine + hydrogen sulfide

Glossary:

3-oxo-L-alanine = formylglycine = Cα-formylglycine = FGly

Other name(s):

anSME; Cys-type anaerobic sulfatase-maturating enzyme; anaerobic sulfatase maturase

Systematic name:

[sulfatase]-L-cysteine:S-adenosyl-L-methionine oxidoreductase (3-oxo-L-alanine-forming)

Comments:

A radical S-adenosylmethionine (AdoMet) enzyme that contains three [4Fe-4S] clusters. The enzyme, found in some bacteria, activates a type I sulfatase enzyme (EC 3.1.6.1) by converting a conserved L-cysteine residue in the active site to a unique 3-oxo-L-alanine residue that is essential for the sulfatase activity. Some enzymes can also act on L-serine, see EC 1.1.98.7, serine-type anaerobic sulfatase-maturating enzyme and EC 1.8.3.7, formylglycine-generating enzyme.

Links to other databases:

References:

1.	Berteau, O., Guillot, A., Benjdia, A. and Rabot, S. A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes. J. Biol. Chem. 281 (2006) 22464–22470. [PMID: 16766528]
2.	Benjdia, A., Subramanian, S., Leprince, J., Vaudry, H., Johnson, M.K. and Berteau, O. Anaerobic sulfatase-maturating enzymes, first dual substrate radical S-adenosylmethionine enzymes. J. Biol. Chem. 283 (2008) 17815–17826. [PMID: 18408004]
3.	Benjdia, A., Leprince, J., Sandstrom, C., Vaudry, H. and Berteau, O. Mechanistic investigations of anaerobic sulfatase-maturating enzyme: direct Cβ H-atom abstraction catalyzed by a radical AdoMet enzyme. J. Am. Chem. Soc. 131 (2009) 8348–8349. [PMID: 19489556]
4.	Benjdia, A., Subramanian, S., Leprince, J., Vaudry, H., Johnson, M.K. and Berteau, O. Anaerobic sulfatase-maturating enzyme^--a mechanistic link with glycyl radical-activating enzymes. FEBS J. 277 (2010) 1906–1920. [PMID: 20218986]
5.	Grove, T.L., Ahlum, J.H., Qin, R.M., Lanz, N.D., Radle, M.I., Krebs, C. and Booker, S.J. Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. Biochemistry 52 (2013) 2874–2887. [PMID: 23477283]

[EC 1.8.98.7 created 2020]

1.9.3.1

Transferred entry:

cytochrome-c oxidase. Now EC 7.1.1.9, cytochrome-c oxidase

[EC 1.9.3.1 created 1961, modified 2000, deleted 2019]

1.10.3.17

Accepted name:

superoxide oxidase

Reaction:

2 O₂ + ubiquinol = 2 superoxide + ubiquinone + 2 H⁺

Other name(s):

SOO; CybB; cytochrome b₅₆₁; superoxide:ubiquinone oxidoreductase

Systematic name:

ubiquinol:oxygen oxidoreductase (superoxide-forming)

Comments:

This membrane-bound, di-heme containing enzyme, identified in the bacterium Escherichia coli, is responsible for the detoxification of superoxide in the periplasm. In vivo the reaction proceeds in the opposite direction of that shown and produces oxygen. Superoxide production was only observed when the enzyme was incubated in vitro with an excess of ubiquinol.

Links to other databases:

References:

1.	Murakami, H., Kita, K. and Anraku, Y. Cloning of cybB, the gene for cytochrome b₅₆₁ of Escherichia coli K12. Mol. Gen. Genet. 198 (1984) 1–6. [PMID: 6097799]
2.	Murakami, H., Kita, K. and Anraku, Y. Purification and properties of a diheme cytochrome b₅₆₁ of the Escherichia coli respiratory chain. J. Biol. Chem. 261 (1986) 548–551. [PMID: 3510204]
3.	Lundgren, C.AK., Sjostrand, D., Biner, O., Bennett, M., Rudling, A., Johansson, A.L., Brzezinski, P., Carlsson, J., von Ballmoos, C. and Hogbom, M. Scavenging of superoxide by a membrane-bound superoxide oxidase. Nat. Chem. Biol. 14 (2018) 788–793. [PMID: 29915379]

[EC 1.10.3.17 created 2019]

1.11.1.15

Transferred entry:

peroxiredoxin. Now described by EC 1.11.1.24, thioredoxin-dependent peroxiredoxin; EC 1.11.1.25, glutaredoxin-dependent peroxiredoxin; EC 1.11.1.26, NADH-dependent peroxiredoxin; EC 1.11.1.27, glutathione-dependent peroxiredoxin; EC 1.11.1.28, lipoyl-dependent peroxiredoxin; and EC 1.11.1.29, mycoredoxin-dependent peroxiredoxin.

[EC 1.11.1.15 created 2004, deleted 2020]

1.11.1.24

Accepted name:

thioredoxin-dependent peroxiredoxin

Reaction:

thioredoxin + ROOH = thioredoxin disulfide + H₂O + ROH

For diagram of reaction, click here and for mechanism, click here

Other name(s):

thioredoxin peroxidase; bcp (gene name); tpx (gene name); PrxQ

Systematic name:

thioredoxin:hydroperoxide oxidoreductase

Comments:

Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [4]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Thioredoxin-dependent peroxiredoxins are the most common. They have been reported from archaea, bacteria, fungi, plants, and animals.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 207137-51-7

References:

1.	Kang, S.W., Chae, H.Z., Seo, M.S., Kim, K., Baines, I.C. and Rhee, S.G. Mammalian peroxiredoxin isoforms can reduce hydrogen peroxide generated in response to growth factors and tumor necrosis factor-α. J. Biol. Chem. 273 (1998) 6297–6302. [PMID: 9497357]
2.	Kong, W., Shiota, S., Shi, Y., Nakayama, H. and Nakayama, K. A novel peroxiredoxin of the plant Sedum lineare is a homologue of Escherichia coli bacterioferritin co-migratory protein (Bcp). Biochem. J. 351 (2000) 107–114. [PMID: 10998352]
3.	Jeong, W., Cha, M.K. and Kim, I.H. Thioredoxin-dependent hydroperoxide peroxidase activity of bacterioferritin comigratory protein (BCP) as a new member of the thiol-specific antioxidant protein (TSA)/alkyl hydroperoxide peroxidase C (AhpC) family. J. Biol. Chem. 275 (2000) 2924–2930. [PMID: 10644761]
4.	Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
5.	Jeon, S.J. and Ishikawa, K. Characterization of novel hexadecameric thioredoxin peroxidase from Aeropyrum pernix K1. J. Biol. Chem. 278 (2003) 24174–24180. [PMID: 12707274]
6.	Perez-Perez, M.E., Mata-Cabana, A., Sanchez-Riego, A.M., Lindahl, M. and Florencio, F.J. A comprehensive analysis of the peroxiredoxin reduction system in the cyanobacterium Synechocystis sp. strain PCC 6803 reveals that all five peroxiredoxins are thioredoxin dependent. J. Bacteriol. 191 (2009) 7477–7489. [PMID: 19820102]

[EC 1.11.1.24 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.24]

1.11.1.25

Accepted name:

glutaredoxin-dependent peroxiredoxin

Reaction:

glutaredoxin + ROOH = glutaredoxin disulfide + H₂O + ROH

For diagram of reaction, click here and for mechanism, click here

Other name(s):

PRXIIB (gene name)

Systematic name:

glutaredoxin:hydroperoxide oxidoreductase

Comments:

Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [2]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. To recycle the disulfide, known atypical 2-Cys Prxs appear to use thioredoxin as an electron donor. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Glutaredoxin-dependent peroxiredoxins have been reported from bacteria, fungi, plants, and animals. These enzymes are often able to use an alternative reductant such as thioredoxin or glutathione.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 207137-51-7

References:

1.	Rouhier, N., Gelhaye, E. and Jacquot, J.P. Glutaredoxin-dependent peroxiredoxin from poplar: protein-protein interaction and catalytic mechanism. J. Biol. Chem. 277 (2002) 13609–13614. [PMID: 11832487]
2.	Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
3.	Pedrajas, J.R., Padilla, C.A., McDonagh, B. and Barcena, J.A. Glutaredoxin participates in the reduction of peroxides by the mitochondrial 1-CYS peroxiredoxin in Saccharomyces cerevisiae. Antioxid Redox Signal 13 (2010) 249–258. [PMID: 20059400]
4.	Hanschmann, E.M., Lonn, M.E., Schutte, L.D., Funke, M., Godoy, J.R., Eitner, S., Hudemann, C. and Lillig, C.H. Both thioredoxin 2 and glutaredoxin 2 contribute to the reduction of the mitochondrial 2-Cys peroxiredoxin Prx3. J. Biol. Chem. 285 (2010) 40699–40705. [PMID: 20929858]
5.	Lim, J.G., Bang, Y.J. and Choi, S.H. Characterization of the Vibrio vulnificus 1-Cys peroxiredoxin Prx3 and regulation of its expression by the Fe-S cluster regulator IscR in response to oxidative stress and iron starvation. J. Biol. Chem. 289 (2014) 36263–36274. [PMID: 25398878]
6.	Couturier, J., Prosper, P., Winger, A.M., Hecker, A., Hirasawa, M., Knaff, D.B., Gans, P., Jacquot, J.P., Navaza, A., Haouz, A. and Rouhier, N. In the absence of thioredoxins, what are the reductants for peroxiredoxins in Thermotoga maritima. Antioxid Redox Signal 18 (2013) 1613–1622. [PMID: 22866991]

[EC 1.11.1.25 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.25]

1.11.1.26

Accepted name:

NADH-dependent peroxiredoxin

Reaction:

NADH + ROOH + H⁺ = NAD⁺ + H₂O + ROH

For diagram of reaction, click here and for mechanism, click here

Other name(s):

ahpC (gene name); ahpF (gene name); alkyl hydroperoxide reductase

Systematic name:

NADH:hydroperoxide oxidoreductase

Comments:

Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. This bacterial peroxiredoxin differs from most other forms by comprising two types of subunits. One subunit (AhpC) is a typical 2-Cys peroxiredoxin. Following the reduction of the substrate, one AhpC subunit forms a disulfide bond with an identical unit. The disulfide bond is reduced by the second type of subunit (AhpF). This second subunit is a flavin-containing protein that uses electrons from NADH to reduce the cysteine residues on the AhpC subunits back to their active state.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 207137-51-7

References:

1.	Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.	Dip, P.V., Kamariah, N., Subramanian Manimekalai, M.S., Nartey, W., Balakrishna, A.M., Eisenhaber, F., Eisenhaber, B. and Gruber, G. Structure, mechanism and ensemble formation of the alkylhydroperoxide reductase subunits AhpC and AhpF from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 2848–2862. [PMID: 25372677]
3.	Nartey, W., Basak, S., Kamariah, N., Manimekalai, M.S., Robson, S., Wagner, G., Eisenhaber, B., Eisenhaber, F. and Gruber, G. NMR studies reveal a novel grab and release mechanism for efficient catalysis of the bacterial 2-Cys peroxiredoxin machinery. FEBS J. 282 (2015) 4620–4638. [PMID: 26402142]

[EC 1.11.1.26 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.26]

1.11.1.27

Accepted name:

glutathione-dependent peroxiredoxin

Reaction:

2 glutathione + ROOH = glutathione disulfide + H₂O + ROH

For diagram of reaction, click here and for mechanism, click here

Other name(s):

PRDX6 (gene name); prx3 (gene name)

Systematic name:

glutathione:hydroperoxide oxidoreductase

Comments:

Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Glutathione-dependent peroxiredoxins have been reported from bacteria and animals, and appear to be 1-Cys enzymes. The mechanism for the mammalian PRDX6 enzyme involves heterodimerization of the enzyme with π-glutathione S-transferase, followed by glutathionylation of the oxidized cysteine residue. Subsequent dissociation of the heterodimer yields glutathionylated peroxiredoxin, which is restored to the active form via spontaneous reduction by a second glutathione molecule.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 207137-51-7

References:

1.	Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.	Pauwels, F., Vergauwen, B., Vanrobaeys, F., Devreese, B. and Van Beeumen, J.J. Purification and characterization of a chimeric enzyme from Haemophilus influenzae Rd that exhibits glutathione-dependent peroxidase activity. J. Biol. Chem. 278 (2003) 16658–16666. [PMID: 12606554]
3.	Manevich, Y., Feinstein, S.I. and Fisher, A.B. Activation of the antioxidant enzyme 1-CYS peroxiredoxin requires glutathionylation mediated by heterodimerization with π GST. Proc. Natl. Acad. Sci. USA 101 (2004) 3780–3785. [PMID: 15004285]
4.	Greetham, D. and Grant, C.M. Antioxidant activity of the yeast mitochondrial one-Cys peroxiredoxin is dependent on thioredoxin reductase and glutathione in vivo. Mol. Cell Biol. 29 (2009) 3229–3240. [PMID: 19332553]
5.	Lim, J.G., Bang, Y.J. and Choi, S.H. Characterization of the Vibrio vulnificus 1-Cys peroxiredoxin Prx3 and regulation of its expression by the Fe-S cluster regulator IscR in response to oxidative stress and iron starvation. J. Biol. Chem. 289 (2014) 36263–36274. [PMID: 25398878]

[EC 1.11.1.27 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.27]

1.11.1.28

Accepted name:

lipoyl-dependent peroxiredoxin

Reaction:

a [lipoyl-carrier protein]-N⁶-[(R)-dihydrolipoyl]-L-lysine + ROOH = a [lipoyl-carrier protein]-N⁶-[(R)-lipoyl]-L-lysine + H₂O + ROH

For diagram of reaction, click here and for mechanism, click here

Other name(s):

Ohr; ahpC (gene name); ahpD (gene name)

Systematic name:

[lipoyl-carrier protein]-N⁶-[(R)-dihydrolipoyl]-L-lysine:hydroperoxide oxidoreductase

Comments:

Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [2]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Two types of lipoyl-dependent peroxiredoxins have been reported from bacteria. One type is the AhpC/AhpD system, originally described from Mycobacterium tuberculosis. In that system, AhpC catalyses reduction of the substrate, resulting in an intramolecular disulfide. AhpD then forms an intermolecular disulfide crosslink with AhpC, reducing it back to active state. AhpD is reduced in turn by lipoylated proteins. The second type, which has been characterized in Xylella fastidiosa, consists of only one type of subunit, which interacts directly with lipoylated proteins.

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 207137-51-7

References:

1.	Hillas, P.J., del Alba, F.S., Oyarzabal, J., Wilks, A. and Ortiz De Montellano, P.R. The AhpC and AhpD antioxidant defense system of Mycobacterium tuberculosis. J. Biol. Chem. 275 (2000) 18801–18809. [PMID: 10766746]
2.	Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
3.	Koshkin, A., Nunn, C.M., Djordjevic, S. and Ortiz de Montellano, P.R. The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics. J. Biol. Chem. 278 (2003) 29502–29508. [PMID: 12761216]
4.	Koshkin, A., Knudsen, G.M. and Ortiz De Montellano, P.R. Intermolecular interactions in the AhpC/AhpD antioxidant defense system of Mycobacterium tuberculosis. Arch. Biochem. Biophys. 427 (2004) 41–47. [PMID: 15178486]
5.	Shi, S. and Ehrt, S. Dihydrolipoamide acyltransferase is critical for Mycobacterium tuberculosis pathogenesis. Infect. Immun. 74 (2006) 56–63. [PMID: 16368957]
6.	Cussiol, J.R., Alegria, T.G., Szweda, L.I. and Netto, L.E. Ohr (organic hydroperoxide resistance protein) possesses a previously undescribed activity, lipoyl-dependent peroxidase. J. Biol. Chem. 285 (2010) 21943–21950. [PMID: 20463026]

[EC 1.11.1.28 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.28]

1.11.1.29

Accepted name:

mycoredoxin-dependent peroxiredoxin

Reaction:

mycoredoxin + ROOH = mycoredoxin disulfide + H₂O + ROH

For diagram of reaction, click here and for mechanism, click here

Other name(s):

ahpE (gene name)

Systematic name:

mycoredoxin:hydroperoxide oxidoreductase

Comments:

Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins. They can be divided into three classes: typical 2-Cys, atypical 2-Cys and 1-Cys peroxiredoxins [1]. The peroxidase reaction comprises two steps centred around a redox-active cysteine called the peroxidatic cysteine. All three peroxiredoxin classes have the first step in common, in which the peroxidatic cysteine attacks the peroxide substrate and is oxidized to S-hydroxycysteine (a sulfenic acid) (see mechanism). The second step of the peroxidase reaction, the regeneration of cysteine from S-hydroxycysteine, distinguishes the three peroxiredoxin classes. For typical 2-Cys Prxs, in the second step, the peroxidatic S-hydroxycysteine from one subunit is attacked by the ‘resolving’ cysteine located in the C-terminus of the second subunit, to form an intersubunit disulfide bond, which is then reduced by one of several cell-specific thiol-containing reductants completing the catalytic cycle. In the atypical 2-Cys Prxs, both the peroxidatic cysteine and its resolving cysteine are in the same polypeptide, so their reaction forms an intrachain disulfide bond. The 1-Cys Prxs conserve only the peroxidatic cysteine, so its regeneration involves direct interaction with a reductant molecule. Mycoredoxin-dependent enzymes are found in Mycobacteria. Following the reduction of the substrate, the sulfenic acid derivative of the peroxidatic cysteine forms a protein mixed disulfide with the N-terminal cysteine of mycoredoxin, which is then reduced by the C-terminal cysteine of mycoredoxin, restoring the peroxiredoxin to active state and resulting in an intra-protein disulfide in mycoredoxin. The disulfide is eventually reduced by mycothiol.

Links to other databases:

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

References:

1.	Wood, Z.A., Schröder, E., Harris, J.R. and Poole, L.B. Structure, mechanism and regulation of peroxiredoxins. Trends Biochem. Sci. 28 (2003) 32–40. [DOI] [PMID: 12517450]
2.	Hugo, M., Turell, L., Manta, B., Botti, H., Monteiro, G., Netto, L.E., Alvarez, B., Radi, R. and Trujillo, M. Thiol and sulfenic acid oxidation of AhpE, the one-cysteine peroxiredoxin from Mycobacterium tuberculosis: kinetics, acidity constants, and conformational dynamics. Biochemistry 48 (2009) 9416–9426. [PMID: 19737009]
3.	Hugo, M., Van Laer, K., Reyes, A.M., Vertommen, D., Messens, J., Radi, R. and Trujillo, M. Mycothiol/mycoredoxin 1-dependent reduction of the peroxiredoxin AhpE from Mycobacterium tuberculosis. J. Biol. Chem. 289 (2014) 5228–5239. [PMID: 24379404]
4.	Kumar, A., Balakrishna, A.M., Nartey, W., Manimekalai, M.SS. and Gruber, G. Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol. Free Radic. Biol. Med. 97 (2016) 588–601. [PMID: 27417938]
5.	Pedre, B., van Bergen, L.A., Pallo, A., Rosado, L.A., Dufe, V.T., Molle, I.V., Wahni, K., Erdogan, H., Alonso, M., Proft, F.D. and Messens, J. The active site architecture in peroxiredoxins: a case study on Mycobacterium tuberculosis AhpE. Chem. Commun. (Camb.) 52 (2016) 10293–10296. [PMID: 27471753]

[EC 1.11.1.29 created 1983 as EC 1.11.1.15, part transferred 2020 to EC 1.11.1.29]

*EC

1.13.11.79

Accepted name:

aerobic 5,6-dimethylbenzimidazole synthase

Reaction:

FMNH₂ + O₂ = 5,6-dimethylbenzimidazole + D-erythrose 4-phosphate + other product(s)

For diagram of FAD biosynthesis, click here

Other name(s):

BluB; flavin destructase

Systematic name:

FMNH₂ oxidoreductase (5,6-dimethylbenzimidazole-forming)

Comments:

The enzyme catalyses a complex oxygen-dependent conversion of reduced flavin mononucleotide to form 5,6-dimethylbenzimidazole, the lower ligand of vitamin B₁₂. This conversion involves many sequential steps in two distinct stages, and an alloxan intermediate that acts as a proton donor, a proton acceptor, and a hydride acceptor [4]. The C-2 of 5,6-dimethylbenzimidazole is derived from C-1′ of the ribityl group of FMNH₂ and 2-H from the ribityl 1′-pro-S hydrogen. While D-erythrose 4-phosphate has been shown to be one of the byproducts, the nature of the other product(s) has not been verified yet.

Links to other databases:

References:

1.	Gray, M.J. and Escalante-Semerena, J.C. Single-enzyme conversion of FMNH₂ to 5,6-dimethylbenzimidazole, the lower ligand of B₁₂. Proc. Natl. Acad. Sci. USA 104 (2007) 2921–2926. [DOI] [PMID: 17301238]
2.	Ealick, S.E. and Begley, T.P. Biochemistry: molecular cannibalism. Nature 446 (2007) 387–388. [DOI] [PMID: 17377573]
3.	Taga, M.E., Larsen, N.A., Howard-Jones, A.R., Walsh, C.T. and Walker, G.C. BluB cannibalizes flavin to form the lower ligand of vitamin B₁₂. Nature 446:449 (2007). [DOI] [PMID: 17377583]
4.	Wang, X.L. and Quan, J.M. Intermediate-assisted multifunctional catalysis in the conversion of flavin to 5,6-dimethylbenzimidazole by BluB: a density functional theory study. J. Am. Chem. Soc. 133 (2011) 4079–4091. [DOI] [PMID: 21344938]
5.	Collins, H.F., Biedendieck, R., Leech, H.K., Gray, M., Escalante-Semerena, J.C., McLean, K.J., Munro, A.W., Rigby, S.E., Warren, M.J. and Lawrence, A.D. Bacillus megaterium has both a functional BluB protein required for DMB synthesis and a related flavoprotein that forms a stable radical species. PLoS One 8:e55708 (2013). [DOI] [PMID: 23457476]

[EC 1.13.11.79 created 2010 as EC 1.14.99.40, transferred 2014 to EC 1.13.11.79, modified 2019]

1.14.11.70

Accepted name:

7-deoxycylindrospermopsin hydroxylase

Reaction:

(1) 7-deoxycylindrospermopsin + 2-oxoglutarate + O₂ = cylindrospermopsin + succinate + CO₂
(2) 7-deoxycylindrospermopsin + 2-oxoglutarate + O₂ = 7-epi-cylindrospermopsin + succinate + CO₂

Glossary:

cylindrospermopsin = (2aS,3R,4S,5aS,7R)-7-[(R)-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)(hydroxy)methyl]-3-methyl-2a,3,4,5,5a,6,7,8-octahydro-2H-1,8,8b-triazaacenaphthylen-4-yl hydrogen sulfate

Other name(s):

cyrI (gene name)

Systematic name:

7-deoxycylindrospermopsin,2-oxoglutarate:oxygen oxidoreductase (7-hydroxylating)

Comments:

Requires iron(II). The enzyme, found in some cyanobacterial species, catalyses the last step in the biosynthesis of the toxins cylindrospermopsin and 7-epi-cylindrospermopsin. The ratio of the two products differs among different strains.

Links to other databases:

References:

1.	Mazmouz, R., Chapuis-Hugon, F., Pichon V., Mejean, A., and Ploux, O. The last step of the biosynthesis of the cyanotoxins cylindrospermopsin and 7-epi-cylindrospermopsin is catalysed by CyrI, a 2-oxoglutarate-dependent iron oxygenase. ChemBioChem 12 (2011) 858–862.
2.	Mazmouz, R., Essadik, I., Hamdane, D., Mejean, A. and Ploux, O. Characterization of CyrI, the hydroxylase involved in the last step of cylindrospermopsin biosynthesis: Binding studies, site-directed mutagenesis and stereoselectivity. Arch. Biochem. Biophys. 647 (2018) 1–9. [PMID: 29653078]

[EC 1.14.11.70 created 2019]

1.14.11.71

Accepted name:

methylphosphonate hydroxylase

Reaction:

methylphosphonate + 2-oxoglutarate + O₂ = hydroxymethylphosphonate + succinate + CO₂

Other name(s):

phnY* (gene name)

Systematic name:

methylphosphonate,2-oxoglutarate:oxygen oxidoreductase (1-hydroxylating)

Comments:

Requires iron(II). The enzyme, characterized from the marine bacterium Gimesia maris, participates in a methylphosphonate degradation pathway.

Links to other databases:

References:

1.	Gama, S.R., Vogt, M., Kalina, T., Hupp, K., Hammerschmidt, F., Pallitsch, K. and Zechel, D.L. An oxidative pathway for microbial utilization of methylphosphonic acid as a phosphate source. ACS Chem. Biol. 14 (2019) 735–741. [PMID: 30810303]

[EC 1.14.11.71 created 2019]

1.14.13.247

Accepted name:

stachydrine N-demethylase

Reaction:

L-proline betaine + NAD(P)H + H⁺ + O₂ = N-methyl-L-proline + formaldehyde + NAD(P)⁺ + H₂O

Other name(s):

L-proline betaine N-demethylase; stc2 (gene name)

Systematic name:

L-proline betaine,NAD(P)H:oxygen oxidoreductase (formaldehyde-forming)

Comments:

The enzyme, characterized from the bacterium Sinorhizobium meliloti 1021, consists of three different types of subunits. The catalytic unit contains a Rieske [2Fe-2S] iron-sulfur cluster, and catalyses the monooxygenation of a methyl group. The resulting N-methoxyl group is unstable and decomposes spontaneously to form formaldehyde. The other subunits are involved in the transfer of electrons from NAD(P)H to the catalytic subunit.

Links to other databases:

References:

1.	Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P. and Allen, K.N. Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J. Am. Chem. Soc. 134 (2012) 2823–2834. [PMID: 22224443]
2.	Kumar, R., Zhao, S., Vetting, M.W., Wood, B.M., Sakai, A., Cho, K., Solbiati, J., Almo, S.C., Sweedler, J.V., Jacobson, M.P., Gerlt, J.A. and Cronan, J.E. Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5 (2014) e00933. [DOI] [PMID: 24520058]

[EC 1.14.13.247 created 2017]

*EC

1.14.14.22

Accepted name:

dibenzothiophene sulfone monooxygenase

Reaction:

dibenzothiophene-5,5-dioxide + FMNH₂ + NADH + O₂ = 2′-hydroxybiphenyl-2-sulfinate + H₂O + FMN + NAD⁺ + H⁺ (overall reaction)
(1a) FMNH₂ + O₂ = FMN-N⁵-peroxide
(1b) dibenzothiophene-5,5-dioxide + FMN-N⁵-peroxide = 2′-hydroxybiphenyl-2-sulfinate + FMN-N⁵-oxide
(1c) FMN-N⁵-oxide + NADH = FMN + H₂O + NAD⁺ + H⁺ (spontaneous)

Glossary:

dibenzothiophene-5,5-dioxide = dibenzothiophene sulfone

Other name(s):

dszA (gene name)

Systematic name:

dibenzothiophene-5,5-dioxide,FMNH₂:oxygen oxidoreductase

Comments:

This bacterial enzyme catalyses a step in the desulfurization pathway of dibenzothiophenes. The enzyme forms a two-component system with a dedicated NADH-dependent FMN reductase (EC 1.5.1.42) encoded by the dszD gene, which also interacts with EC 1.14.14.21, dibenzothiophene monooxygenase. The flavin-N⁵-oxide that is formed by the enzyme reacts spontaneously with NADH to give oxidized flavin, releasing a water molecule.

Links to other databases:

References:

1.	Gray, K.A., Pogrebinsky, O.S., Mrachko, G.T., Xi, L., Monticello, D.J. and Squires, C.H. Molecular mechanisms of biocatalytic desulfurization of fossil fuels. Nat. Biotechnol. 14 (1996) 1705–1709. [DOI] [PMID: 9634856]
2.	Ohshiro, T., Kojima, T., Torii, K., Kawasoe, H. and Izumi, Y. Purification and characterization of dibenzothiophene (DBT) sulfone monooxygenase, an enzyme involved in DBT desulfurization, from Rhodococcus erythropolis D-1. J. Biosci. Bioeng. 88 (1999) 610–616. [DOI] [PMID: 16232672]
3.	Konishi, J., Ishii, Y., Onaka, T., Ohta, Y., Suzuki, M. and Maruhashi, K. Purification and characterization of dibenzothiophene sulfone monooxygenase and FMN-dependent NADH oxidoreductase from the thermophilic bacterium Paenibacillus sp. strain A11-2. J. Biosci. Bioeng. 90 (2000) 607–613. [DOI] [PMID: 16232919]
4.	Ohshiro, T., Ishii, Y., Matsubara, T., Ueda, K., Izumi, Y., Kino, K. and Kirimura, K. Dibenzothiophene desulfurizing enzymes from moderately thermophilic bacterium Bacillus subtilis WU-S₂B: purification, characterization and overexpression. J. Biosci. Bioeng. 100 (2005) 266–273. [DOI] [PMID: 16243275]
5.	Adak, S. and Begley, T.P. Dibenzothiophene catabolism proceeds via a flavin-N⁵-oxide intermediate. J. Am. Chem. Soc. 138 (2016) 6424–6426. [PMID: 27120486]
6.	Adak, S. and Begley, T.P. Flavin-N⁵-oxide: A new, catalytic motif in flavoenzymology. Arch. Biochem. Biophys. 632 (2017) 4–10. [PMID: 28784589]
7.	Matthews, A., Saleem-Batcha, R., Sanders, J.N., Stull, F., Houk, K.N. and Teufel, R. Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat. Chem. Biol. 16 (2020) 556–563. [DOI] [PMID: 32066967]

[EC 1.14.14.22 created 2016, modified 2019]

*EC

1.14.16.1

Accepted name:

phenylalanine 4-monooxygenase

Reaction:

L-phenylalanine + a 5,6,7,8-tetrahydropteridine + O₂ = L-tyrosine + a 4a-hydroxy-5,6,7,8-tetrahydropteridine

For diagram of phenylalanine and tyrosine biosynthesis, click here, of biopterin biosynthesis, click here and for mechanism of reaction, click here

Other name(s):

phenylalaninase; phenylalanine 4-hydroxylase; phenylalanine hydroxylase

Systematic name:

L-phenylalanine,tetrahydropteridine:oxygen oxidoreductase (4-hydroxylating)

Comments:

The active centre contains mononuclear iron(II). The reaction involves an arene oxide that rearranges to give the phenolic hydroxy group. This results in the hydrogen at C-4 migrating to C-3 and in part being retained. This process is known as the NIH-shift. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9029-73-6

References:

1.	Guroff, G. and Rhoads, C.A. Phenylalanine hydroxylation by Pseudomonas species (ATCC 11299a). Nature of the cofactor. J. Biol. Chem. 244 (1969) 142–146. [PMID: 5773277]
2.	Kaufman, S. Studies on the mechanism of the enzymic conversion of phenylalanine to tyrosine. J. Biol. Chem. 234 (1959) 2677–2682. [PMID: 14404870]
3.	Mitoma, C. Studies on partially purified phenylalanine hydroxylase. Arch. Biochem. Biophys. 60 (1956) 476–484. [DOI] [PMID: 13292928]
4.	Udenfriend, S. and Cooper, J.R. The enzymic conversion of phenylalanine to tyrosine. J. Biol. Chem. 194 (1952) 503–511. [PMID: 14927641]
5.	Carr, R.T., Balasubramanian, S., Hawkins, P.C. and Benkovic, S.J. Mechanism of metal-independent hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase. Biochemistry 34 (1995) 7525–7532. [PMID: 7779797]
6.	Andersen, O.A., Flatmark, T. and Hough, E. High resolution crystal structures of the catalytic domain of human phenylalanine hydroxylase in its catalytically active Fe(II) form and binary complex with tetrahydrobiopterin. J. Mol. Biol. 314 (2001) 266–278. [DOI] [PMID: 11718561]
7.	Erlandsen, H., Kim, J.Y., Patch, M.G., Han, A., Volner, A., Abu-Omar, M.M. and Stevens, R.C. Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: similar fold, different stability and reaction rates. J. Mol. Biol. 320 (2002) 645–661. [DOI] [PMID: 12096915]

[EC 1.14.16.1 created 1961 as EC 1.99.1.2, transferred 1965 to EC 1.14.3.1, transferred 1972 to EC 1.14.16.1, modified 2002, modified 2003, modified 2019]

*EC

1.14.16.2

Accepted name:

tyrosine 3-monooxygenase

Reaction:

L-tyrosine + a 5,6,7,8-tetrahydropteridine + O₂ = L-dopa + a 4a-hydroxy-5,6,7,8-tetrahydropteridine

For diagram of dopa biosynthesis, click here and for diagram of biopterin biosynthesis, click here

Glossary:

L-dopa = 3,4-dihydroxy-L-phenylalanine

Other name(s):

L-tyrosine hydroxylase; tyrosine 3-hydroxylase; tyrosine hydroxylase

Systematic name:

L-tyrosine,tetrahydropteridine:oxygen oxidoreductase (3-hydroxylating)

Comments:

The active centre contains mononuclear iron(II). The enzyme is activated by phosphorylation, catalysed by EC 2.7.11.31, [hydroxymethylglutaryl-CoA reductase (NADPH)] kinase. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9036-22-0

References:

1.	El Mestikawy, S., Glowinski, J. and Hamon, M. Tyrosine hydroxylase activation in depolarized dopaminergic terminals -involvement of Ca²⁺-dependent phosphorylation. Nature (Lond.) 302 (1983) 830–832. [PMID: 6133218]
2.	Ikeda, M., Levitt, M. and Udenfriend, S. Phenylalanine as substrate and inhibitor of tyrosine hydroxylase. Arch. Biochem. Biophys. 120 (1967) 420–427. [DOI] [PMID: 6033458]
3.	Nagatsu, T., Levitt, M. and Udenfriend, S. Tyrosine hydroxylase. The initial step in norepinephrine biosynthesis. J. Biol. Chem. 239 (1964) 2910–2917. [PMID: 14216443]
4.	Pigeon, D., Drissi-Daoudi, R., Gros, F. and Thibault, J. Copurification of tyrosine hydroxylase from rat pheochromocytoma by protein kinase. C. R. Acad. Sci. III 302 (1986) 435–438. [PMID: 2872947]
5.	Goodwill, K.E., Sabatier, C., Marks, C., Raag, R., Fitzpatrick, P.F. and Stevens, R.C. Crystal structure of tyrosine hydroxylase at 2.3 Å and its implications for inherited neurodegenerative diseases. Nat. Struct. Biol. 4 (1997) 578–585. [PMID: 9228951]

[EC 1.14.16.2 created 1972, modified 2003, modified 2019]

*EC

1.14.16.4

Accepted name:

tryptophan 5-monooxygenase

Reaction:

L-tryptophan + a 5,6,7,8-tetrahydropteridine + O₂ = 5-hydroxy-L-tryptophan + a 4a-hydroxy-5,6,7,8-tetrahydropteridine

For diagram of biopterin biosynthesis, click here

Other name(s):

L-tryptophan hydroxylase; indoleacetic acid-5-hydroxylase; tryptophan 5-hydroxylase; tryptophan hydroxylase

Systematic name:

L-tryptophan,tetrahydropteridine:oxygen oxidoreductase (5-hydroxylating)

Comments:

The active centre contains mononuclear iron(II). The enzyme is activated by phosphorylation, catalysed by a Ca²⁺-activated protein kinase. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9037-21-2

References:

1.	Friedman, P.A., Kappelman, A.H. and Kaufman, S. Partial purification and characterization of tryptophan hydroxylase from rabbit hindbrain. J. Biol. Chem. 247 (1972) 4165–4173. [PMID: 4402511]
2.	Hamon, M., Bourgoin, S., Artaud, F. and Glowinski, J. The role of intraneuronal 5-HT and of tryptophan hydroxylase activation in the control of 5-HT synthesis in rat brain slices incubated in K⁺-enriched medium. J. Neurochem. 33 (1979) 1031–1042. [DOI] [PMID: 315449]
3.	Ichiyama, A., Nakamura, S., Nishizuka, Y. and Hayaishi, O. Enzymic studies on the biosynthesis of serotonin in mammalian brain. J. Biol. Chem. 245 (1970) 1699–1709. [PMID: 5309585]
4.	Jequier, E., Robinson, B.S., Lovenberg, W. and Sjoerdsma, A. Further studies on tryptophan hydroxylase in rat brainstem and beef pineal. Biochem. Pharmacol. 18 (1969) 1071–1081. [DOI] [PMID: 5789774]
5.	Wang, L., Erlandsen, H., Haavik, J., Knappskog, P.M. and Stevens, R.C. Three-dimensional structure of human tryptophan hydroxylase and its implications for the biosynthesis of the neurotransmitters serotonin and melatonin. Biochemistry 41 (2002) 12569–12574. [DOI] [PMID: 12379098]

[EC 1.14.16.4 created 1972, modified 2003, modified 2019]

*EC

1.14.16.5

Accepted name:

alkylglycerol monooxygenase

Reaction:

1-O-alkyl-sn-glycerol + a 5,6,7,8-tetrahydropteridine + O₂ = 1-O-(1-hydroxyalkyl)-sn-glycerol + a 4a-hydroxy-5,6,7,8-tetrahydropteridine

Other name(s):

glyceryl-ether monooxygenase; glyceryl-ether cleaving enzyme; glyceryl ether oxygenase; glyceryl etherase; O-alkylglycerol monooxygenase

Systematic name:

1-alkyl-sn-glycerol,tetrahydrobiopteridine:oxygen oxidoreductase

Comments:

The enzyme cleaves alkylglycerols, but does not cleave alkenylglycerols (plasmalogens). Requires non-heme iron [7], reduced glutathione and phospholipids for full activity. The product spontaneously breaks down to form a fatty aldehyde and glycerol. The co-product, 4a-hydroxytetrahydropteridine, is rapidly dehydrated to 6,7-dihydropteridine, either spontaneously or by EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 37256-82-9

References:

1.	Ishibashi, T. and Imai, Y. Solubilization and partial characterization of alkylglycerol monooxygenase from rat liver microsomes. Eur. J. Biochem. 132 (1983) 23–27. [DOI] [PMID: 6840084]
2.	Pfleger, E.C., Piantadosi, C. and Snyder, F. The biocleavage of isomeric glyceryl ethers by soluble liver enzymes in a variety of species. Biochim. Biophys. Acta 144 (1967) 633–648. [DOI] [PMID: 4383918]
3.	Snyder, F., Malone, B. and Piantadosi, C. Tetrahydropteridine-dependent cleavage enzyme for O-alkyl lipids: substrate specificity. Biochim. Biophys. Acta 316 (1973) 259–265. [DOI] [PMID: 4355017]
4.	Soodsma, J.F., Piantadosi, C. and Snyder, F. Partial characterization of the alkylglycerol cleavage enzyme system of rat liver. J. Biol. Chem. 247 (1972) 3923–3929. [PMID: 4402391]
5.	Tietz, A., Lindberg, M. and Kennedy, E.P. A new pteridine-requiring enzyme system for the oxidation of glyceryl ethers. J. Biol. Chem. 239 (1964) 4081–4090. [PMID: 14247652]
6.	Taguchi, H. and Armarego, W.L. Glyceryl-ether monooxygenase [EC 1.14.16.5]. A microsomal enzyme of ether lipid metabolism. Med. Res. Rev. 18 (1998) 43–89. [DOI] [PMID: 9436181]
7.	Watschinger, K., Keller, M.A., Hermetter, A., Golderer, G., Werner-Felmayer, G. and Werner, E.R. Glyceryl ether monooxygenase resembles aromatic amino acid hydroxylases in metal ion and tetrahydrobiopterin dependence. Biol. Chem. 390 (2009) 3–10. [DOI] [PMID: 19007315]
8.	Werner, E.R., Hermetter, A., Prast, H., Golderer, G. and Werner-Felmayer, G. Widespread occurrence of glyceryl ether monooxygenase activity in rat tissues detected by a novel assay. J. Lipid Res. 48 (2007) 1422–1427. [DOI] [PMID: 17303893]

[EC 1.14.16.5 created 1972 as EC 1.14.99.17, transferred 1976 to EC 1.14.16.5, modified 2010, modified 2020]

*EC

1.14.16.6

Accepted name:

mandelate 4-monooxygenase

Reaction:

(S)-2-hydroxy-2-phenylacetate + a 5,6,7,8-tetrahydropteridine + O₂ = (S)-4-hydroxymandelate + a 4a-hydroxy-5,6,7,8-tetrahydropteridine

Glossary:

(S)-4-hydroxymandelate = (S)-2-hydroxy-2-(4-hydroxyphenyl)acetate

Other name(s):

L-mandelate 4-hydroxylase; mandelic acid 4-hydroxylase

Systematic name:

(S)-2-hydroxy-2-phenylacetate,tetrahydropteridine:oxygen oxidoreductase (4-hydroxylating)

Comments:

Requires Fe²⁺. The enzyme has been characterized from the bacterium Pseudomonas putida. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.

Links to other databases:

BRENDA, EXPASY, KEGG, CAS registry number: 39459-82-0

References:

1.	Bhat, S.G. and Vaidyanathan, C.S. Purifications and properties of L-mandelate-4-hydroxylase from Pseudomonas convexa. Arch. Biochem. Biophys. 176 (1976) 314–323. [DOI] [PMID: 9909]

[EC 1.14.16.6 created 1984, modified 2020]

*EC

1.14.16.7

Accepted name:

phenylalanine 3-monooxygenase

Reaction:

L-phenylalanine + a 5,6,7,8-tetrahydropteridine + O₂ = 3-hydroxy-L-phenylalanine + a 4a-hydroxy-5,6,7,8-tetrahydropteridine

Glossary:

3-hydroxy-L-phenylalanine = meta-L-tyrosine = 3-(3-hydroxyphenyl)-L-alanine

Other name(s):

PacX; phenylalanine 3-hydroxylase

Systematic name:

L-phenylalanine,tetrahydropteridine:oxygen oxidoreductase (3-hydroxylating)

Comments:

The enzyme, characterized from the bacterium Streptomyces coeruleorubidus, forms 3-hydroxy-L-phenylalanine (i.e. m-L-tyrosine), which is one of the building blocks in the biosynthesis of the uridyl peptide antibiotics pacidamycins. The 4a-hydroxytetrahydropteridine formed can dehydrate to 6,7-dihydropteridine, both spontaneously and by the action of EC 4.2.1.96, 4a-hydroxytetrahydrobiopterin dehydratase. The 6,7-dihydropteridine must be enzymically reduced back to tetrahydropteridine, by EC 1.5.1.34, 6,7-dihydropteridine reductase, before it slowly rearranges into the more stable but inactive compound 7,8-dihydropteridine.

Links to other databases:

References:

1.	Zhang, W., Ames, B.D. and Walsh, C.T. Identification of phenylalanine 3-hydroxylase for meta-tyrosine biosynthesis. Biochemistry 50 (2011) 5401–5403. [DOI] [PMID: 21615132]

[EC 1.14.16.7 created 2014, modified 2019]

*EC

1.14.17.1

Accepted name:

dopamine β-monooxygenase

Reaction:

dopamine + 2 ascorbate + O₂ = noradrenaline + 2 monodehydroascorbate + H₂O

For diagram of dopa biosynthesis, click here

Glossary:

dopamine = 4-(2-aminoethyl)benzene-1,2-diol

Other name(s):

dopamine β-hydroxylase; MDBH (membrane-associated dopamine β-monooxygenase); SDBH (soluble dopamine β-monooxygenase); dopamine-B-hydroxylase; 3,4-dihydroxyphenethylamine β-oxidase; 4-(2-aminoethyl)pyrocatechol β-oxidase; dopa β-hydroxylase; dopamine β-oxidase; dopamine hydroxylase; phenylamine β-hydroxylase; (3,4-dihydroxyphenethylamine)β-mono-oxygenase; DβM (gene name)

Systematic name:

dopamine,ascorbate:oxygen oxidoreductase (β-hydroxylating)

Comments:

A copper protein. The enzyme, found in animals, binds two copper ions with distinct roles during catalysis. Stimulated by fumarate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9013-38-1

References:

1.	Levin, E.Y., Levenberg, B. and Kaufman, S. The enzymatic conversion of 3,4-dihydroxyphenylethylamine to norepinephrine. J. Biol. Chem. 235 (1960) 2080–2086. [PMID: 14416204]
2.	Friedman, S. and Kaufman, S. 3,4-Dihydroxyphenylethylamine β-hydroxylase. Physical properties, copper content, and role of copper in the catalytic activity. J. Biol. Chem. 240 (1965) 4763–4773. [PMID: 5846992]
3.	Skotland, T. and Ljones, T. Direct spectrophotometric detection of ascorbate free radical formed by dopamine β-monooxygenase and by ascorbate oxidase. Biochim. Biophys. Acta 630 (1980) 30–35. [PMID: 7388045]
4.	Evans, J.P., Ahn, K. and Klinman, J.P. Evidence that dioxygen and substrate activation are tightly coupled in dopamine β-monooxygenase. Implications for the reactive oxygen species. J. Biol. Chem. 278 (2003) 49691–49698. [PMID: 12966104]

[EC 1.14.17.1 created 1965 as EC 1.14.2.1, transferred 1972 to EC 1.14.17.1, modified 2020]

*EC

1.14.17.3

Accepted name:

peptidylglycine monooxygenase

Reaction:

[peptide]-glycine + 2 ascorbate + O₂ = [peptide]-(2S)-2-hydroxyglycine + 2 monodehydroascorbate + H₂O

Other name(s):

peptidylglycine 2-hydroxylase; peptidyl α-amidating enzyme; peptide-α-amide synthetase; peptide α-amidating enzyme; peptide α-amide synthase; peptidylglycine α-hydroxylase; peptidylglycine α-amidating monooxygenase; PAM-A; PAM-B; PAM; peptidylglycine,ascorbate:oxygen oxidoreductase (2-hydroxylating)

Systematic name:

[peptide]-glycine,ascorbate:oxygen oxidoreductase (2-hydroxylating)

Comments:

A copper protein. The enzyme binds two copper ions with distinct roles during catalysis. Peptidylglycines with a neutral amino acid residue in the penultimate position are the best substrates for the enzyme. The product is unstable and dismutates to glyoxylate and the corresponding desglycine peptide amide, a reaction catalysed by EC 4.3.2.5 peptidylamidoglycolate lyase. In mammals, the two activities are part of a bifunctional protein. Involved in the final step of biosynthesis of α-melanotropin and related biologically active peptides.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 90597-47-0

References:

1.	Bradbury, A.F., Finnie, M.D.A. and Smyth, D.G. Mechanism of C-terminal amide formation by pituitary enzymes. Nature (Lond.) 298 (1982) 686–688. [PMID: 7099265]
2.	Glembotski, C.G. Further characterization of the peptidyl α-amidating enzyme in rat anterior pituitary secretory granules. Arch. Biochem. Biophys. 241 (1985) 673–683. [DOI] [PMID: 2994573]
3.	Murthy, A.S.N., Mains, R.E. and Eipper, B.A. Purification and characterization of peptidylglycine α-amidating monooxygenase from bovine neurointermediate pituitary. J. Biol. Chem. 261 (1986) 1815–1822. [PMID: 3944110]
4.	Bradbury, A.F. and Smyth, D.G. Enzyme-catalysed peptide amidation. Isolation of a stable intermediate formed by reaction of the amidating enzyme with an imino acid. Eur. J. Biochem. 169 (1987) 579–584. [DOI] [PMID: 3691506]
5.	Murthy, A.S.N., Keutmann, H.T. and Eipper, B.A. Further characterization of peptidylglycine α-amidating monooxygenase from bovine neurointermediate pituitary. Mol. Endocrinol. 1 (1987) 290–299. [DOI] [PMID: 3453894]
6.	Katopodis, A.G., Ping, D. and May, S.W. A novel enzyme from bovine neurointermediate pituitary catalyzes dealkylation of α-hydroxyglycine derivatives, thereby functioning sequentially with peptidylglycine α-amidating monooxygenase in peptide amidation. Biochemistry 29 (1990) 6115–6120. [PMID: 2207061]
7.	Prigge, S.T., Kolhekar, A.S., Eipper, B.A., Mains, R.E. and Amzel, L.M. Amidation of bioactive peptides: the structure of peptidylglycine α-hydroxylating monooxygenase. Science 278 (1997) 1300–1305. [PMID: 9360928]
8.	Prigge, S.T., Eipper, B.A., Mains, R.E. and Amzel, L.M. Dioxygen binds end-on to mononuclear copper in a precatalytic enzyme complex. Science 304 (2004) 864–867. [PMID: 15131304]
9.	Chufan, E.E., Prigge, S.T., Siebert, X., Eipper, B.A., Mains, R.E. and Amzel, L.M. Differential reactivity between two copper sites in peptidylglycine α-hydroxylating monooxygenase. J. Am. Chem. Soc. 132 (2010) 15565–15572. [PMID: 20958070]
10.	Chauhan, S., Hosseinzadeh, P., Lu, Y. and Blackburn, N.J. Stopped-flow studies of the reduction of the copper centers suggest a bifurcated electron transfer pathway in peptidylglycine monooxygenase. Biochemistry 55 (2016) 2008–2021. [PMID: 26982589]

[EC 1.14.17.3 created 1989, modified 2019]

1.14.18.12

Accepted name:

2-hydroxy fatty acid dioxygenase

Reaction:

a (2R)-2-hydroxy C_n-fatty acid + O₂ = a C_n-1-fatty acid + H₂O + CO₂

Other name(s):

MPO1 (gene name)

Systematic name:

2-hydroxyfatty acid:oxygen oxidoreductase (CO₂,H₂O-forming)

Comments:

Requires iron(II). The enzyme, characterized from yeast, is involved in phytosphingosine metabolism. The reaction is mediated by iron(IV) peroxide and results in the release of a water molecule and a carbon dioxide molecule, shortening the substrate by a single carbon atom and forming an odd-numbered fatty acid. Both oxygen atoms of the original carboxylate group are released - one as the leaving water molecule, the other as one of the oxygens of the carbon dioxide molecule. The two oxygen atoms in the newly-formed carboxylate originate from the 2-hydroxy group and from molecular oxygen, respectively. The other oxygen atom of the molecular oxygen is incorporated into the leaving CO₂ molecule. The enzyme from the yeast Saccharomyces cerevisiae is active at least toward C₁₄ to C₂₆ 2-hydroxyfatty acids, but not against C₈ 2-hydroxyfatty acid.

Links to other databases:

References:

1.	Kondo, N., Ohno, Y., Yamagata, M., Obara, T., Seki, N., Kitamura, T., Naganuma, T. and Kihara, A. Identification of the phytosphingosine metabolic pathway leading to odd-numbered fatty acids. Nat. Commun. 5:5338 (2014). [PMID: 25345524]
2.	Seki, N., Mori, K., Kitamura, T., Miyamoto, M. and Kihara, A. Yeast Mpo1 is a novel dioxygenase that catalyzes the α-oxidation of a 2-hydroxy fatty acid in an Fe²⁺-dependent manner. Mol. Cell Biol. 39:e00428-18 (2019). [DOI] [PMID: 30530523]

[EC 1.14.18.12 created 2020]

*EC

1.14.99.46

Accepted name:

pyrimidine oxygenase

Reaction:

(1) uracil + FMNH₂ + O₂ + NADH = (Z)-3-ureidoacrylate + H₂O + FMN + NAD⁺ + H⁺ (overall reaction)
(1a) FMNH₂ + O₂ = FMN-N⁵-peroxide
(1b) uracil + FMN-N⁵-peroxide = (Z)-3-ureidoacrylate + FMN-N⁵-oxide
(1c) FMN-N⁵-oxide + NADH = FMN + H₂O + NAD⁺ + H⁺ (spontaneous)
(2) thymine + FMNH₂ + O₂ + NADH = (Z)-2-methylureidoacrylate + H₂O + FMN + NAD⁺ + H⁺ (overall reaction)
(2a) FMNH₂ + O₂ = FMN-N⁵-peroxide
(2b) thymine + FMN-N⁵-peroxide = (Z)-2-methylureidoacrylate + FMN-N⁵-oxide
(2c) FMN-N⁵-oxide + NADH = FMN + H₂O + NAD⁺ + H⁺ (spontaneous)

For diagram of pyrimidine catabolism, click here

Glossary:

(Z)-3-ureidoacrylate = (2Z)-3-(carbamoylamino)prop-2-enoate
(Z)-2-methylureidoacrylate = (2Z)-3-(carbamoylamino)-2-methylprop-2-enoate

Other name(s):

rutA (gene name)

Systematic name:

uracil,FMNH₂:oxygen oxidoreductase (uracil hydroxylating, ring-opening)

Comments:

The enzyme participates in the Rut pyrimidine catabolic pathway. The flavin-N⁵-oxide that is formed by the enzyme reacts spontaneously with NADH to give oxidized flavin, releasing a water molecule.

Links to other databases:

References:

1.	Mukherjee, T., Zhang, Y., Abdelwahed, S., Ealick, S.E. and Begley, T.P. Catalysis of a flavoenzyme-mediated amide hydrolysis. J. Am. Chem. Soc. 132 (2010) 5550–5551. [DOI] [PMID: 20369853]
2.	Kim, K.S., Pelton, J.G., Inwood, W.B., Andersen, U., Kustu, S. and Wemmer, D.E. The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems. J. Bacteriol. 192 (2010) 4089–4102. [DOI] [PMID: 20400551]
3.	Adak, S. and Begley, T.P. RutA-catalyzed oxidative cleavage of the uracil amide involves formation of a flavin-N⁵-oxide. Biochemistry 56 (2017) 3708–3709. [PMID: 28661684]
4.	Adak, S. and Begley, T.P. Flavin-N⁵-oxide: A new, catalytic motif in flavoenzymology. Arch. Biochem. Biophys. 632 (2017) 4–10. [PMID: 28784589]
5.	Matthews, A., Saleem-Batcha, R., Sanders, J.N., Stull, F., Houk, K.N. and Teufel, R. Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases. Nat. Chem. Biol. 16 (2020) 556–563. [DOI] [PMID: 32066967]

[EC 1.14.99.46 created 2012, modified 2019]

*EC

1.16.1.8

Accepted name:

[methionine synthase] reductase

Reaction:

2 [methionine synthase]-methylcob(III)alamin + 2 S-adenosyl-L-homocysteine + NADP⁺ = 2 [methionine synthase]-cob(II)alamin + NADPH + H⁺ + 2 S-adenosyl-L-methionine

For diagram of reaction, click here

Other name(s):

methionine synthase cob(II)alamin reductase (methylating); methionine synthase reductase; [methionine synthase]-cobalamin methyltransferase (cob(II)alamin reducing); [methionine synthase]-methylcob(I)alamin,S-adenosylhomocysteine:NADP⁺ oxidoreductase

Systematic name:

[methionine synthase]-methylcob(III)alamin,S-adenosyl-L-homocysteine:NADP⁺ oxidoreductase

Comments:

In humans, the enzyme is a flavoprotein containing FAD and FMN. The substrate of the enzyme is the inactivated cobalt(II) form of EC 2.1.1.13, methionine synthase. Electrons are transferred from NADPH to FAD to FMN. Defects in this enzyme lead to hereditary hyperhomocysteinemia.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 207004-87-3

References:

1.	Leclerc, D., Wilson, A., Dumas, R., Gafuik, C., Song, D., Watkins, D., Heng, H.H.Q., Rommens, J.M., Scherer, S.W., Rosenblatt, D.S., Gravel, R.A. Cloning and mapping of a cDNA for methionine synthase reductase, a flavoprotein defective in patients with homocystinuria. Proc. Natl. Acad. Sci. USA 95 (1998) 3059–3064. [DOI] [PMID: 9501215]
2.	Olteanu, H. and Banerjee, R. Human methionine synthase reductase, a soluble P-450 reductase-like dual flavoprotein, is sufficient for NADPH-dependent methionine synthase activation. J. Biol. Chem. 276 (2001) 35558–35563. [DOI] [PMID: 11466310]
3.	Olteanu, H., Munson, T. and Banerjee, R. Differences in the efficiency of reductive activation of methionine synthase and exogenous electron acceptors between the common polymorphic variants of human methionine synthase reductase. Biochemistry 41 (2002) 13378–13385. [DOI] [PMID: 12416982]

[EC 1.16.1.8 created 1999 as EC 2.1.1.135, transferred 2003 to EC 1.16.1.8, modified 2020]

1.16.8.1

Deleted entry:

cob(II)yrinic acid a,c-diamide reductase. This activity is now known to be catalyzed by EC 2.5.1.17, corrinoid adenosyltransferase

[EC 1.16.8.1 created 2004, deleted 2019]

*EC

1.17.1.8

Accepted name:

4-hydroxy-tetrahydrodipicolinate reductase

Reaction:

(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)⁺ + H₂O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H⁺

For diagram of lysine biosynthesis (early stages), click here

Glossary:

(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate = (2S)-2,3,4,5-tetrahydrodipicolinate

Other name(s):

dihydrodipicolinate reductase (incorrect); dihydrodipicolinic acid reductase (incorrect); 2,3,4,5-tetrahydrodipicolinate:NAD(P)⁺ oxidoreductase (incorrect); dapB (gene name)

Systematic name:

(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate:NAD(P)⁺ 4-oxidoreductase

Comments:

The substrate of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1], and the enzyme was classified accordingly as EC 1.3.1.26, dihydrodipicolinate reductase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual substrate of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate, and that its activity includes a dehydration step [2], and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate reductase. However, the identity of the substrate is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all [3].

Links to other databases:

References:

1.	Farkas, W. and Gilvarg, C. The reduction step in diaminopimelic acid biosynthesis. J. Biol. Chem. 240 (1965) 4717–4722. [PMID: 4378965]
2.	Devenish, S.R., Blunt, J.W. and Gerrard, J.A. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J. Med. Chem. 53 (2010) 4808–4812. [DOI] [PMID: 20503968]
3.	Karsten, W.E., Nimmo, S.A., Liu, J. and Chooback, L. Identification of 2,3-dihydrodipicolinate as the product of the dihydrodipicolinate synthase reaction from Escherichia coli. Arch. Biochem. Biophys. 653 (2018) 50–62. [PMID: 29944868]

[EC 1.17.1.8 created 1976 as EC 1.3.1.26, transferred 2013 to EC 1.17.1.8, modified 2020]

1.17.99.8

Accepted name:

limonene dehydrogenase

Reaction:

(1) (S)-limonene + H₂O + acceptor = (–)-perillyl alcohol + reduced acceptor
(2) (R)-limonene + H₂O + acceptor = (+)-perillyl alcohol + reduced acceptor

Glossary:

limonene = 1-methyl-4-(prop-1-en-2-yl)cyclohex-1-ene
perillyl alcohol = [4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol
(–)-perillyl alcohol = (S)-perillyl alcohol = [(4S)-4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol
(+)-perillyl alcohol = (R)-perillyl alcohol = [(4R)-4-(prop-1-en-2-yl)cyclohex-1-en-1-yl]methanol
(–)-limonene = (S)-limonene = (4S)-1-methyl-4-(prop-1-en-2-yl)cyclohexene
(+)-limonene = (R)-limonene = (4R)-1-methyl-4-(prop-1-en-2-yl)cyclohexene

Other name(s):

ctmAB (gene names)

Systematic name:

limonene:acceptor oxidoreductase (7-hydroxylating)

Comments:

Contains FAD. The enzyme, characterized from the bacterium Castellaniella defragrans 65Phen, hydroxylates the R- and S-enantiomers at a similar rate. The in vivo electron acceptor may be a heterodimeric electron transfer flavoprotein (ETF).

Links to other databases:

References:

1.	Petasch, J., Disch, E.M., Markert, S., Becher, D., Schweder, T., Huttel, B., Reinhardt, R. and Harder, J. The oxygen-independent metabolism of cyclic monoterpenes in Castellaniella defragrans 65Phen. BMC Microbiol. 14:164 (2014). [PMID: 24952578]
2.	Puentes-Cala, E., Liebeke, M., Markert, S. and Harder, J. Limonene dehydrogenase hydroxylates the allylic methyl group of cyclic monoterpenes in the anaerobic terpene degradation by Castellaniella defragrans. J. Biol. Chem. 293 (2018) 9520–9529. [PMID: 29716998]

[EC 1.17.99.8 created 2020]

*EC

1.20.4.1

Accepted name:

arsenate reductase (glutathione/glutaredoxin)

Reaction:

arsenate + glutathione + glutaredoxin = arsenite + a glutaredoxin-glutathione disulfide + H₂O

For diagram of arsenate catabolism, click here

Other name(s):

ArsC (ambiguous); arsenate:glutaredoxin oxidoreductase; arsenate reductase (glutaredoxin)

Systematic name:

arsenate:glutathione/glutaredoxin oxidoreductase

Comments:

The enzyme is part of a system for detoxifying arsenate. The substrate binds to a catalytic cysteine residue, forming a covalent thiolate—As(V) intermediate. A tertiary intermediate is then formed between the arsenic, the enzyme’s cysteine, and a glutathione cysteine. This intermediate is reduced by glutaredoxin, which forms a dithiol with the glutathione, leading to the dissociation of arsenite. Thus reduction of As(V) is mediated by three cysteine residues: one in ArsC, one in glutathione, and one in glutaredoxin. Although the arsenite formed is more toxic than arsenate, it can be extruded from some bacteria by EC 7.3.2.7, arsenite-transporting ATPase; in other organisms, arsenite can be methylated by EC 2.1.1.137, arsenite methyltransferase, in a pathway that produces non-toxic organoarsenical compounds. cf. EC 1.20.4.4, arsenate reductase (thioredoxin).

Links to other databases:

BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB, CAS registry number: 146907-46-2

References:

1.	Gladysheva, T., Liu, J.Y. and Rosen, B.P. His-8 lowers the pKa of the essential Cys-12 residue of the ArsC arsenate reductase of plasmid R773. J. Biol. Chem. 271 (1996) 33256–33260. [DOI] [PMID: 8969183]
2.	Gladysheva, T.B., Oden, K.L. and Rosen, B.P. Properties of the arsenate reductase of plasmid R773. Biochemistry 33 (1994) 7288–7293. [PMID: 8003492]
3.	Holmgren, A. and Aslund, F. Glutaredoxin. Methods Enzymol. 252 (1995) 283–292. [DOI] [PMID: 7476363]
4.	Krafft, T. and Macy, J.M. Purification and characterization of the respiratory arsenate reductase of Chrysiogenes arsenatis. Eur. J. Biochem. 255 (1998) 647–653. [DOI] [PMID: 9738904]
5.	Martin, J.L. Thioredoxin - a fold for all reasons. Structure 3 (1995) 245–250. [DOI] [PMID: 7788290]
6.	Radabaugh, T.R. and Aposhian, H.V. Enzymatic reduction of arsenic compounds in mammalian systems: reduction of arsenate to arsenite by human liver arsenate reductase. Chem. Res. Toxicol. 13 (2000) 26–30. [DOI] [PMID: 10649963]
7.	Sato, T. and Kobayashi, Y. The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J. Bacteriol. 180 (1998) 1655–1661. [PMID: 9537360]
8.	Shi, J., Vlamis-Gardikas, V., Aslund, F., Holmgren, A. and Rosen, B.P. Reactivity of glutaredoxins 1, 2, and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction. J. Biol. Chem. 274 (1999) 36039–36042. [DOI] [PMID: 10593884]
9.	Mukhopadhyay, R. and Rosen, B.P. Arsenate reductases in prokaryotes and eukaryotes. Environ Health Perspect 110 Suppl 5 (2002) 745–748. [PMID: 12426124]
10.	Messens, J. and Silver, S. Arsenate reduction: thiol cascade chemistry with convergent evolution. J. Mol. Biol. 362 (2006) 1–17. [PMID: 16905151]

[EC 1.20.4.1 created 2000 as EC 1.97.1.5, transferred 2001 to EC 1.20.4.1, modified 2015, modified 2019, modified 2020]

*EC

2.1.1.74

Accepted name:

methylenetetrahydrofolate—tRNA-(uracil⁵⁴-C⁵)-methyltransferase [NAD(P)H-oxidizing]

Reaction:

5,10-methylenetetrahydrofolate + uracil⁵⁴ in tRNA + NAD(P)H + H⁺ = tetrahydrofolate + 5-methyluracil⁵⁴ in tRNA + NAD(P)⁺

Glossary:

Ψ = pseudouridine
T = ribothymidine = 5-methyluridine

Other name(s):

folate-dependent ribothymidyl synthase; methylenetetrahydrofolate-transfer ribonucleate uracil 5-methyltransferase; 5,10-methylenetetrahydrofolate:tRNA-UΨC (uracil-5-)-methyl-transferase; 5,10-methylenetetrahydrofolate:tRNA (uracil-5-)-methyl-transferase; TrmFO; folate/FAD-dependent tRNA T54 methyltransferase; methylenetetrahydrofolate—tRNA-(uracil⁵⁴-C⁵)-methyltransferase (FADH₂-oxidizing)

Systematic name:

5,10-methylenetetrahydrofolate:tRNA (uracil⁵⁴-C⁵)-methyltransferase

Comments:

A flavoprotein (FAD). Up to 25% of the bases in mature tRNA are post-translationally modified or hypermodified. One almost universal post-translational modification is the conversion of U⁵⁴ into ribothymidine in the TΨC loop, and this modification is found in most species studied to date [2]. Unlike this enzyme, which uses 5,10-methylenetetrahydrofolate and NAD(P)H to supply the atoms for methylation of U⁵⁴, EC 2.1.1.35, tRNA (uracil⁵⁴-C⁵)-methyltransferase, uses S-adenosyl-L-methionine.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 56831-74-4

References:

1.	Delk, A.S., Nagle, D.P., Jr. and Rabinowitz, J.C. Methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH₂. J. Biol. Chem. 255 (1980) 4387–4390. [PMID: 6768721]
2.	Becker, H.F., Motorin, Y., Sissler, M., Florentz, C. and Grosjean, H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs. J. Mol. Biol. 274 (1997) 505–518. [DOI] [PMID: 9417931]
3.	Nishimasu, H., Ishitani, R., Yamashita, K., Iwashita, C., Hirata, A., Hori, H. and Nureki, O. Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase. Proc. Natl. Acad. Sci. USA 106 (2009) 8180–8185. [DOI] [PMID: 19416846]
4.	Yamagami, R., Yamashita, K., Nishimasu, H., Tomikawa, C., Ochi, A., Iwashita, C., Hirata, A., Ishitani, R., Nureki, O. and Hori, H. The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO). J. Biol. Chem. 287 (2012) 42480–42494. [PMID: 23095745]

[EC 2.1.1.74 created 1983 as EC 2.1.2.12, transferred 1984 to EC 2.1.1.74, modified 2011, modified 2019]

2.1.1.363

Accepted name:

pre-sodorifen synthase

Reaction:

S-adenosyl-L-methionine + (2E,6E)-farnesyl diphosphate = S-adenosyl-L-homocysteine + pre-sodorifen diphosphate

Glossary:

pre-sodorifen diphosphate = [(2E)-3-methyl-5-[(1S,4R,5R)-1,2,3,4,5-pentamethylcyclopent-2-en-1-yl]pent-2-en-1-yl phosphonato]oxyphosphonate
sodorifen = (1S,2S,4R,5S,8s)-1,2,4,5,6,7,8-heptamethyl-3-methylenebicyclo[3.2.1]oct-6-ene

Other name(s):

sodC (gene name)

Systematic name:

(2E,6E)-farnesyl diphosphate 10-C-methyltransferase (cyclyzing, pre-sodorifen diphosphate producing)

Comments:

The enzyme, characterized from the bacterium Serratia plymuthica, participates in biosynthesis of sodorifen.

Links to other databases:

References:

1.	Domik, D., Magnus, N. and Piechulla, B. Analysis of a new cluster of genes involved in the synthesis of the unique volatile organic compound sodorifen of Serratia plymuthica 4Rx13. FEMS Microbiol. Lett. 363(14): fnw139 (2016). [DOI] [PMID: 27231241]
2.	Schmidt, R., Jager, V., Zuhlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., Ijcken, W.V., Sleutels, F., Boer, W., Riedel, K. and Garbeva, P. Fungal volatile compounds induce production of the secondary metabolite sodorifen in Serratia plymuthica PRI-2C. Sci. Rep. 7:862 (2017). [PMID: 28408760]
3.	von Reuss, S., Domik, D., Lemfack, M.C., Magnus, N., Kai, M., Weise, T. and Piechulla, B. Sodorifen biosynthesis in the rhizobacterium Serratia plymuthica involves methylation and cyclization of MEP-derived farnesyl pyrophosphate by a SAM-dependent C-methyltransferase. J. Am. Chem. Soc. 140 (2018) 11855–11862. [PMID: 30133268]

[EC 2.1.1.363 created 2019]

*EC

2.3.1.291

Accepted name:

sphingoid base N-palmitoyltransferase

Reaction:

palmitoyl-CoA + a sphingoid base = an N-(palmitoyl)-sphingoid base + CoA

Other name(s):

mammalian ceramide synthase 5; CERS5 (gene name); LASS5 (gene name)

Systematic name:

palmitoyl-CoA:sphingoid base N-palmitoyltransferase

Comments:

Mammals have six ceramide synthases that exhibit relatively strict specificity regarding the chain-length of their acyl-CoA substrates. Ceramide synthase 5 (CERS5) is specific for palmitoyl-CoA as the acyl donor. It can use multiple sphingoid bases including sphinganine, sphingosine, and phytosphingosine.

Links to other databases:

References:

1.	Lahiri, S. and Futerman, A.H. LASS5 is a bona fide dihydroceramide synthase that selectively utilizes palmitoyl-CoA as acyl donor. J. Biol. Chem. 280 (2005) 33735–33738. [PMID: 16100120]
2.	Xu, Z., Zhou, J., McCoy, D.M. and Mallampalli, R.K. LASS5 is the predominant ceramide synthase isoform involved in de novo sphingolipid synthesis in lung epithelia. J. Lipid Res. 46 (2005) 1229–1238. [PMID: 15772421]
3.	Mizutani, Y., Kihara, A. and Igarashi, Y. Mammalian Lass6 and its related family members regulate synthesis of specific ceramides. Biochem. J. 390 (2005) 263–271. [PMID: 15823095]

[EC 2.3.1.291 created 2019, modified 2019]

2.3.2.33

Accepted name:

RCR-type E3 ubiquitin transferase

Reaction:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-threonine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-3-O-ubiquitinyl-L-threonine (overall reaction)
(1a) [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [RCR-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [RCR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine
(1b) [RCR-type E3 ubiquitin transferase]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-threonine = [RCR-type E3 ubiquitin transferase]-L-cysteine + [acceptor protein]-3-O-ubiquitinyl-L-threonine

Glossary:

RCR = RIN^G-Cys-Relay
RING = Really Interesting New Gene

Other name(s):

MYCBP2; PHR1

Systematic name:

[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:acceptor protein ubiquitin transferase (isopeptide bond-forming; RCR-type)

Comments:

RCR-type E3 ubiquitin transferases is a class of RING-type E3 ubiquitin transferase (see EC 2.3.2.27) that mediates ubiquitylation of acceptor proteins via an internal cysteine residue. The RING1 domain binds an EC 2.3.2.23, E2 ubiquitin-conjugating enzyme, and transfers the ubiquitin that is bound to it to an internal cysteine residue on a mediator loop of the RCR-type ligase. The ubiquitin may be transferred to a second internal cysteine before the transfer of the ubiquitin from the RCR-type ligase to the substrate.

Links to other databases:

References:

1.	Pao, K.C., Wood, N.T., Knebel, A., Rafie, K., Stanley, M., Mabbitt, P.D., Sundaramoorthy, R., Hofmann, K., van Aalten, D.MF. and Virdee, S. Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity. Nature 556 (2018) 381–385. [PMID: 29643511]

[EC 2.3.2.33 created 2019]

2.4.1.371

Accepted name:

polymannosyl GlcNAc-diphospho-ditrans,octacis-undecaprenol 2,3-α-mannosylpolymerase

Reaction:

(1) 2 GDP-α-D-mannose + [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 = 2 GDP + 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
(2) 2 GDP-α-D-mannose + 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 = 2 GDP + [α-D-Man-(1→3)-α-D-Man-(1→3)-α-D-Man-(1→2)-α-D-Man-(1→2)]_n+1-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):

WbdA

Systematic name:

GDP-α-D-mannose: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 2,3-α-mannosyltransferase (configuration-retaining)

Comments:

The enzyme is involved in the biosynthesis of polymannose O-polysaccharide in the outer leaflet of the membrane of Escherichia coli serotype O9a. The enzymes consists of two domains that are responsible for the 1→2 and 1→3 linkages, respectively.

Links to other databases:

References:

1.	Greenfield, L.K., Richards, M.R., Li, J., Wakarchuk, W.W., Lowary, T.L. and Whitfield, C. Biosynthesis of the polymannose lipopolysaccharide O-antigens from Escherichia coli serotypes O8 and O9a requires a unique combination of single- and multiple-active site mannosyltransferases. J. Biol. Chem. 287 (2012) 35078–35091. [DOI] [PMID: 22875852]
2.	Greenfield, L.K., Richards, M.R., Vinogradov, E., Wakarchuk, W.W., Lowary, T.L. and Whitfield, C. Domain organization of the polymerizing mannosyltransferases involved in synthesis of the Escherichia coli O8 and O9a lipopolysaccharide O-antigens. J. Biol. Chem. 287 (2012) 38135–38149. [PMID: 22989876]
3.	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 2.4.1.371 created 2019]

2.4.1.372

Accepted name:

mutansucrase

Reaction:

sucrose + [(1→3)-α-D-glucosyl]_n = D-fructose + [(1→3)-α-D-glucosyl]_n+1

Other name(s):

gtfJ (gene name)

Systematic name:

sucrose:(1→3)-α-D-glucan 3-α-D-glucosyltransferase

Comments:

The glucansucrases transfer a D-glucosyl residue from sucrose to a glucan chain. They are classified based on the linkage by which they attach the transferred residue. In some cases, in which the enzyme forms more than one linkage type, classification relies on the relative proportion of the linkages that are generated. This enzyme extends the glucan chain by an α(1→3) linkage.

Links to other databases:

References:

1.	Simpson, C.L., Cheetham, N.W., Giffard, P.M. and Jacques, N.A. Four glucosyltransferases, GtfJ, GtfK, GtfL and GtfM, from Streptococcus salivarius ATCC 25975. Microbiology 141 (1995) 1451–1460. [PMID: 7545511]
2.	Puanglek, S., Kimura, S., Enomoto-Rogers, Y., Kabe, T., Yoshida, M., Wada, M. and Iwata, T. In vitro synthesis of linear α-1,3-glucan and chemical modification to ester derivatives exhibiting outstanding thermal properties. Sci. Rep. 6:30479 (2016). [PMID: 27469976]

[EC 2.4.1.372 created 2019]

2.4.1.373

Accepted name:

α-(1→2) branching sucrase

Reaction:

sucrose + a (1→6)-α-D-glucan = D-fructose + a (1→6)-α-D-glucan containing a (1→2)-α-D-glucose branch

Systematic name:

sucrose:(1→6)-α-D-glucan 2-α-D-glucosyl-transferase

Comments:

Links to other databases:

References:

1.	Fabre, E., Bozonnet, S., Arcache, A., Willemot, R.M., Vignon, M., Monsan, P. and Remaud-Simeon, M. Role of the two catalytic domains of DSR-E dextransucrase and their involvement in the formation of highly α-1,2 branched dextran. J. Bacteriol. 187 (2005) 296–303. [PMID: 15601714]
2.	Brison, Y., Laguerre, S., Lefoulon, F., Morel, S., Monties, N., Potocki-Veronese, G., Monsan, P. and Remaud-Simeon, M. Branching pattern of gluco-oligosaccharides and 1.5kDa dextran grafted by the α-1,2 branching sucrase GBD-CD2. Carbohydr. Polym. 94 (2013) 567–576. [PMID: 23544576]
3.	Passerini, D., Vuillemin, M., Ufarte, L., Morel, S., Loux, V., Fontagne-Faucher, C., Monsan, P., Remaud-Simeon, M. and Moulis, C. Inventory of the GH70 enzymes encoded by Leuconostoc citreum NRRL B-1299 - identification of three novel α-transglucosylases. FEBS J. 282 (2015) 2115–2130. [PMID: 25756290]

[EC 2.4.1.373 created 2019]

2.4.1.374

Accepted name:

β-1,2-mannooligosaccharide synthase

Reaction:

GDP-α-D-mannose + [(1→2)-β-D-mannosyl]_n = GDP + [(1→2)-β-D-mannosyl]_n+1

Other name(s):

MTP1 (gene name); MTP2 (gene name)

Systematic name:

GDP-α-D-mannose:(1→2)-β-D-mannan mannosyltransferase (configuration-inverting)

Comments:

The enzyme, characterized from Leishmania parasites, is involved in synthesis of mannogen, a β-(1→2)-mannan oligosaccharide used by the organisms as a carbohydrate reserve.

Links to other databases:

References:

Sernee, M.F., Ralton, J.E., Nero, T.L., Sobala, L.F., Kloehn, J., Vieira-Lara, M.A., Cobbold, S.A., Stanton, L., Pires, D.EV., Hanssen, E., Males, A., Ward, T., Bastidas, L.M., van der Peet, P.L., Parker, M.W., Ascher, D.B., Williams, S.J., Davies, G.J. and McConville, M.J. A family of dual-activity glycosyltransferase-phosphorylases mediates mannogen turnover and virulence in Leishmania parasites. Cell Host Microbe 26 (2019) 385–399.e9. [PMID: 31513773]

[EC 2.4.1.374 created 2019]

*EC

2.4.2.42

Accepted name:

UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase

Reaction:

UDP-α-D-xylose + [protein with EGF-like domain]-3-O-(β-D-glucosyl)-L-serine = UDP + [protein with EGF-like domain]-3-O-[α-D-xylosyl-(1→3)-β-D-glucosyl]-L-serine

Other name(s):

β-glucoside α-1,3-xylosyltransferase; UDP-α-D-xylose:β-D-glucoside 3-α-D-xylosyltransferase; GXYLT1 (gene name); GXYLT2 (gene name)

Systematic name:

UDP-α-D-xylose:[protein with EGF-like domain]-3-O-(β-D-glucosyl)-L-serine 3-α-D-xylosyltransferase (configuration-retaining)

Comments:

The enzyme, found in animals and insects, is involved in the biosynthesis of the α-D-xylosyl-(1→3)-α-D-xylosyl-(1→3)-β-D-glucosyl trisaccharide on epidermal growth factor-like (EGF-like) domains [2,3]. When present on Notch proteins, the trisaccharide functions as a modulator of the signalling activity of this protein.

Links to other databases:

References:

1.	Omichi, K., Aoki, K., Minamida, S. and Hase, S. Presence of UDP-D-xylose: β-D-glucoside α-1,3-D-xylosyltransferase involved in the biosynthesis of the Xyl α 1-3Glc β-Ser structure of glycoproteins in the human hepatoma cell line HepG2. Eur. J. Biochem. 245 (1997) 143–146. [DOI] [PMID: 9128735]
2.	Ishimizu, T., Sano, K., Uchida, T., Teshima, H., Omichi, K., Hojo, H., Nakahara, Y. and Hase, S. Purification and substrate specificity of UDP-D-xylose:β-D-glucoside α-1,3-D-xylosyltransferase involved in the biosynthesis of the Xyl α1-3Xyl α1-3Glc β1-O-Ser on epidermal growth factor-like domains. J. Biochem. 141 (2007) 593–600. [DOI] [PMID: 17317689]
3.	Sethi, M.K., Buettner, F.F., Krylov, V.B., Takeuchi, H., Nifantiev, N.E., Haltiwanger, R.S., Gerardy-Schahn, R. and Bakker, H. Identification of glycosyltransferase 8 family members as xylosyltransferases acting on O-glucosylated notch epidermal growth factor repeats. J. Biol. Chem. 285 (2010) 1582–1586. [PMID: 19940119]

[EC 2.4.2.42 created 2010, modified 2020]

2.6.1.118

Accepted name:

[amino-group carrier protein]-γ-(L-lysyl)-L-glutamate aminotransferase

Reaction:

an [amino-group carrier protein]-C-terminal-[γ-(L-lysyl)-L-glutamate] + 2-oxoglutarate = an [amino-group carrier protein]-C-terminal-[N-(1-carboxy-5-oxopentyl)-L-glutamine] + L-glutamate

Other name(s):

lysJ (gene name)

Systematic name:

2-oxoglutarate:[amino-group carrier protein]-C-terminal-[γ-(L-lysyl)-L-glutamate] aminotransferase

Comments:

The enzyme participates in an L-lysine biosynthesis pathway in certain species of archaea and bacteria.

Links to other databases:

References:

1.	Miyazaki, J., Kobashi, N., Nishiyama, M. and Yamane, H. Functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through α-aminoadipate. J. Bacteriol. 183 (2001) 5067–5073. [PMID: 11489859]
2.	Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673–679. [DOI] [PMID: 19620981]

[EC 2.6.1.118 created 2019]

*EC

2.7.1.8

Accepted name:

glucosamine kinase

Reaction:

ATP + D-glucosamine = ADP + D-glucosamine 6-phosphate

Glossary:

D-glucosamine 6-phosphate = 2-amino-2-deoxy-D-glucose 6-phosphate

Other name(s):

glucosamine kinase (phosphorylating); ATP:2-amino-2-deoxy-D-glucose-6-phosphotransferase; aminodeoxyglucose kinase; ATP:D-glucosamine phosphotransferase

Systematic name:

ATP:D-glucosamine 6-phosphotransferase

Comments:

The enzyme is specific for glucosamine and has only a minor activity with D-glucose. Two unrelated enzymes with this activity have been described. One type was studied in the bacterium Vibrio cholerae, where it participates in a chitin degradation pathway. The other type has been described from actinobacteria, where it is involved in the incorporation of environmental glucosamine into antibiotic biosynthesis pathways. cf. EC 2.7.1.147, ADP-specific glucose/glucosamine kinase.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9031-90-7

References:

1.	Bueding, E. and MacKinnon, J.A. Hexokinases of Schistosoma mansoni. J. Biol. Chem. 215 (1955) 495–506. [PMID: 13242546]
2.	Park, J.K., Wang, L.X. and Roseman, S. Isolation of a glucosamine-specific kinase, a unique enzyme of Vibrio cholerae. J. Biol. Chem. 277 (2002) 15573–15578. [DOI] [PMID: 11850417]
3.	Manso, J.A., Nunes-Costa, D., Macedo-Ribeiro, S., Empadinhas, N. and Pereira, P.J.B. Molecular fingerprints for a novel enzyme family in actinobacteria with glucosamine kinase activity. MBio 10:e00239-19 (2019). [PMID: 31088917]

[EC 2.7.1.8 created 1961, modified 2014, modified 2020]

*EC

2.7.1.147

Accepted name:

ADP-specific glucose/glucosamine kinase

Reaction:

(1) ADP + D-glucose = AMP + D-glucose 6-phosphate
(2) ADP + D-glucosamine = AMP + D-glucosamine 6-phosphate

Other name(s):

ADP-specific glucokinase; ADP-dependent glucokinase

Systematic name:

ADP:D-glucose/D-glucosamine 6-phosphotransferase

Comments:

Requires Mg²⁺. The enzyme, characterized from a number of hyperthermophilic archaeal species, is highly specific for ADP. No activity is detected when ADP is replaced by ATP, GDP, phosphoenolpyruvate, diphosphate or polyphosphate.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 173585-07-4

References:

1.	Kengen, S.W., Tuininga, J.E., de Bok, F.A., Stams, A.J. and de Vos, W.M. Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 270 (1995) 30453–30457. [DOI] [PMID: 8530474]
2.	Koga, S., Yoshioka, I., Sakuraba, H., Takahashi, M., Sakasegawa, S., Shimizu, S. and Ohshima, T. Biochemical characterization, cloning, and sequencing of ADP-dependent (AMP-forming) glucokinase from two hyperthermophilic archaea, Pyrococcus furiosus and Thermococcus litoralis. J. Biochem. 128 (2000) 1079–1085. [PMID: 11098152]
3.	Aslam, M., Takahashi, N., Matsubara, K., Imanaka, T., Kanai, T. and Atomi, H. Identification of the glucosamine kinase in the chitinolytic pathway of Thermococcus kodakarensis. J. Biosci. Bioeng. 125:S1389-1723( (2018). [PMID: 29146530]

[EC 2.7.1.147 created 2001, modified 2020]

2.7.1.230

Accepted name:

amicoumacin kinase

Reaction:

ATP + amicoumacin A = ADP + amicoumacin A 2-phosphate

Other name(s):

amiN (gene name); yerI (gene name)

Systematic name:

ATP:amicoumacin A 2-phosphotransferase

Comments:

The enzyme, found in some bacterial species, inactivates the antibiotic amicoumacin A by phosphorylating it, conferring resistance on the bacteria.

Links to other databases:

References:

Terekhov, S.S., Smirnov, I.V., Malakhova, M.V., Samoilov, A.E., Manolov, A.I., Nazarov, A.S., Danilov, D.V., Dubiley, S.A., Osterman, I.A., Rubtsova, M.P., Kostryukova, E.S., Ziganshin, R.H., Kornienko, M.A., Vanyushkina, A.A., Bukato, O.N., Ilina, E.N., Vlasov, V.V., Severinov, K.V., Gabibov, A.G. and Altman, S. Ultrahigh-throughput functional profiling of microbiota communities. Proc. Natl. Acad. Sci. USA 115 (2018) 9551–9556. [PMID: 30181282]

[EC 2.7.1.230 created 2019]

2.7.2.16

Accepted name:

2-phosphoglycerate kinase

Reaction:

ATP + 2-phospho-D-glycerate = ADP + 2,3-diphospho-D-glycerate

Other name(s):

pgk2 (gene name)

Systematic name:

ATP:2-phosphoglycerate 3-phosphotransferase

Comments:

The enzyme, found in a number of methanogenic archaeal genera, is involved in the biosynthesis of cyclic 2,3-bisphosphoglycerate, a thermoprotectant. Activity is stimulated by potassium ions.

Links to other databases:

References:

1.	Lehmacher, A., Vogt, A.B. and Hensel, R. Biosynthesis of cyclic 2,3-diphosphoglycerate. Isolation and characterization of 2-phosphoglycerate kinase and cyclic 2,3-diphosphoglycerate synthetase from Methanothermus fervidus. FEBS Lett. 272 (1990) 94–98. [PMID: 2226838]
2.	Lehmacher, A. and Hensel, R. Cloning, sequencing and expression of the gene encoding 2-phosphoglycerate kinase from Methanothermus fervidus. Mol. Gen. Genet. 242 (1994) 163–168. [PMID: 8159166]

[EC 2.7.2.16 created 2019]

2.7.2.17

Accepted name:

[amino-group carrier protein]-L-2-aminoadipate 6-kinase

Reaction:

ATP + an [amino-group carrier protein]-C-terminal-[N-(1,4-dicarboxybutyl)-L-glutamine] = ADP + an [amino-group carrier protein]-C-terminal-{N-[1-carboxy-5-oxo-5-(phosphooxy)pentyl]-L-glutamine}

Other name(s):

lysZ (gene name); [amino group carrier protein]-C-terminal-N-(1,4-dicarboxybutan-1-yl)-L-glutamine 5-O-kinase; [amino group carrier protein]-L-2-aminoadipate 6-kinase

Systematic name:

[amino-group carrier protein]-C-terminal-[N-(1,4-dicarboxybutyl)-L-glutamine] 5-O-kinase

Comments:

The enzyme participates in an L-lysine biosynthetic pathway in certain species of bacteria and archaea.

Links to other databases:

References:

1.	Nishida, H., Nishiyama, M., Kobashi, N., Kosuge, T., Hoshino, T. and Yamane, H. A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Genome Res. 9 (1999) 1175–1183. [PMID: 10613839]
2.	Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673–679. [DOI] [PMID: 19620981]
3.	Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277–283. [DOI] [PMID: 23434852]

[EC 2.7.2.17 created 2020]

*EC

2.7.7.2

Accepted name:

FAD synthase

Reaction:

ATP + FMN = diphosphate + FAD

For diagram of FAD biosynthesis, click here

Other name(s):

FAD pyrophosphorylase; riboflavin mononucleotide adenylyltransferase; adenosine triphosphate-riboflavin mononucleotide transadenylase; adenosine triphosphate-riboflavine mononucleotide transadenylase; riboflavin adenine dinucleotide pyrophosphorylase; riboflavine adenine dinucleotide adenylyltransferase; flavin adenine dinucleotide synthetase; FADS; FMN adenylyltransferase; FAD synthetase (misleading)

Systematic name:

ATP:FMN adenylyltransferase

Comments:

Requires Mg²⁺ and is highly specific for ATP as phosphate donor [5]. The cofactors FMN and FAD participate in numerous processes in all organisms, including mitochondrial electron transport, photosynthesis, fatty-acid oxidation, and metabolism of vitamin B₆, vitamin B₁₂ and folates [3]. While monofunctional FAD synthetase is found in eukaryotes and in some prokaryotes, most prokaryotes have a bifunctional enzyme that exhibits both this activity and that of EC 2.7.1.26, riboflavin kinase [3,5].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9026-37-3

References:

1.	Giri, K.V., Rao, N.A., Cama, H.R. and Kumar, S.A. Studies on flavinadenine dinucleotide-synthesizing enzyme in plants. Biochem. J. 75 (1960) 381–386. [PMID: 13828163]
2.	Schrecker, A.W. and Kornberg, A. Reversible enzymatic synthesis of flavin-adenine dinucleotide. J. Biol. Chem. 182 (1950) 795–803. [PMID: 19994476]
3.	Sandoval, F.J. and Roje, S. An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Biol. Chem. 280 (2005) 38337–38345. [DOI] [PMID: 16183635]
4.	Oka, M. and McCormick, D.B. Complete purification and general characterization of FAD synthetase from rat liver. J. Biol. Chem. 262 (1987) 7418–7422. [PMID: 3034893]
5.	Brizio, C., Galluccio, M., Wait, R., Torchetti, E.M., Bafunno, V., Accardi, R., Gianazza, E., Indiveri, C. and Barile, M. Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase. Biochem. Biophys. Res. Commun. 344 (2006) 1008–1016. [DOI] [PMID: 16643857]

[EC 2.7.7.2 created 1961, modified 2007, modified 2020]

2.8.3.26

Accepted name:

succinyl-CoA:mesaconate CoA transferase

Reaction:

succinyl-CoA + mesaconate = 2-methylfumaryl-CoA + succinate

Glossary:

2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA
mesaconate = 2-methylbut-2-enedioic acid

Other name(s):

mct (gene name)

Systematic name:

succinyl-CoA:mesaconate CoA transferase

Comments:

The enzyme participates in the methylaspartate cycle, an anaplerotic pathway that operates in some members of the haloarchaea and forms malate from acetyl-CoA.

Links to other databases:

References:

1.	Khomyakova, M., Bukmez, O., Thomas, L.K., Erb, T.J. and Berg, I.A. A methylaspartate cycle in haloarchaea. Science 331 (2011) 334–337. [PMID: 21252347]
2.	Borjian, F., Johnsen, U., Schonheit, P. and Berg, I.A. Succinyl-CoA:mesaconate CoA-transferase and mesaconyl-CoA hydratase, enzymes of the methylaspartate cycle in Haloarcula hispanica. Front. Microbiol. 8:1683 (2017). [PMID: 28932214]

[EC 2.8.3.26 created 2020]

2.9.1.3

Accepted name:

tRNA 2-selenouridine synthase

Reaction:

selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine³⁴ in tRNA + H₂O = 5-methylaminomethyl-2-selenouridine³⁴ in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate (overall reaction)
(1a) geranyl diphosphate + 5-methylaminomethyl-2-thiouridine³⁴ in tRNA = 5-methylaminomethyl-2-(S-geranyl)thiouridine³⁴ in tRNA + diphosphate
(1b) selenophosphate + 5-methylaminomethyl-2-(S-geranyl)thiouridine³⁴ in tRNA = 5-methylaminomethyl-2-(Se-phospho)selenouridine³⁴ in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol
(1c) 5-methylaminomethyl-2-(Se-phospho)selenouridine³⁴ in tRNA + H₂O = 5-methylaminomethyl-2-selenouridine³⁴ in tRNA + phosphate

Other name(s):

selU (gene name); mnmH (gene name); ybbB (gene name); sufY (gene name)

Systematic name:

geranyl diphosphate/selenophosphate:tRNA 5-methylaminomethyl-2-thiouridine³⁴ geranyl/selenophosphatetransferase

Comments:

This bacterial enzyme converts 5-methylaminomethyl-2-uridine and 5-carboxymethylaminomethyl-2-uridine to the respective selenouridine forms in a two-step process that involves geranylation and subsequent phosphoselenation of the resulting geranylated intermediates. The resultant seleno-phosphorylated uridine intermediates further react with a water molecule to release a phosphate anion and 2-selenouridine tRNA. The enzyme contains a rhodanese domain.

Links to other databases:

References:

1.	Bartos, P., Maciaszek, A., Rosinska, A., Sochacka, E. and Nawrot, B. Transformation of a wobble 2-thiouridine to 2-selenouridine via S-geranyl-2-thiouridine as a possible cellular pathway. Bioorg. Chem. 56 (2014) 49–53. [PMID: 24971911]
2.	Jager, G., Chen, P. and Bjork, G.R. Transfer RNA bound to mnmh protein is enriched with geranylated tRNA—a possible intermediate in its selenation. PLoS One 11:e0153488 (2016). [PMID: 27073879]
3.	Sierant, M., Leszczynska, G., Sadowska, K., Komar, P., Radzikowska-Cieciura, E., Sochacka, E. and Nawrot, B. Escherichia coli tRNA 2-selenouridine synthase (SelU) converts S₂U-RNA to Se₂U-RNA via S-geranylated-intermediate. FEBS Lett. 592 (2018) 2248–2258. [PMID: 29862510]

[EC 2.9.1.3 created 2020]

3.1.3.107

Accepted name:

amicoumacin phosphatase

Reaction:

amicoumacin A 2-phosphate + H₂O = amicoumacin A + phosphate

Other name(s):

amiO (gene name)

Systematic name:

amicoumacin 2-phosphate phosphohydrolase

Comments:

This bacterial enzyme activates the antibiotic amicoumacin A by removing a phosphate group that is added by EC 2.7.1.230, amicoumacin kinase.

Links to other databases:

References:

[EC 3.1.3.107 created 2019]

3.1.3.108

Accepted name:

nocturnin

Reaction:

(1) NADPH + H₂O = NADH + phosphate
(2) NADP⁺ + H₂O = NAD⁺ + phosphate

Other name(s):

NOCT (gene name); nocturnin (curled); MJ0109 (gene name); NADP phosphatase; NADPase

Systematic name:

NADPH 2′-phosphohydrolase

Comments:

The mammalian mitochondrial enzyme is a rhythmically expressed protein that regulates metabolism under the control of circadian clock. It has a slight preference for NADPH over NADP⁺. The archaeal enzyme, identified in Methanocaldococcus jannaschii, is bifunctional acting as NAD⁺ kinase (EC 2.7.1.23) and NADP⁺ phosphatase with a slight preference for NADP⁺ over NADPH.

Links to other databases:

References:

1.	Kawai, S. and Murata, K. Structure and function of NAD kinase and NADP phosphatase: key enzymes that regulate the intracellular balance of NAD(H) and NADP(H). Biosci. Biotechnol. Biochem. 72 (2008) 919–930. [DOI] [PMID: 18391451]
2.	Abshire, E.T., Chasseur, J., Bohn, J.A., Del Rizzo, P.A., Freddolino, P.L., Goldstrohm, A.C. and Trievel, R.C. The structure of human nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Nucleic Acids Res. 46 (2018) 6257–6270. [PMID: 29860338]
3.	Estrella, M.A., Du, J. and Korennykh, A. Crystal structure of human nocturnin catalytic domain. Sci. Rep. 8:16294 (2018). [PMID: 30389976]
4.	Estrella, M.A., Du, J., Chen, L., Rath, S., Prangley, E., Chitrakar, A., Aoki, T., Schedl, P., Rabinowitz, J. and Korennykh, A. The metabolites NADP⁺ and NADPH are the targets of the circadian protein nocturnin (curled). Nat. Commun. 10:2367 (2019). [PMID: 31147539]

[EC 3.1.3.108 created 2020]

3.1.11.7

Transferred entry:

adenosine-5′-diphospho-5′-[DNA] diphosphatase. Now EC 3.6.1.71, adenosine-5′-diphospho-5′-[DNA] diphosphatase

[EC 3.1.11.7 created 2017, deleted 2019]

3.1.11.8

Transferred entry:

guanosine-5′-diphospho-5′-[DNA] diphosphatase. Now EC 3.6.1.70, guanosine-5′-diphospho-5′-[DNA] diphosphatase

[EC 3.1.11.8 created 2017, deleted 2019]

3.1.12.2

Transferred entry:

DNA-3-diphospho-5-guanosine diphosphatase. Now EC 3.6.1.72, DNA-3-diphospho-5-guanosine diphosphatase

[EC 3.1.12.2 created 2017, deleted 2019]

3.1.27.3

Transferred entry:

ribonuclease T₁. Now EC 4.6.1.24, ribonuclease T₁, since the primary reaction is that of a lyase

[EC 3.1.27.3 created 1961 as EC 3.1.4.8, transferred 1965 to EC 2.7.7.26, reinstated 1972 as EC 3.1.4.8, transferred 1978 to EC 3.1.27.3, deleted 2020]

3.2.1.44

Transferred entry:

fucoidanase. Now EC 3.2.1.211, endo-(13)-fucoidanase and EC 3.2.1.212, endo-(14)-fucoidanase

[EC 3.2.1.44 created 1972, deleted 2020]

*EC

3.2.1.155

Accepted name:

xyloglucan-specific endo-processive β-1,4-glucanase

Reaction:

Hydrolysis of (1→4)-D-glucosidic linkages in xyloglucans so as to successively remove oligosaccharides from the newly-formed chain end after endo-initiation on a polymer molecule

Other name(s):

Cel74A; [(1→6)-α-D-xylo]-(1→4)-β-D-glucan exo-glucohydrolase (ambiguous); xyloglucan-specific exo-β-1,4-glucanase (ambiguous)

Systematic name:

[(1→6)-α-D-xylo]-(1→4)-β-D-glucan endo-processive glucohydrolase

Comments:

The enzyme removes branched oligosaccharides, containing preferentially four glucoside residues in the main chain, from xyloglucan molecules in a processive manner after the initial endo-type attack on a polysaccharide [1-5]. Hydrolysis occurs at either the unsubstituted D-glucopyranose residue in the main backbone and/or the D-glucopyranose residue bearing a xylosyl group [1-5]. The enzyme does not display activity, or shows very low activity, towards other β-D-glucans [1,2,4,5].

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, CAS registry number: 1000598-79-7

References:

1.	Grishutin, S.G., Gusakov, A.V., Markov, A.V., Ustinov, B.B., Semenova, M.V. and Sinitsyn, A.P. Specific xyloglucanases as a new class of polysaccharide-degrading enzymes. Biochim. Biophys. Acta 1674 (2004) 268–281. [DOI] [PMID: 15541296]
2.	Ichinose, H., Araki, Y., Michikawa, M., Harazono, K., Yaoi, K., Karita, S. and Kaneko, S. Characterization of an endo-processive-type xyloglucanase having a β-1,4-glucan-binding module and an endo-type xyloglucanase from Streptomyces avermitilis. Appl. Environ. Microbiol. 78 (2012) 7939–7945. [PMID: 22941084]
3.	Matsuzawa, T., Saito, Y. and Yaoi, K. Key amino acid residues for the endo-processive activity of GH74 xyloglucanase. FEBS Lett. 588 (2014) 1731–1738. [PMID: 24657616]
4.	Arnal, G., Stogios, P.J., Asohan, J., Skarina, T., Savchenko, A. and Brumer, H. Structural enzymology reveals the molecular basis of substrate regiospecificity and processivity of an exemplar bacterial glycoside hydrolase family 74 endo-xyloglucanase. Biochem. J. 475 (2018) 3963–3978. [PMID: 30463871]
5.	Arnal, G., Stogios, P.J., Asohan, J., Attia, M.A., Skarina, T., Viborg, A.H., Henrissat, B., Savchenko, A. and Brumer, H. Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J. Biol. Chem. 294 (2019) 13233–13247. [PMID: 31324716]
6.	Gusakov, A.V. Additional sequence and structural characterization of an endo-processive GH74 xyloglucanase from Myceliophthora thermophila and the revision of the EC 3.2.1.155 entry. Biochim. Biophys. Acta. 1864:129511 (2020). [PMID: 31911243]

[EC 3.2.1.155 created 2005, withdrawn at public-review stage, modified and reinstated 2006, modified 2020]

3.2.1.211

Accepted name:

endo-(1→3)-fucoidanase

Reaction:

endohydrolysis of (1→3)-α-L-fucoside linkages in fucan

Other name(s):

α-L-fucosidase (incorrect); poly(1,3-α-L-fucoside-2/4-sulfate) glycanohydrolase

Systematic name:

poly[(1→3)-α-L-fucoside-2/4-sulfate] glycanohydrolase

Comments:

The enzyme specifically hydrolyses (1→3)-α-L-fucoside linkages in fucan. Fucans are found mainly in different species of seaweed and are sulfated polysaccharides with a backbone of (1→3)-linked or alternating (1→3)- and (1→4)-linked α-L-fucopyranosyl residues. In the literature, the sulfated polysaccharides are often called fucoidans. Fucoidans include polysaccharides with a relatively low proportion of fucose and some polysaccharides that have a backbone composed of other saccharides with fucose in the branching side chains. The sulfation of the α-L-fucopyranosyl residues may occur at positions 2 and 4. The enzyme degrades fucan to sulfated α-L-fucooligosaccharides but neither L-fucose nor small fucooligosaccharides are produced.

Links to other databases:

References:

1.	Thanassi, N.M. and Nakada, H.I. Enzymic degradation of fucoidan by enzymes from the hepatopancreas of abalone, Halotus species. Arch. Biochem. Biophys. 118 (1967) 172–177.
2.	Bakunina, I.Iu, Nedashkovskaia, O.I., Alekseeva, S.A., Ivanova, E.P., Romanenko, L.A., Gorshkova, N.M., Isakov, V.V., Zviagintseva, T.N. and Mikhailov, V.V. [Degradation of fucoidan by the marine proteobacterium Pseudoalteromonas citrea] Mikrobiologiia 71 (2002) 49–55. [PMID: 11910806] (in Russian)
3.	Berteau, O. and Mulloy, B. Sulfated fucans, fresh perspectives: structures, functions, and biological properties of sulfated fucans and an overview of enzymes active toward this class of polysaccharide. Glycobiology 13 (2003) 29R–40R. [PMID: 12626402]
4.	Bilan, M.I., Kusaykin, M.I., Grachev, A.A., Tsvetkova, E.A., Zvyagintseva, T.N., Nifantiev, N.E. and Usov, A.I. Effect of enzyme preparation from the marine mollusk Littorina kurila on fucoidan from the brown alga Fucus distichus. Biochemistry (Mosc.) 70 (2005) 1321–1326. [PMID: 16417453]

[EC 3.2.1.211 created 1972 as EC 3.2.1.44, part transferred 2020 to EC 3.2.1.211 ]

3.2.1.212

Accepted name:

endo-(1→4)-fucoidanase

Reaction:

endohydrolysis of (1→4)-α-L-fucoside linkages in fucan

Other name(s):

α-L-fucosidase (incorrect); poly(1,4-α-L-fucoside-2/3-sulfate) glycanohydrolase

Systematic name:

poly[(1→4)-α-L-fucoside-2/3-sulfate] glycanohydrolase

Comments:

The enzyme specifically hydrolyses (1→4)-α-L-fucoside linkages in fucan. Fucans are found mainly in different species of seaweed and are sulfated polysaccharides with a backbone of (1→3)-linked or alternating (1→3)- and (1→4)-linked α-L-fucopyranosyl residues. In the literature, the sulfated polysaccharides are often called fucoidans. Fucoidans include polysaccharides with a relatively low proportion of fucose and some polysaccharides that have a backbone composed of other saccharides with fucose in the branching side chains. The sulfation of the α-L-fucopyranosyl residues may occur at positions 2 and 3. The enzyme degrades fucan to sulfated α-L-fucooligosaccharides but neither L-fucose nor small fucooligosaccharides are produced.

Links to other databases:

References:

1.	Thanassi, N.M. and Nakada, H.I. Enzymic degradation of fucoidan by enzymes from the hepatopancreas of abalone, Halotus species. Arch. Biochem. Biophys. 118 (1967) 172–177.
2.	Berteau, O. and Mulloy, B. Sulfated fucans, fresh perspectives: structures, functions, and biological properties of sulfated fucans and an overview of enzymes active toward this class of polysaccharide. Glycobiology 13 (2003) 29R–40R. [PMID: 12626402]
3.	Descamps, V., Colin, S., Lahaye, M., Jam, M., Richard, C., Potin, P., Barbeyron, T., Yvin, J.C. and Kloareg, B. Isolation and culture of a marine bacterium degrading the sulfated fucans from marine brown algae. Mar Biotechnol (NY) 8 (2006) 27–39. [PMID: 16222488]
4.	Kim, W.J., Kim, S.M., Lee, Y.H., Kim, H.G., Kim, H.K., Moon, S.H., Suh, H.H., Jang, K.H. and Park, Y.I. Isolation and characterization of marine bacterial strain degrading fucoidan from Korean Undaria pinnatifida Sporophylls. J. Microbiol. Biotechnol. 18 (2008) 616–623. [PMID: 18467852]
5.	Silchenko, A.S., Kusaykin, M.I., Kurilenko, V.V., Zakharenko, A.M., Isakov, V.V., Zaporozhets, T.S., Gazha, A.K. and Zvyagintseva, T.N. Hydrolysis of fucoidan by fucoidanase isolated from the marine bacterium, Formosa algae. Mar. Drugs 11 (2013) 2413–2430. [PMID: 23852092]
6.	Silchenko, A.S., Kusaykin, M.I., Zakharenko, A.M., Menshova, R.V., Khanh, H.H.N., Dmitrenok, P.S., Isakov, V.V., Zvyagintseva, T.N. Endo-1,4-fucoidanase from vietnamese marine mollusk Lambis sp. which producing sulphated fucooligosaccharides. J. Mol. Catal. B 102 (2014) 154–160.
7.	Silchenko, A.S., Ustyuzhanina, N.E., Kusaykin, M.I., Krylov, V.B., Shashkov, A.S., Dmitrenok, A.S., Usoltseva, R.V., Zueva, A.O., Nifantiev, N.E. and Zvyagintseva, T.N. Expression and biochemical characterization and substrate specificity of the fucoidanase from Formosa algae. Glycobiology 27 (2017) 254–263. [PMID: 28031251]

[EC 3.2.1.212 created 1972 as EC 3.2.1.44, part transferred 2020 to EC 3.2.1.212]

3.2.1.213

Accepted name:

galactan exo-1,6-β-galactobiohydrolase (non-reducing end)

Reaction:

Hydrolysis of (1→6)-β-D-galactosidic linkages in arabinogalactan proteins and (1→3):(1→6)-β-galactans to yield (1→6)-β-galactobiose as the final product.

Other name(s):

exo-β-1,6-galactobiohydrolase; 1,6Gal (gene name)

Systematic name:

exo-β-(1→6)-galactobiohydrolase (non-reducing end)

Comments:

The enzyme, characterized from the bacterium Bifidobacterium longum, specifically hydrolyses (1→6)-β-galactobiose from the non-reducing terminal of (1→6)-β-D-galactooligosaccharides with a degree of polymerization (DP) of 3 or higher, using an exo mode of action. The enzyme cannot hydrolyse α-L-arabinofuranosylated (1→6)-β-galactans (as found in arabinogalactans) and does not act on (1→3)-β-D- or (1→4)-β-D-galactans. cf. EC 3.2.1.164, galactan endo-1,6-β-galactosidase.

Links to other databases:

References:

1.	Fujita, K., Sakamoto, A., Kaneko, S., Kotake, T., Tsumuraya, Y. and Kitahara, K. Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl. Microbiol. Biotechnol. 103 (2019) 1299–1310. [PMID: 30564851]

[EC 3.2.1.213 created 2020]

3.4.17.24

Accepted name:

tubulin-glutamate carboxypeptidase

Reaction:

This is a subfamily of enzymes that cleave C-terminal and/or side chain amino acids from tubulins. The dual-specificity enzymes can cleave both α- and γ-linked L-glutamate from tubulins, removing the posttranslationally added polyglutamyl side chains from the C-terminal regions. In addition, the enzyme removes two glutamate residues from the C-terminus of β-tubulin and detyrosinated α-tubulin (from which the C-terminal L-tyrosine has been removed by EC 3.4.17.17, tubulinyl-Tyr carboxypeptidase). The latter is cleaved to δ2-tubulin and further to δ3-tubulin.

Other name(s):

cytosolic carboxypeptidase 5; CCP5; Agtpbp1 (gene name); AGBL5 (gene name)

Links to other databases:

References:

1.	Rogowski, K., van Dijk, J., Magiera, M.M., Bosc, C., Deloulme, J.C., Bosson, A., Peris, L., Gold, N.D., Lacroix, B., Bosch Grau, M., Bec, N., Larroque, C., Desagher, S., Holzer, M., Andrieux, A., Moutin, M.J. and Janke, C. A family of protein-deglutamylating enzymes associated with neurodegeneration. Cell 143 (2010) 564–578. [PMID: 21074048]
2.	Kimura, Y., Kurabe, N., Ikegami, K., Tsutsumi, K., Konishi, Y., Kaplan, O.I., Kunitomo, H., Iino, Y., Blacque, O.E. and Setou, M. Identification of tubulin deglutamylase among Caenorhabditis elegans and mammalian cytosolic carboxypeptidases (CCPs). J. Biol. Chem. 285 (2010) 22936–22941. [PMID: 20519502]
3.	Pathak, N., Austin-Tse, C.A., Liu, Y., Vasilyev, A. and Drummond, I.A. Cytoplasmic carboxypeptidase 5 regulates tubulin glutamylation and zebrafish cilia formation and function. Mol. Biol. Cell 25 (2014) 1836–1844. [PMID: 24743595]

[EC 3.4.17.24 created 2020]

3.6.1.69

Accepted name:

8-oxo-(d)GTP phosphatase

Reaction:

(1) 8-oxo-GTP + H₂O = 8-oxo-GDP + phosphate
(2) 8-oxo-dGTP + H₂O = 8-oxo-dGDP + phosphate

Glossary:

8-oxo-dGTP = 2′-deoxy-7,8-dihydro-8-oxoguanosine 5′-triphosphate

Other name(s):

mutT1 (gene name)

Systematic name:

8-oxo-dGTP diphosphohydrolase

Comments:

The enzyme, characterized from the bacterium Mycobacterium tuberculosis, catalyses the hydrolysis of both 8-oxo-GTP and 8-oxo-dGTP, thereby preventing transcriptional and translational errors caused by oxidative damage. The enzyme is highly specific. Unlike EC 3.6.1.55, 8-oxo-dGTP diphosphatase, it removes only a single phosphate group. The nucleoside diphosphate products are hydrolysed further by EC 3.6.1.58, 8-oxo-dGDP phosphatase.

Links to other databases:

References:

Patil, A.G., Sang, P.B., Govindan, A. and Varshney, U. Mycobacterium tuberculosis MutT1 (Rv2985) and ADPRase (Rv1700) proteins constitute a two-stage mechanism of 8-oxo-dGTP and 8-oxo-GTP detoxification and adenosine to cytidine mutation avoidance. J. Biol. Chem. 288 (2013) 11252–11262. [PMID: 23463507]

[EC 3.6.1.69 created 2019]

3.6.1.70

Accepted name:

guanosine-5′-diphospho-5′-[DNA] diphosphatase

Reaction:

guanosine-5′-diphospho-5′-[DNA] + H₂O = phospho-5′-[DNA] + GMP

Other name(s):

aprataxin; pp5′G5′DNA diphosphatase; pp5′G5′-DNA guanylate hydrolase; APTX (gene name); HNT3 (gene name)

Systematic name:

guanosine-5′-diphospho-5′-[DNA] hydrolase (guanosine 5′-phosphate-forming)

Comments:

Aprataxin is a DNA-binding protein that catalyses (among other activities) the 5′ decapping of Gpp-DNA (formed by homologs of RtcB3 from the bacterium Myxococcus xanthus). The enzyme binds the guanylate group to a histidine residue at its active site, forming a covalent enzyme-nucleotide phosphate intermediate, followed by the hydrolysis of the guanylate from the nucleic acid and eventual release. The enzyme forms a 5′-phospho terminus that can be efficiently joined by "classical" ligases. The enzyme also possesses the activitiy of EC 3.6.1.71, adenosine-5′-diphospho-5′-[DNA] diphosphatase and EC 3.6.1.72, DNA-3′-diphospho-5′-guanosine diphosphatase.

Links to other databases:

References:

1.	Maughan, W.P. and Shuman, S. Characterization of 3′-phosphate RNA ligase paralogs RtcB1, RtcB2, and RtcB3 from Myxococcus xanthus highlights DNA and RNA 5′-phosphate capping activity of RtcB3. J. Bacteriol. 197 (2015) 3616–3624. [DOI] [PMID: 26350128]

[EC 3.6.1.70 created 2017 as EC 3.1.11.8, transferred 2019 to EC 3.6.1.70]

3.6.1.71

Accepted name:

adenosine-5′-diphospho-5′-[DNA] diphosphatase

Reaction:

(1) adenosine-5′-diphospho-5′-[DNA] + H₂O = AMP + phospho-5′-[DNA]
(2) adenosine-5′-diphospho-5′-(ribonucleotide)-[DNA] + H₂O = AMP + 5′-phospho-(ribonucleotide)-[DNA]

Other name(s):

aprataxin; 5′-App5′-DNA adenylate hydrolase; APTX (gene name); HNT3 (gene name)

Systematic name:

adenosine-5′-diphospho-5′-[DNA] hydrolase (adenosine 5′-phosphate-forming)

Comments:

Aprataxin is a DNA-binding protein involved in different types of DNA break repair. The enzyme acts (among other activities) on abortive DNA ligation intermediates that contain an adenylate covalently linked to the 5′-phosphate DNA terminus. It also acts when the adenylate is covalently linked to the 5′-phosphate of a ribonucleotide linked to a DNA strand, which is the result of abortive ligase activty on products of EC 3.1.26.4, ribonuclease H, an enzyme that cleaves RNA-DNA hybrids on the 5′ side of the ribonucleotide found in the 5′-RNA-DNA-3′ junction. Aprataxin binds the adenylate group to a histidine residue within the active site, followed by its hydrolysis from the nucleic acid and eventual release, leaving a 5′-phosphate terminus that can be efficiently rejoined. The enzyme also possesses the activities of EC 3.6.1.70, guanosine-5′-diphospho-5′-[DNA] diphosphatase, and EC 3.6.1.72, DNA-3′-diphospho-5′-guanosine diphosphatase.

Links to other databases:

References:

1.	Ahel, I., Rass, U., El-Khamisy, S.F., Katyal, S., Clements, P.M., McKinnon, P.J., Caldecott, K.W. and West, S.C. The neurodegenerative disease protein aprataxin resolves abortive DNA ligation intermediates. Nature 443 (2006) 713–716. [DOI] [PMID: 16964241]
2.	Tumbale, P., Williams, J.S., Schellenberg, M.J., Kunkel, T.A. and Williams, R.S. Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity. Nature 506 (2014) 111–115. [DOI] [PMID: 24362567]

[EC 3.6.1.71 created 2017 as EC 3.1.11.7, transferred 2019 to EC 3.6.1.71]

3.6.1.72

Accepted name:

DNA-3′-diphospho-5′-guanosine diphosphatase

Reaction:

[DNA]-3′-diphospho-5′-guanosine + H₂O = [DNA]-3′-phosphate + GMP

Other name(s):

aprataxin; DNA-3′pp5′G guanylate hydrolase; APTX (gene name); HNT3 (gene name)

Systematic name:

[DNA]-3′-diphospho-5′-guanosine hydrolase (guanosine 5′-phosphate-forming)

Comments:

Aprataxin is a DNA-binding protein that catalyses (among other activities) the 3′ decapping of DNA-ppG (formed by EC 6.5.1.8, 3′-phosphate/5′-hydroxy nucleic acid ligase) [1]. The enzyme binds the guanylate group to a histidine residue at its active site, forming a covalent enzyme-nucleotide phosphate intermediate, followed by the hydrolysis of the guanylate from the nucleic acid and its eventual release. The enzyme also possesses the activity of EC 3.6.1.71, adenosine-5′-diphospho-5′-[DNA] diphosphatase, and EC 3.6.1.70, guanosine-5′-diphospho-5′-[DNA] diphosphatase.

Links to other databases:

References:

1.	Das, U., Chauleau, M., Ordonez, H. and Shuman, S. Impact of DNA3′pp5′G capping on repair reactions at DNA 3′ ends. Proc. Natl. Acad. Sci. USA 111 (2014) 11317–11322. [DOI] [PMID: 25049385]
2.	Chauleau, M., Jacewicz, A. and Shuman, S. DNA3′pp5′G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition. Nucleic Acids Res. 43 (2015) 6075–6083. [DOI] [PMID: 26007660]

[EC 3.6.1.72 created 2017 as EC 3.1.12.2, transferred 2019 to EC 3.6.1.72]

3.6.1.73

Accepted name:

inosine/xanthosine triphosphatase

Reaction:

(1) inosine 5′-triphosphate + H₂O = inosine 5′-diphosphate + phosphate
(2) xanthosine 5′-triphosphate + H₂O = xanthosine 5′-diphosphate + phosphate

Glossary:

inosine 5′-triphosphate = ITP
xanthosine 5′-triphosphate = XTP

Other name(s):

yjjX (gene name)

Systematic name:

inosine/xanthosine 5′-triphosphate phosphohydrolase

Comments:

The enzyme, characterized from the bacterium Escherichia coli, preferentially hydrolyses inosine triphosphate and xanthosine triphosphate, which are formed by oxidative deamination damage. By hydrolysing these damaged nucleotides, the enzyme prevents their incorporation into RNA.

Links to other databases:

References:

1.	Zheng, J., Singh, V.K. and Jia, Z. Identification of an ITPase/XTPase in Escherichia coli by structural and biochemical analysis. Structure 13 (2005) 1511–1520. [PMID: 16216582]

[EC 3.6.1.73 created 2020]

3.7.1.26

Accepted name:

2,4-didehydro-3-deoxy-L-rhamnonate hydrolase

Reaction:

2,4-didehydro-3-deoxy-L-rhamnonate + H₂O = pyruvate + (S)-lactate

For diagram of L-rhamnose metabolism, click here

Other name(s):

L-2,4-diketo-3-deoxyrhamnonate hydrolase; lra6 (gene name)

Systematic name:

2,4-didehydro-3-deoxy-L-rhamnonate hydrolase

Comments:

The enzyme, characterized from the bacterium Sphingomonas sp. SKA58, participates in an L-rhamnose degradation pathway.

Links to other databases:

References:

1.	Watanabe, S. and Makino, K. Novel modified version of nonphosphorylated sugar metabolism - an alternative L-rhamnose pathway of Sphingomonas sp. FEBS J. 276 (2009) 1554–1567. [DOI] [PMID: 19187228]

[EC 3.7.1.26 created 2020]

3.13.1.9

Accepted name:

S-inosyl-L-homocysteine hydrolase

Reaction:

S-inosyl-L-homocysteine + H₂O = inosine + L-homocysteine

Other name(s):

SIHH

Systematic name:

S-inosyl-L-homocysteine hydrolase (inosine-forming)

Comments:

The enzyme, characterized from the methanogenic archaeon Methanocaldococcus jannaschii, binds an NAD⁺ cofactor. It participates in an alternative pathway for the regeneration of S-adenosyl-L-methionine from S-adenosyl-L-homocysteine that involves the deamination of the latter to S-inosyl-L-homocysteine.

Links to other databases:

References:

1.	Miller, D., Xu, H. and White, R.H. S-Inosyl-L-homocysteine hydrolase, a novel enzyme involved in S-adenosyl-L-methionine recycling. J. Bacteriol. 197 (2015) 2284–2291. [DOI] [PMID: 25917907]

[EC 3.13.1.9 created 2020]

4.1.1.119

Accepted name:

phenylacetate decarboxylase

Reaction:

phenylacetate = toluene + CO₂

Other name(s):

phdB (gene name)

Systematic name:

phenylacetate carboxy-lyase

Comments:

This bacterial enzyme, isolated from anoxic, toluene-producing microbial communities, is a glycyl radical enzyme. It needs to be activated by a dedicated activating enzyme (PhdA). The activase catalyses the reductive cleavage of AdoMet, producing a 5′-deoxyadenosyl radical that leads to the production of the glycyl radical in PhdB.

Links to other databases:

References:

1.	Zargar, K., Saville, R., Phelan, R.M., Tringe, S.G., Petzold, C.J., Keasling, J.D. and Beller, H.R. In vitro characterization of phenylacetate decarboxylase, a novel enzyme catalyzing toluene biosynthesis in an anaerobic microbial community. Sci. Rep. 6:31362 (2016). [PMID: 27506494]
2.	Beller, H.R., Rodrigues, A.V., Zargar, K., Wu, Y.W., Saini, A.K., Saville, R.M., Pereira, J.H., Adams, P.D., Tringe, S.G., Petzold, C.J. and Keasling, J.D. Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nat. Chem. Biol. 14 (2018) 451–457. [PMID: 29556105]
3.	Rodrigues, A.V., Tantillo, D.J., Mukhopadhyay, A., Keasling, J.D. and Beller, H. Insights into the mechanism of phenylacetate decarboxylase (PhdB), a toluene-producing glycyl radical enzyme. ChemBioChem (2019) . [PMID: 31512343]

[EC 4.1.1.119 created 2019]

4.1.2.41

Transferred entry:

vanillin synthase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase

[EC 4.1.2.41 created 2000, deleted 2019]

4.1.2.61

Accepted name:

feruloyl-CoA hydratase/lyase

Reaction:

feruloyl-CoA + H₂O = vanillin + acetyl-CoA (overall reaction)
(1a) feruloyl-CoA + H₂O = 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA
(1b) 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA = vanillin + acetyl-CoA

For diagram of vanillin biosynthesis, click here

Other name(s):

hydroxycinnamoyl-CoA hydratase lyase; enoyl-CoA hydratase/aldolase; HCHL; ferB (gene name); couA (gene name)

Systematic name:

feruloyl-CoA hydro-lyase/vanillin-lyase (acetyl-CoA-forming)

Comments:

The enzyme is a member of the enoyl-CoA hydratase/isomerase superfamily. It catalyses a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant β-hydroxy thioester by retro-aldol reaction. (E)-caffeoyl-CoA and (E)-4-coumaroyl-CoA are also substrates.

Links to other databases:

References:

1.	Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582–1585. [PMID: 6870241]
2.	Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397–1405. [DOI] [PMID: 9611814]
3.	Gasson, M.J., Kitamura, Y., McLauchlan, W.R., Narbad, A., Parr, A.J., Parsons, E.L., Payne, J., Rhodes, M.J. and Walton, N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J. Biol. Chem. 273 (1998) 4163–4170. [PMID: 9461612]
4.	Overhage, J., Priefert, H. and Steinbuchel, A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. Strain HR199. Appl. Environ. Microbiol. 65 (1999) 4837–4847. [PMID: 10543794]
5.	Bennett, J.P., Bertin, L., Moulton, B., Fairlamb, I.J., Brzozowski, A.M., Walton, N.J. and Grogan, G. A ternary complex of hydroxycinnamoyl-CoA hydratase-lyase (HCHL) with acetyl-CoA and vanillin gives insights into substrate specificity and mechanism. Biochem. J. 414 (2008) 281–289. [PMID: 18479250]
6.	Hirakawa, H., Schaefer, A.L., Greenberg, E.P. and Harwood, C.S. Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J. Bacteriol. 194 (2012) 1960–1967. [PMID: 22328668]
7.	Yang, W., Tang, H., Ni, J., Wu, Q., Hua, D., Tao, F. and Xu, P. Characterization of two Streptomyces enzymes that convert ferulic acid to vanillin. PLoS One 8:e67339 (2013). [PMID: 23840666]

[EC 4.1.2.61 created 2020 (EC 4.1.2.41 created 2000, incorporated 2020, EC 4.2.1.101 created 2000, incorporated 2020)]

*EC

4.2.1.96

Accepted name:

4a-hydroxytetrahydrobiopterin dehydratase

Reaction:

4a-hydroxytetrahydrobiopterin = 6,7-dihydrobiopterin + H₂O

For diagram of biopterin biosynthesis, click here

Glossary:

4a-hydroxytetrahydrobiopterin = 6-[(1R,2S)-1,2-dihydroxypropyl]-5,6,7,8-tetrahydro-4a-hydroxypterin
6,7-dihydrobiopterin = 6-[(1R,2S)-1,2-dihydroxypropyl]-6,7-dihydropterin

Other name(s):

4α-hydroxy-tetrahydropterin dehydratase; 4a-carbinolamine dehydratase; pterin-4α-carbinolamine dehydratase; 4a-hydroxytetrahydrobiopterin hydro-lyase

Systematic name:

4a-hydroxytetrahydrobiopterin hydro-lyase (6,7-dihydrobiopterin-forming)

Comments:

In concert with EC 1.5.1.34, 6,7-dihydropteridine reductase, the enzyme recycles 4a-hydroxytetrahydrobiopterin back to tetrahydrobiopterin, a cosubstrate for several enzymes, including aromatic amino acid hydroxylases. The enzyme is bifunctional, and also acts as a dimerization cofactor of hepatocyte nuclear factor-1α (HNF-1).

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 87683-70-3

References:

1.	Citron, B.A., Davis, M.D., Milstien, S., Gutierrez, J., Mendel, D.B., Crabtree, G.R. and Kaufman, S. Identity of 4a-carbinolamine dehydratase, a component of the phenylalanine hydroxylation system, and DCoH, a transregulator of homeodomain proteins. Proc. Natl. Acad. Sci. USA 89 (1992) 11891–11894. [PMID: 1465414]
2.	Hauer, C.R., Rebrin, I., Thöny, B., Neuheiser, F., Curtius, H.C., Hunziker, P., Blau, N., Ghisla, S., Heizmann, C.W. Phenylalanine hydroxylase-stimulating protein: pterin-4α-carbinolamine dehydratase from rat and human liver. J. Biol. Chem. 268 (1993) 4828–4831. [PMID: 8444860]
3.	Thony, B., Neuheiser, F., Blau, N. and Heizmann, C.W. Characterization of the human PCBD gene encoding the bifunctional protein pterin-4 α-carbinolamine dehydratase/dimerization cofactor for the transcription factor HNF-1 α. Biochem. Biophys. Res. Commun. 210 (1995) 966–973. [PMID: 7763270]
4.	Endrizzi, J.A., Cronk, J.D., Wang, W., Crabtree, G.R. and Alber, T. Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator. Science 268 (1995) 556–559. [PMID: 7725101]
5.	Cronk, J.D., Endrizzi, J.A. and Alber, T. High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue. Protein Sci. 5 (1996) 1963–1972. [PMID: 8897596]

[EC 4.2.1.96 created 1999, modified 2020]

4.2.1.101

Transferred entry:

trans-feruloyl-CoA hydratase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase

[EC 4.2.1.101 created 2000, deleted 2020]

4.2.2.27

Accepted name:

pectin monosaccharide-lyase

Reaction:

(1,4-α-D-galacturonosyl methyl ester)_n = (1,4-α-D-galacturonosyl methyl ester)_n-1 + 4-deoxy-6-O-methyl-L-threo-hex-4-enopyranuronate

Other name(s):

exo-pectin lyase; PLIII

Systematic name:

poly(1,4-α-D-galacturonosyl methyl ester) non-reducing-end-monosaccharide-lyase

Comments:

The enzyme, isolated from the fungus Aspergillus giganteus, acts on the non-reducing end of methyl-esterified polygalacturonan, releasing either 4-deoxy^--L-threo-hex-4-enopyranuronate or 4-deoxy-6-O-methyl-L-threo-hex-4-enopyranuronate. The enzyme is stimulated by divalent cations, with Co²⁺ having the strongest effect. It is able to act on substrates as short as a disaccharide, and was active on substrates with degrees of methyl esterification ranging between 34% and 90%.

Links to other databases:

References:

1.	Pedrolli, D.B. and Carmona, E.C. Purification and characterization of a unique pectin lyase from Aspergillus giganteus able to release unsaturated monogalacturonate during pectin degradation. Enzyme Res. 2014:353915 (2014). [PMID: 25610636]

[EC 4.2.2.27 created 2020]

*EC

4.3.2.5

Accepted name:

peptidylamidoglycolate lyase

Reaction:

[peptide]-(2S)-2-hydroxyglycine = [peptide]-amide + glyoxylate

Other name(s):

α-hydroxyglycine amidating dealkylase; peptidyl-α-hydroxyglycine α-amidating lyase; HGAD; PGL; PAL; peptidylamidoglycolate peptidylamide-lyase

Systematic name:

[peptide]-(2S)-2-hydroxyglycine peptidyl-amide-lyase (glyoxylate-forming)

Comments:

Requires zinc. The enzyme acts on the product of the reaction catalysed by EC 1.14.17.3 peptidylglycine monooxygenase, thus removing a terminal glycine residue and leaving a des-glycine peptide amide. In mammals, the two activities are part of a bifunctional protein.

Links to other databases:

BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 131689-50-4

References:

1.	Katapodis, A.G., Ping, D. and May, S.W. A novel enzyme from bovine neurointermediate pituitary catalyzes dealkylation of α-hydroxyglycine derivatives, thereby functioning sequentially with peptidylglycine α-amidating monooxygenase in peptide amidation. Biochemistry 29 (1990) 6115–6120. [PMID: 2207061]
2.	Bell, J., Ash, D.E., Snyder, L.M., Kulathila, R., Blackburn, N.J. and Merkler, D.J. Structural and functional investigations on the role of zinc in bifunctional rat peptidylglycine α-amidating enzyme. Biochemistry 36 (1997) 16239–16246. [PMID: 9405058]

[EC 4.3.2.5 created 1992, modified 2019]

*EC

4.3.3.7

Accepted name:

4-hydroxy-tetrahydrodipicolinate synthase

Reaction:

pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H₂O

For diagram of lysine biosynthesis (early stages), click here

Glossary:

(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

Other name(s):

dihydrodipicolinate synthase (incorrect); dihydropicolinate synthetase (incorrect); dihydrodipicolinic acid synthase (incorrect); L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing); dapA (gene name).

Systematic name:

L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate-forming]

Comments:

The reaction can be divided into three consecutive steps: Schiff base formation with pyruvate, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product. The product of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1,2], and the enzyme was classified accordingly as EC 4.2.1.52, dihydrodipicolinate synthase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual product of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate [3], and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate synthase. However, the identity of the product is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all [5].

Links to other databases:

References:

1.	Yugari, Y. and Gilvarg, C. The condensation step in diaminopimelate synthesis. J. Biol. Chem. 240 (1965) 4710–4716. [PMID: 5321309]
2.	Blickling, S., Renner, C., Laber, B., Pohlenz, H.D., Holak, T.A. and Huber, R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 36 (1997) 24–33. [DOI] [PMID: 8993314]
3.	Devenish, S.R., Blunt, J.W. and Gerrard, J.A. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J. Med. Chem. 53 (2010) 4808–4812. [DOI] [PMID: 20503968]
4.	Soares da Costa, T.P., Muscroft-Taylor, A.C., Dobson, R.C., Devenish, S.R., Jameson, G.B. and Gerrard, J.A. How essential is the ’essential’ active-site lysine in dihydrodipicolinate synthase. Biochimie 92 (2010) 837–845. [DOI] [PMID: 20353808]
5.	Karsten, W.E., Nimmo, S.A., Liu, J. and Chooback, L. Identification of 2,3-dihydrodipicolinate as the product of the dihydrodipicolinate synthase reaction from Escherichia coli. Arch. Biochem. Biophys. 653 (2018) 50–62. [PMID: 29944868]

[EC 4.3.3.7 created 1972 as EC 4.2.1.52, transferred 2012 to EC 4.3.3.7, modified 2020]

4.6.1.24

Accepted name:

ribonuclease T₁

Reaction:

[RNA] containing guanosine + H₂O = an [RNA fragment]-3′-guanosine-3′-phosphate + a 5′-hydroxy-ribonucleotide-3′-[RNA fragment] (overall reaction)
(1a) [RNA] containing guanosine = [RNA fragment]-3′-guanosine-2′,3′-cyclophosphate + a 5′-hydroxy-ribonucleotide-3′-[RNA fragment]
(1b) [RNA fragment]-3′-guanosine-2′,3′-cyclophosphate + H₂O = [RNA fragment]-3′-guanosine-3′-phosphate

Other name(s):

barnase; bacterial ribonuclease Sa; guanyloribonuclease; Aspergillus oryzae ribonuclease; RNase N₁; RNase N₂; ribonuclease N₃; ribonuclease U₁; ribonuclease F₁; ribonuclease Ch; ribonuclease PP1; ribonuclease SA; RNase F₁; ribonuclease C2; binase; RNase Sa; guanyl-specific RNase; RNase G; RNase T₁; ribonuclease guaninenucleotido-2′-transferase (cyclizing); ribonuclease N₁

Systematic name:

[RNA]-guanosine 5′-hydroxy-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′-guanosine-2′,3′-cyclophosphate-forming and hydrolysing)

Comments:

A family of related enzymes found in some fungi and bacteria. The enzyme is specific for cleavage at the 3′-phosphate group of guanosine in single stranded RNA, and catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5′-hydroxy-phosphooligonucletides and 3′-phosphooligonucleotides ending in Gp with 2′,3′-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3′,5′-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5′-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3′-nucleotides.

Links to other databases:

References:

1.	Takahashi, K. The structure and function of ribonuclease T₁. I. Chromatographic purification and properties of ribonuclease T₁. J. Biochem. (Tokyo) 49 (1961) 1–8. [DOI]
2.	Kasai, K., Uchida, T., Egami, F., Yoshida, K. and Nomoto, M. Purification and crystallization of ribonuclease N₁ from Neurospora crassa. J. Biochem. (Tokyo) 66 (1969) 389–396. [PMID: 5348588]
3.	Loverix, S., Laus, G., Martins, J.C., Wyns, L. and Steyaert, J. Reconsidering the energetics of ribonuclease catalysed RNA hydrolysis. Eur. J. Biochem. 257 (1998) 286–290. [PMID: 9799130]

[EC 4.6.1.24 created 1961 as EC 3.1.4.8, transferred 1965 to EC 2.7.7.26, reinstated 1972 as EC 3.1.4.8, transferred 1978 to EC 3.1.27.3, transferred 2020 to EC 4.6.1.24]

4.6.1.25

Accepted name:

bacteriophage T₄ restriction endoribonuclease RegB

Reaction:

a [pre-mRNA]-containing guanosine-adenosine + H₂O = a 5′ hydroxy-guanosine-[pre-mRNA fragment] + a [pre-mRNA fragment]-3′-adenosine-3′-phosphate (overall reaction)
(1a) a [pre-mRNA]-containing guanosine-adenosine + H₂O = a 5′ hydroxy-guanosine-[pre-mRNA fragment] + a [pre-mRNA fragment]-adenosine-2′,3′-cyclophosphate
(1b) a [pre-mRNA fragment]- adenosine-2′,3′-cyclophosphate + H₂O = a [pre-mRNAfragment]-3′-adenosine-3′-phosphate

Other name(s):

RegB

Systematic name:

[pre-mRNA]-guanosine-adenosine 5′-hydroxy-guanosine-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′- adenosine -2′,3′-cyclophosphate-forming and hydrolysing)

Comments:

The enzyme from bacteriophage T₄ cleaves early mRNAs between Ap and Gp at one specific specific GpGpApGp site, favouring their further transition to middle-phase mRNA. The activity is enhanced by Ribosomal S1 protein. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5′-hydroxy-phosphooligonucletides and 3′-phosphooligonucleotides ending with 2′,3′-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3′,5′-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5′-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3′-nucleotides.

Links to other databases:

References:

1.	Sanson, B., Hu, R.M., Troitskayadagger, E., Mathy, N. and Uzan, M. Endoribonuclease RegB from bacteriophage T₄ is necessary for the degradation of early but not middle or late mRNAs. J. Mol. Biol. 297 (2000) 1063–1074. [PMID: 10764573]
2.	Saida, F., Uzan, M. and Bontems, F. The phage T₄ restriction endoribonuclease RegB: a cyclizing enzyme that requires two histidines to be fully active. Nucleic Acids Res. 31 (2003) 2751–2758. [PMID: 12771201]
3.	Odaert, B., Saida, F., Aliprandi, P., Durand, S., Crechet, J.B., Guerois, R., Laalami, S., Uzan, M. and Bontems, F. Structural and functional studies of RegB, a new member of a family of sequence-specific ribonucleases involved in mRNA inactivation on the ribosome. J. Biol. Chem. 282 (2007) 2019–2028. [PMID: 17046813]

[EC 4.6.1.25 created 2020]

5.5.1.34

Accepted name:

(+)-cis,trans-nepetalactol synthase

Reaction:

(S)-8-oxocitronellyl enol = (+)-cis,trans-nepetalactol

For diagram of secologanin biosynthesis, click here

Glossary:

(S)-8-oxocitronellyl enol = (2E,6S,7E)-8-hydroxy-2,6-dimethylocta-2,7-dienal
(+)-cis,trans-nepetalactol = (+)-iridodial lactol = (4aS,7S,7aR)-4,7-dimethyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-1-ol

Other name(s):

NEPS1 (gene name); NEPS2 (gene name)

Systematic name:

(S)-8-oxocitronellyl enol cyclase [(+)-cis,trans-nepetalactol-forming]

Comments:

The enzyme, characterized from the plant Nepeta mussinii, binds an NAD⁺ cofactor. The product is a precursor of (+)-cis,trans-nepetalactone, the primary ingredient responsible for the psychoactive effects catnip has on cats.

Links to other databases:

References:

1.	Lichman, B.R., Kamileen, M.O., Titchiner, G.R., Saalbach, G., Stevenson, C.EM., Lawson, D.M. and O'Connor, S.E. Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis. Nat. Chem. Biol. 15 (2019) 71–79. [PMID: 30531909]
2.	Lichman, B.R., O'Connor, S.E. and Kries, H. Biocatalytic strategies towards [4+2] cycloadditions. Chemistry 25 (2019) 6864–6877. [PMID: 30664302]

[EC 5.5.1.34 created 2019]

5.5.1.35

Accepted name:

(+)-cis,cis-nepetalactol synthase

Reaction:

(S)-8-oxocitronellyl enol = (+)-cis,cis-nepetalactol

For diagram of secologanin biosynthesis, click here

Glossary:

(S)-8-oxocitronellyl enol = (2E,6S,7E)-8-hydroxy-2,6-dimethylocta-2,7-dienal
(+)-cis,cis-nepetalactol =(4aR,7S,7aS)-4,7-dimethyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-1-ol

Other name(s):

NEPS3 (gene name)

Systematic name:

(S)-8-oxocitronellyl enol cyclase [(+)-cis,cis-nepetalactol-forming]

Comments:

The enzyme, characterized from the plant Nepeta mussinii, binds an NAD⁺ cofactor. The product is a precursor of (+)-cis,cis-nepetalactone, one of the stereoisomers responsible for the psychoactive effects catnip has on cats.

Links to other databases:

References:

1.	Lichman, B.R., Kamileen, M.O., Titchiner, G.R., Saalbach, G., Stevenson, C.EM., Lawson, D.M. and O'Connor, S.E. Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis. Nat. Chem. Biol. 15 (2019) 71–79. [PMID: 30531909]
2.	Lichman, B.R., O'Connor, S.E. and Kries, H. Biocatalytic strategies towards [4+2] cycloadditions. Chemistry 25 (2019) 6864–6877. [PMID: 30664302]

[EC 5.5.1.35 created 2019]

6.2.1.61

Accepted name:

salicylate—[aryl-carrier protein] ligase

Reaction:

ATP + salicylate + holo-[non-ribosomal peptide synthase] = AMP + diphosphate + salicyl-[non-ribosomal peptide synthase] (overall reaction)
(1a) ATP + salicylate = diphosphate + (salicyl)adenylate
(1b) (salicyl)adenylate + holo-[non-ribosomal peptide synthase] = AMP + salicyl-[non-ribosomal peptide synthase]

Other name(s):

pmsE (gene name); pchD (gene name)

Systematic name:

salicylate:holo-[non-ribosomal peptide synthase] ligase

Comments:

The enzyme catalyses the activation of salicylate to (salicyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of an aryl-carrier protein, which is often a domain of a larger non-ribosimal peptide synthase. The PmsE enzyme is involved in pseudomonine biosynthesis and transfers the activated salicylate first to itself, and then to a PmsG protein. The PchD enzyme is involved in pyochelin biosynthesis and transfers the activated salicylate directly to the PchE protein.

Links to other databases:

References:

1.	Quadri, L.E., Keating, T.A., Patel, H.M. and Walsh, C.T. Assembly of the Pseudomonas aeruginosa nonribosomal peptide siderophore pyochelin: In vitro reconstitution of aryl-4, 2-bisthiazoline synthetase activity from PchD, PchE, and PchF. Biochemistry 38 (1999) 14941–14954. [PMID: 10555976]
2.	Sattely, E.S. and Walsh, C.T. A latent oxazoline electrophile for N-O-C bond formation in pseudomonine biosynthesis. J. Am. Chem. Soc. 130 (2008) 12282–12284. [DOI] [PMID: 18710233]

[EC 6.2.1.61 created 2019]

6.2.1.62

Accepted name:

3,4-dihydroxybenzoate—[aryl-carrier protein] ligase

Reaction:

ATP + 3,4-dihydroxybenzoate + holo-[aryl-carrier protein] = AMP + diphosphate + 3,4-dihydroxybenzoyl-[aryl-carrier protein] (overall reaction)
(1a) ATP + 3,4-dihydroxybenzoate = diphosphate + (3,4-dihydroxybenzoyl)adenylate
(1b) (3,4-dihydroxybenzoyl)adenylate + holo-[aryl-carrier protein] = AMP + 3,4-dihydroxybenzoyl-[aryl-carrier protein]

Other name(s):

asbC (gene name)

Systematic name:

3,4-dihydroxybenzoate:[aryl-carrier protein] ligase (AMP-forming)

Comments:

The adenylation domain of the enzyme catalyses the activation of 3,4-dihydroxybenzoate to (3,4-dihydroxybenzoyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of an aryl-carrier protein domain. The aryl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.

Links to other databases:

References:

1.	Pfleger, B.F., Lee, J.Y., Somu, R.V., Aldrich, C.C., Hanna, P.C. and Sherman, D.H. Characterization and analysis of early enzymes for petrobactin biosynthesis in Bacillus anthracis. Biochemistry 46 (2007) 4147–4157. [PMID: 17346033]

[EC 6.2.1.62 created 2020]

6.2.1.63

Accepted name:

L-arginine—[L-arginyl-carrier protein] ligase

Reaction:

ATP + L-arginine + holo-[L-arginyl-carrier protein] = AMP + diphosphate + L-arginyl-[L-arginyl-carrier protein] (overall reaction)
(1a) ATP + L-arginine = diphosphate + (L-arginyl)adenylate
(1b) (L-arginyl)adenylate + holo-[L-arginyl-carrier protein] = AMP + L-arginyl-[L-arginyl-carrier protein]

Other name(s):

vabF (gene name)

Systematic name:

L-arginine:[L-arginyl-carrier protein] ligase (AMP-forming)

Comments:

The adenylation domain of the enzyme catalyses the activation of L-arginine to (L-arginyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.

Links to other databases:

References:

1.	Balado, M., Osorio, C.R. and Lemos, M.L. A gene cluster involved in the biosynthesis of vanchrobactin, a chromosome-encoded siderophore produced by Vibrio anguillarum. Microbiology 152 (2006) 3517–3528. [PMID: 17159203]

[EC 6.2.1.63 created 2020]

*EC

6.3.2.43

Accepted name:

[amino-group carrier protein]—L-2-aminoadipate ligase

Reaction:

ATP + an [amino-group carrier protein]-C-terminal-L-glutamate + L-2-aminoadipate = ADP + phosphate + an [amino-group carrier protein]-C-terminal-[N-(1,4-dicarboxybutyl)-L-glutamine]

Other name(s):

α-aminoadipate-lysW ligase; lysX (gene name); LysX (ambiguous); AAA—LysW ligase; [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate:L-2-aminoadipate ligase (ADP-forming); [lysine-biosynthesis-protein LysW]—L-2-aminoadipate ligase

Systematic name:

[amino-group carrier protein]-C-terminal-L-glutamate:L-2-aminoadipate ligase (ADP-forming)

Comments:

The enzymes from the thermophilic bacterium Thermus thermophilus and the thermophilic archaea Sulfolobus acidocaldarius and Sulfolobus tokodaii protect the amino group of L-2-aminoadipate by conjugation to the carrier protein LysW. This reaction is part of the lysine biosynthesis pathway in these organisms.

Links to other databases:

References:

1.	Vassylyeva, M.N., Sakai, H., Matsuura, T., Sekine, S., Nishiyama, M., Terada, T., Shirouzu, M., Kuramitsu, S., Vassylyev, D.G. and Yokoyama, S. Cloning, expression, purification, crystallization and initial crystallographic analysis of the lysine-biosynthesis LysX protein from Thermus thermophilus HB8. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 1651–1652. [PMID: 12925802]
2.	Horie, A., Tomita, T., Saiki, A., Kono, H., Taka, H., Mineki, R., Fujimura, T., Nishiyama, C., Kuzuyama, T. and Nishiyama, M. Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus. Nat. Chem. Biol. 5 (2009) 673–679. [DOI] [PMID: 19620981]
3.	Ouchi, T., Tomita, T., Horie, A., Yoshida, A., Takahashi, K., Nishida, H., Lassak, K., Taka, H., Mineki, R., Fujimura, T., Kosono, S., Nishiyama, C., Masui, R., Kuramitsu, S., Albers, S.V., Kuzuyama, T. and Nishiyama, M. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat. Chem. Biol. 9 (2013) 277–283. [DOI] [PMID: 23434852]

[EC 6.3.2.43 created 2014, modified 2019]

*EC

6.3.2.52

Accepted name:

jasmonoyl—L-amino acid ligase

Reaction:

ATP + jasmonate + an L-amino acid = AMP + diphosphate + a jasmonoyl-L-amino acid

Other name(s):

JAR1 (gene name); JAR4 (gene name); JAR6 (gene name); jasmonoyl—L-amino acid synthetase

Systematic name:

jasmonate:L-amino acid ligase

Comments:

Two jasmonoyl-L-amino acid synthetases have been described from Nicotiana attenuata [3] and one from Arabidopsis thaliana [1]. The N. attenuata enzymes generate jasmonoyl-L-isoleucine, jasmonoyl-L-leucine, and jasmonoyl-L-valine. The enzyme from A. thaliana could catalyse the addition of many different amino acids to jasmonate in vitro [1,4,5]. While the abundant form of jasmonate in plants is (–)-jasmonate, the active form of jasmonoyl-L-isoleucine is (+)-7-iso-jasmonoyl-L-isoleucine.

Links to other databases:

References:

1.	Staswick, P.E. and Tiryaki, I. The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. Plant Cell 16 (2004) 2117–2127. [DOI] [PMID: 15258265]
2.	Kang, J.H., Wang, L., Giri, A. and Baldwin, I.T. Silencing threonine deaminase and JAR4 in Nicotiana attenuata impairs jasmonic acid-isoleucine-mediated defenses against Manduca sexta. Plant Cell 18 (2006) 3303–3320. [DOI] [PMID: 17085687]
3.	Wang, L., Halitschke, R., Kang, J.H., Berg, A., Harnisch, F. and Baldwin, I.T. Independently silencing two JAR family members impairs levels of trypsin proteinase inhibitors but not nicotine. Planta 226 (2007) 159–167. [DOI] [PMID: 17273867]
4.	Guranowski, A., Miersch, O., Staswick, P.E., Suza, W. and Wasternack, C. Substrate specificity and products of side-reactions catalyzed by jasmonate:amino acid synthetase (JAR1). FEBS Lett. 581 (2007) 815–820. [DOI] [PMID: 17291501]
5.	Suza, W.P. and Staswick, P.E. The role of JAR1 in jasmonoyl-L-isoleucine production during Arabidopsis wound response. Planta 227 (2008) 1221–1232. [DOI] [PMID: 18247047]

[EC 6.3.2.52 created 2018, modified 2019]

*EC

7.1.1.7

Accepted name:

quinol oxidase (electrogenic, proton-motive force generating)

Reaction:

2 quinol + O₂_{[side 2]} + 4 H⁺_{[side 2]} = 2 quinone + 2 H₂O_{[side 2]} + 4 H⁺_{[side 1]} (overall reaction)
(1a) 2 quinol = 2 quinone + 4 H⁺_{[side 1]} + 4 e^-
(1b) O₂_{[side 2]} + 4 H⁺_{[side 2]} + 4 e^- = 2 H₂O_{[side 2]}

Other name(s):

cydAB (gene names); appBC (gene names); cytochrome bd oxidase; cytochrome bd-I oxidase; cytochrome bd-II oxidase; ubiquinol:O₂ oxidoreductase (electrogenic, non H⁺-transporting); ubiquinol oxidase (electrogenic, proton-motive force generating); ubiquinol oxidase (electrogenic, non H⁺-transporting)

Systematic name:

quinol:oxygen oxidoreductase (electrogenic, non H⁺-transporting)

Comments:

This terminal oxidase enzyme is unable to pump protons but generates a proton motive force by transmembrane charge separation resulting from utilizing protons and electrons originating from opposite sides of the membrane to generate water. The bioenergetic efficiency (the number of charges driven across the membrane per electron used to reduce oxygen to water) is 1. The bd-I oxidase from the bacterium Escherichia coli is the predominant respiratory oxygen reductase that functions under microaerophilic conditions in that organism. cf. EC 7.1.1.3, ubiquinol oxidase (H⁺-transporting).

Links to other databases:

References:

1.	Miller, M.J., Hermodson, M. and Gennis, R.B. The active form of the cytochrome d terminal oxidase complex of Escherichia coli is a heterodimer containing one copy of each of the two subunits. J. Biol. Chem. 263 (1988) 5235–5240. [PMID: 3281937]
2.	Puustinen, A., Finel, M., Haltia, T., Gennis, R.B. and Wikstrom, M. Properties of the two terminal oxidases of Escherichia coli. Biochemistry 30 (1991) 3936–3942. [PMID: 1850294]
3.	Belevich, I., Borisov, V.B., Zhang, J., Yang, K., Konstantinov, A.A., Gennis, R.B. and Verkhovsky, M.I. Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site. Proc. Natl. Acad. Sci. USA 102 (2005) 3657–3662. [DOI] [PMID: 15728392]
4.	Lenn, T., Leake, M.C. and Mullineaux, C.W. Clustering and dynamics of cytochrome bd-I complexes in the Escherichia coli plasma membrane in vivo. Mol. Microbiol. 70 (2008) 1397–1407. [DOI] [PMID: 19019148]
5.	Shepherd, M., Sanguinetti, G., Cook, G.M. and Poole, R.K. Compensations for diminished terminal oxidase activity in Escherichia coli: cytochrome bd-II-mediated respiration and glutamate metabolism. J. Biol. Chem. 285 (2010) 18464–18472. [DOI] [PMID: 20392690]
6.	Borisov, V.B., Murali, R., Verkhovskaya, M.L., Bloch, D.A., Han, H., Gennis, R.B. and Verkhovsky, M.I. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc. Natl. Acad. Sci. USA 108 (2011) 17320–17324. [DOI] [PMID: 21987791]
7.	Borisov, V.B., Gennis, R.B., Hemp, J. and Verkhovsky, M.I. The cytochrome bd respiratory oxygen reductases. Biochim. Biophys. Acta 1807 (2011) 1398–1413. [PMID: 21756872]

[EC 7.1.1.7 created 2014 as EC 1.10.3.14, modified 2017, transferred 2018 to EC 7.1.1.7, modified 2020]

7.1.1.9

Accepted name:

cytochrome-c oxidase

Reaction:

4 ferrocytochrome c + O₂ + 8 H⁺_{[side 1]} = 4 ferricytochrome c + 2 H₂O + 4 H⁺_{[side 2]}

For diagram, click here

Other name(s):

cytochrome aa₃; cytochrome caa₃; cytochrome bb₃; cytochrome cbb₃; cytochrome ba₃; cytochrome a₃; Warburg's respiratory enzyme; indophenol oxidase; indophenolase; complex IV (mitochondrial electron transport); ferrocytochrome c oxidase; cytochrome oxidase (ambiguous); NADH cytochrome c oxidase (incorrect)

Systematic name:

ferrocytochrome-c:oxygen oxidoreductase

Comments:

An oligomeric membrane heme-Cu:O₂ reductase-type enzyme that terminates the respiratory chains of aerobic and facultative aerobic organisms. The reduction of O₂ to water is accompanied by the extrusion of four protons. The cytochrome-aa₃ enzymes of mitochondria and many bacterial species are the most abundant group, but other variations, such as the bacterial cytochrome-cbb₃ enzymes, also exist. All of the variants have a conserved catalytic core subunit (subunit I) that contains a low-spin heme (of a- or b-type), a binuclear metal centre composed of a high-spin heme iron (of a-, o-, or b-type heme, referred to as a₃, o₃ or b₃ heme), and a Cu atom (CuB). Besides subunit I, the enzyme usually has at least two other core subunits: subunit II is the primary electron acceptor; subunit III usually does not contain any cofactors, but in the case of cbb₃-type enzymes it is a diheme c-type cytochrome. While most bacterial enzymes consist of only 3–4 subunits, the mitochondrial enzyme is much more complex and contains 14 subunits.

Links to other databases:

BRENDA, EXPASY, Gene, GTD, KEGG, PDB, CAS registry number: 9001-16-5

References:

1.	Keilin, D. and Hartree, E.F. Cytochrome oxidase. Proc. R. Soc. Lond. B Biol. Sci. 125 (1938) 171–186.
2.	Keilin, D. and Hartree, E.F. Cytochrome and cytochrome oxidase. Proc. R. Soc. Lond. B Biol. Sci. 127 (1939) 167–191.
3.	Wainio, W.W., Eichel, B. and Gould, A. Ion and pH optimum for the oxidation of ferrocytochrome c by cytochrome c oxidase in air. J. Biol. Chem. 235 (1960) 1521–1525.
4.	Yonetani, T. Studies on cytochrome oxidase. II. Steady state properties. J. Biol. Chem. 235 (1960) 3138–3243. [PMID: 13787372]
5.	Yonetani, T. Studies on cytochrome oxidase. III. Improved purification and some properties. J. Biol. Chem. 236 (1961) 1680–1688. [PMID: 13787373]
6.	Henning, W., Vo, L., Albanese, J. and Hill, B.C. High-yield purification of cytochrome aa₃ and cytochrome caa3 oxidases from Bacillus subtilis plasma membranes. Biochem. J. 309 (1995) 279–283. [DOI] [PMID: 7619069]
7.	Keightley, J.A., Zimmermann, B.H., Mather, M.W., Springer, P., Pastuszyn, A., Lawrence, D.M. and Fee, J.A. Molecular genetic and protein chemical characterization of the cytochrome ba₃ from Thermus thermophilus HB8. J. Biol. Chem. 270 (1995) 20345–20358. [DOI] [PMID: 7657607]
8.	Ducluzeau, A.L., Ouchane, S. and Nitschke, W. The cbb3 oxidases are an ancient innovation of the domain bacteria. Mol. Biol. Evol. 25 (2008) 1158–1166. [DOI] [PMID: 18353797]

[EC 7.1.1.9 created 1961 as EC 1.9.3.1, modified 2000, transferred 2019 to EC 7.1.1.9, modified 2021]

7.4.2.13

Accepted name:

ABC-type tyrosine transporter

Reaction:

ATP + H₂O + L-tyrosinyl-[tyrosine-binding protein]_{[side 1]} = ADP + phosphate + L-tyrosine_{[side 2]} + [tyrosine-binding protein]_{[side 1]}

Systematic name:

ATP phosphohydrolase (ABC-type, L-tyrosine-importing)

Comments:

An ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. The enzyme, found in Clostridioides, interacts with an extracytoplasmic substrate binding lipoprotein and mediates the import of L-tyrosine. L-phenylalanine is also tranported however with lower efficiency.

Links to other databases: