The Enzyme Database

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Ron Caspi, Ture Damhus, Shinya Fushinobu, Julia Hauenstein, Antje Jäde, Ingrid Keseler, Masaaki Kotera, Andrew McDonald, Gerry Moss, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before 'EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.

Contents

EC 1.1.1.128 deleted
*EC 1.1.3.6 cholesterol oxidase
*EC 1.2.1.74 abieta-7,13-dien-18-al dehydrogenase
*EC 1.2.99.4 formaldehyde dismutase
*EC 1.4.1.13 glutamate synthase (NADPH)
*EC 1.4.7.1 glutamate synthase (ferredoxin)
EC 1.5.8.3 sarcosine dehydrogenase
EC 1.5.8.4 dimethylglycine dehydrogenase
EC 1.5.99.1 transferred
EC 1.5.99.2 transferred
EC 1.13.11.13 deleted
*EC 1.14.13.108 abieta-7,13-diene hydroxylase
*EC 1.14.13.109 abieta-7,13-dien-18-ol hydroxylase
EC 1.14.13.137 indole-2-monooxygenase
EC 1.14.13.138 indolin-2-one monooxygenase
EC 1.14.13.139 3-hydroxyindolin-2-one monooxygenase
EC 1.14.13.140 2-hydroxy-1,4-benzoxazin-3-one monooxygenase
EC 1.14.13.141 cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]
EC 1.14.13.142 3-ketosteroid 9α-monooxygenase
EC 1.14.13.143 ent-isokaurene C2/3-hydroxylase
EC 1.14.13.144 9β-pimara-7,15-diene oxidase
EC 1.14.13.145 ent-cassa-12,15-diene 11-hydroxylase
EC 1.14.13.146 taxoid 14β-hydroxylase
EC 1.14.13.147 taxoid 7β-hydroxylase
EC 1.14.13.148 trimethylamine monooxygenase
EC 1.14.13.149 phenylacetyl-CoA 1,2-epoxidase
EC 1.14.20.2 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase
*EC 1.16.1.9 ferric-chelate reductase (NADPH)
EC 2.1.1.239 L-olivosyl-oleandolide 3-O-methyltransferase
EC 2.1.1.240 trans-resveratrol di-O-methyltransferase
EC 2.1.1.241 2,4,7-trihydroxy-1,4-benzoxazin-3-one-glucoside 7-O-methyltransferase
EC 2.1.1.242 16S rRNA (guanine1516-N2)-methyltransferase
*EC 2.1.2.9 methionyl-tRNA formyltransferase
EC 2.3.1.197 dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose 3-N-acetyltransferase
EC 2.4.1.278 3-α-mycarosylerythronolide B desosaminyl transferase
*EC 2.5.1.95 xanthan ketal pyruvate transferase
EC 2.5.1.98 Rhizobium leguminosarum exopolysaccharide glucosyl ketal-pyruvate-transferase
EC 2.7.7.81 pseudaminic acid cytidylyltransferase
EC 3.1.7.10 (13E)-labda-7,13-dien-15-ol synthase
*EC 3.2.1.172 unsaturated rhamnogalacturonyl hydrolase
EC 3.4.19.14 leukotriene-C4 hydrolase
EC 3.5.4.32 8-oxoguanine deaminase
EC 3.6.1.30 deleted
EC 3.6.1.58 8-oxo-dGDP phosphatase
EC 3.6.1.59 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] diphosphatase
EC 3.6.1.60 diadenosine hexaphosphate hydrolase (AMP-forming)
EC 3.6.1.61 diadenosine hexaphosphate hydrolase (ATP-forming)
EC 3.6.1.62 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] hydrolase
EC 3.7.1.17 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
*EC 4.2.1.88 synephrine dehydratase
*EC 4.2.3.18 abieta-7,13-diene synthase
*EC 4.2.3.68 β-eudesmol synthase
*EC 4.2.3.69 (+)-α-barbatene synthase
EC 4.2.3.94 γ-curcumene synthase
EC 4.2.3.95 (-)-α-cuprenene synthase
EC 4.2.3.96 avermitilol synthase
EC 4.2.3.97 (-)-δ-cadinene synthase
EC 4.2.3.98 (+)-T-muurolol synthase
EC 4.2.3.99 labdatriene synthase
EC 4.2.3.100 bicyclogermacrene synthase
EC 4.2.3.101 7-epi-sesquithujene synthase
EC 4.2.3.102 sesquithujene synthase
EC 4.2.3.103 ent-isokaurene synthase
EC 4.2.3.104 α-humulene synthase
*EC 5.3.1.17 5-dehydro-4-deoxy-D-glucuronate isomerase
*EC 5.4.4.4 geraniol isomerase
EC 5.4.99.57 baruol synthase
*EC 5.5.1.16 halimadienyl-diphosphate synthase
*EC 6.3.2.14 enterobactin synthase
*EC 6.3.5.6 asparaginyl-tRNA synthase (glutamine-hydrolysing)

EC 1.1.1.128
Deleted entry: L-idonate 2-dehydrogenase. The reaction described is covered by EC 1.1.1.264.
[EC 1.1.1.128 created 1972, modified 1976, deleted 2012]
 
 
*EC 1.1.3.6
Accepted name: cholesterol oxidase
Reaction: cholesterol + O2 = cholest-5-en-3-one + H2O2
For diagram of cholesterol catabolism (rings A, B and C), click here
Other name(s): cholesterol- O2 oxidoreductase; 3β-hydroxy steroid oxidoreductase; 3β-hydroxysteroid:oxygen oxidoreductase
Systematic name: cholesterol:oxygen oxidoreductase
Comments: Contains FAD. Cholesterol oxidases are secreted bacterial bifunctional enzymes that catalyse the first two steps in the degradation of cholesterol. The enzyme catalyses the oxidation of the 3β-hydroxyl group to a keto group, and the isomerization of the double bond in the oxidized steroid ring system from the Δ5 position to Δ6 position (cf. EC 5.3.3.1, steroid Δ-isomerase).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9028-76-6
References:
1.  Richmond, W. Preparation and properties of a cholesterol oxidase from Nocardia sp. and its application to the enzymatic assay of total cholesterol in serum. Clin. Chem. 19 (1973) 1350–1356. [PMID: 4757363]
2.  Stadtman, T.C., Cherkes, A. and Anfinsen, C.B. Studies on the microbiological degradation of cholesterol. J. Biol. Chem. 206 (1954) 511–523. [PMID: 13143010]
3.  MacLachlan, J., Wotherspoon, A.T., Ansell, R.O. and Brooks, C.J. Cholesterol oxidase: sources, physical properties and analytical applications. J. Steroid Biochem. Mol. Biol. 72 (2000) 169–195. [DOI] [PMID: 10822008]
4.  Vrielink, A. Cholesterol oxidase: structure and function. Subcell. Biochem. 51 (2010) 137–158. [DOI] [PMID: 20213543]
[EC 1.1.3.6 created 1961, modified 1982, modified 2012]
 
 
*EC 1.2.1.74
Accepted name: abieta-7,13-dien-18-al dehydrogenase
Reaction: abieta-7,13-dien-18-al + H2O + NAD+ = abieta-7,13-dien-18-oate + NADH + H+
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here
Glossary: abieta-7,13-dien-18-al = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carbaldehyde
abieta-7,13-dien-18-oate = (1R,4aR,4bR,10aR)-7-isopropyl-1,4a-dimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene-1-carboxylate
Other name(s): abietadienal dehydrogenase (ambiguous)
Systematic name: abieta-7,13-dien-18-al:NAD+ oxidoreductase
Comments: Abietic acid is the principle component of conifer resin. This enzyme catalyses the last step of the pathway of abietic acid biosynthesis in Abies grandis (grand fir). The activity has been demonstrated in cell-free stem extracts of A. grandis, was present in the cytoplasm, and required NAD+ as cofactor [1]. The enzyme is expressed constitutively at a high level, and is not inducible by wounding of the plant tissue [2].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Funk, C. and Croteau, R. Diterpenoid resin acid biosynthesis in conifers: characterization of two cytochrome P450-dependent monooxygenases and an aldehyde dehydrogenase involved in abietic acid biosynthesis. Arch. Biochem. Biophys. 308 (1994) 258–266. [DOI] [PMID: 8311462]
2.  Funk, C., Lewinsohn, E., Vogel, B.S., Steele, C.L. and Croteau, R. Regulation of oleoresinosis in grand fir (Abies grandis) (coordinate induction of monoterpene and diterpene cyclases and two cytochrome P450-dependent diterpenoid hydroxylases by stem wounding). Plant Physiol. 106 (1994) 999–1005. [PMID: 12232380]
[EC 1.2.1.74 created 2009, modified 2012]
 
 
*EC 1.2.99.4
Transferred entry: formaldehyde dismutase. Now EC 1.2.98.1, formaldehyde dismutase.
[EC 1.2.99.4 created 1986, modified 2012, deleted 2015]
 
 
*EC 1.4.1.13
Accepted name: glutamate synthase (NADPH)
Reaction: 2 L-glutamate + NADP+ = L-glutamine + 2-oxoglutarate + NADPH + H+ (overall reaction)
(1a) L-glutamate + NH3 = L-glutamine + H2O
(1b) L-glutamate + NADP+ + H2O = NH3 + 2-oxoglutarate + NADPH + H+
For diagram of glutamic acid biosynthesis, click here
Other name(s): glutamate (reduced nicotinamide adenine dinucleotide phosphate) synthase; L-glutamate synthase; L-glutamate synthetase; glutamate synthetase (NADP); NADPH-dependent glutamate synthase; glutamine-ketoglutaric aminotransferase; NADPH-glutamate synthase; NADPH-linked glutamate synthase; glutamine amide-2-oxoglutarate aminotransferase (oxidoreductase, NADP); L-glutamine:2-oxoglutarate aminotransferase, NADPH oxidizing; GOGAT
Systematic name: L-glutamate:NADP+ oxidoreductase (transaminating)
Comments: Binds FMN, FAD, 2 [4Fe-4S] clusters and 1 [3Fe-4S] cluster. The reaction takes place in the direction of L-glutamate production. The protein is composed of two subunits, α and β. The α subunit is composed of two domains, one hydrolysing L-glutamine to NH3 and L-glutamate (cf. EC 3.5.1.2, glutaminase), the other combining the produced NH3 with 2-oxoglutarate to produce a second molecule of L-glutamate (cf. EC 1.4.1.4, glutamate dehydrogenase [NADP+]). The β subunit transfers electrons from the cosubstrate. The NH3 is channeled within the α subunit through a 31 Å channel. The chanelling is very efficient and in the intact α-β complex ammonia is produced only within the complex. In the absence of the β subunit, coupling between the two domains of the α subunit is compromised and some ammonium can leak.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37213-53-9
References:
1.  Miller, R.E. and Stadtman, E.R. Glutamate synthase from Escherichia coli. An iron-sulfide flavoprotein. J. Biol. Chem. 247 (1972) 7407–7419. [PMID: 4565085]
2.  Tempest, D.W., Meers, J.L. and Brown, C.M. Synthesis of glutamate in Aerobacter aerogenes by a hitherto unknown route. Biochem. J. 117 (1970) 405–407. [PMID: 5420057]
3.  Vanoni, M.A. and Curti, B. Glutamate synthase: a complex iron-sulfur flavoprotein. Cell. Mol. Life Sci. 55 (1999) 617–638. [DOI] [PMID: 10357231]
4.  Ravasio, S., Curti, B. and Vanoni, M.A. Determination of the midpoint potential of the FAD and FMN flavin cofactors and of the 3Fe-4S cluster of glutamate synthase. Biochemistry 40 (2001) 5533–5541. [DOI] [PMID: 11331018]
[EC 1.4.1.13 created 1972 as EC 2.6.1.53, transferred 1976 to EC 1.4.1.13, modified 2001, modified 2012]
 
 
*EC 1.4.7.1
Accepted name: glutamate synthase (ferredoxin)
Reaction: 2 L-glutamate + 2 oxidized ferredoxin = L-glutamine + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+ (overall reaction)
(1a) L-glutamate + NH3 = L-glutamine + H2O
(1b) L-glutamate + 2 oxidized ferredoxin + H2O = NH3 + 2-oxoglutarate + 2 reduced ferredoxin + 2 H+
For diagram of glutamic acid biosynthesis, click here
Other name(s): ferredoxin-dependent glutamate synthase; ferredoxin-glutamate synthase; glutamate synthase (ferredoxin-dependent)
Systematic name: L-glutamate:ferredoxin oxidoreductase (transaminating)
Comments: Binds a [3Fe-4S] cluster as well as FAD and FMN. The protein is composed of two domains, one hydrolysing L-glutamine to NH3 and L-glutamate (cf. EC 3.5.1.2, glutaminase), the other combining the produced NH3 with 2-oxoglutarate to produce a second molecule of L-glutamate. The NH3 is channeled through a 24 Å channel in the active protein. No hydrolysis of glutamine takes place without ferredoxin and 2-oxoglutarate being bound to the protein [5,6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 62213-56-3
References:
1.  Galván, F., Márquez, A.J. and Vega, J.M. Purification and molecular properties of ferredoxin-glutamate synthase from Chlamydomonas reinhardii. Planta 162 (1984) 180–187. [PMID: 24254054]
2.  Lea, P.J. and Miflin, B.J. Alternative route for nitrogen assimilation in higher plants. Nature (Lond.) 251 (1974) 614–616. [PMID: 4423889]
3.  Ravasio, S., Dossena, L., Martin-Figueroa, E., Florencio, F.J., Mattevi, A., Morandi, P., Curti, B. and Vanoni, M.A. Properties of the recombinant ferredoxin-dependent glutamate synthase of Synechocystis PCC6803. Comparison with the Azospirillum brasilense NADPH-dependent enzyme and its isolated α subunit. Biochemistry 41 (2002) 8120–8133. [DOI] [PMID: 12069605]
4.  Navarro, F., Martin-Figueroa, E., Candau, P. and Florencio, F.J. Ferredoxin-dependent iron-sulfur flavoprotein glutamate synthase (GlsF) from the cyanobacterium Synechocystis sp. PCC 6803: expression and assembly in Escherichia coli. Arch. Biochem. Biophys. 379 (2000) 267–276. [DOI] [PMID: 10898944]
5.  van den Heuvel, R.H., Ferrari, D., Bossi, R.T., Ravasio, S., Curti, B., Vanoni, M.A., Florencio, F.J. and Mattevi, A. Structural studies on the synchronization of catalytic centers in glutamate synthase. J. Biol. Chem. 277 (2002) 24579–24583. [DOI] [PMID: 11967268]
6.  van den Heuvel, R.H., Svergun, D.I., Petoukhov, M.V., Coda, A., Curti, B., Ravasio, S., Vanoni, M.A. and Mattevi, A. The active conformation of glutamate synthase and its binding to ferredoxin. J. Mol. Biol. 330 (2003) 113–128. [DOI] [PMID: 12818206]
[EC 1.4.7.1 created 1976, modified 2012]
 
 
EC 1.5.8.3
Accepted name: sarcosine dehydrogenase
Reaction: sarcosine + 5,6,7,8-tetrahydrofolate + oxidized [electron-transfer flavoprotein] = glycine + 5,10-methylenetetrahydrofolate + reduced [electron-transfer flavoprotein]
Other name(s): sarcosine N-demethylase; monomethylglycine dehydrogenase; sarcosine:(acceptor) oxidoreductase (demethylating); sarcosine:electron-transfer flavoprotein oxidoreductase (demethylating)
Systematic name: sarcosine, 5,6,7,8-tetrahydrofolate:electron-transferflavoprotein oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
Comments: A flavoprotein (FMN) found in eukaryotes. In the absence of tetrahydrofolate the enzyme produces formaldehyde. cf. EC 1.5.3.1, sarcosine oxidase (formaldehyde-forming), and EC 1.5.3.24, sarcosine oxidase (5,10-methylenetetrahydrofolate-forming).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 37228-65-2, 93389-49-2
References:
1.  Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177–183. [DOI] [PMID: 13716069]
2.  Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94–98. [DOI] [PMID: 13895406]
3.  Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Flavoprotein nature and enzymatic properties of the purified proteins. J. Biol. Chem. 256 (1981) 4109–4115. [DOI] [PMID: 6163778]
4.  Steenkamp, D.J. and Husain, M. The effect of tetrahydrofolate on the reduction of electron transfer flavoprotein by sarcosine and dimethylglycine dehydrogenases. Biochem. J. 203 (1982) 707–715. [DOI] [PMID: 6180732]
[EC 1.5.8.3 created 1972 as EC 1.5.99.1, transferred 2012 to EC 1.5.8.3, modified 2022]
 
 
EC 1.5.8.4
Accepted name: dimethylglycine dehydrogenase
Reaction: N,N-dimethylglycine + 5,6,7,8-tetrahydrofolate + electron-transfer flavoprotein = sarcosine + 5,10-methylenetetrahydrofolate + reduced electron-transfer flavoprotein
Glossary: sarcosine = N-methylglycine
Other name(s): N,N-dimethylglycine oxidase; N,N-dimethylglycine:(acceptor) oxidoreductase (demethylating); Me2GlyDH; N,N-dimethylglycine:electron-transfer flavoprotein oxidoreductase (demethylating)
Systematic name: N,N-dimethylglycine,5,6,7,8-tetrahydrofolate:electron-transferflavoprotein oxidoreductase (demethylating,5,10-methylenetetrahydrofolate-forming)
Comments: A flavoprotein, containing a histidyl(Nπ)-(8α)FAD linkage at position 91 in the human protein. An imine intermediate is channeled from the FAD binding site to the 5,6,7,8-tetrahydrofolate binding site through a 40 Å tunnel [5,8,9]. In the absence of 5,6,7,8-tetrahydrofolate the enzyme forms formaldehyde [5,9].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37256-30-7
References:
1.  Frisell, W.R. and MacKenzie, C.G. Separation and purification of sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 237 (1962) 94–98. [DOI] [PMID: 13895406]
2.  Hoskins, D.D. and MacKenzie, C.G. Solubilization and electron transfer flavoprotein requirement of mitochondrial sarcosine dehydrogenase and dimethylglycine dehydrogenase. J. Biol. Chem. 236 (1961) 177–183. [DOI] [PMID: 13716069]
3.  Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Purification and folate-binding characteristics. J. Biol. Chem. 256 (1981) 4102–4108. [PMID: 6163777]
4.  Wittwer, A.J. and Wagner, C. Identification of the folate-binding proteins of rat liver mitochondria as dimethylglycine dehydrogenase and sarcosine dehydrogenase. Flavoprotein nature and enzymatic properties of the purified proteins. J. Biol. Chem. 256 (1981) 4109–4115. [DOI] [PMID: 6163778]
5.  Porter, D.H., Cook, R.J. and Wagner, C. Enzymatic properties of dimethylglycine dehydrogenase and sarcosine dehydrogenase from rat liver. Arch. Biochem. Biophys. 243 (1985) 396–407. [DOI] [PMID: 2417560]
6.  Brizio, C., Brandsch, R., Bufano, D., Pochini, L., Indiveri, C. and Barile, M. Over-expression in Escherichia coli, functional characterization and refolding of rat dimethylglycine dehydrogenase. Protein Expr. Purif. 37 (2004) 434–442. [DOI] [PMID: 15358367]
7.  Brizio, C., Brandsch, R., Douka, M., Wait, R. and Barile, M. The purified recombinant precursor of rat mitochondrial dimethylglycine dehydrogenase binds FAD via an autocatalytic reaction. Int. J. Biol. Macromol. 42 (2008) 455–462. [DOI] [PMID: 18423846]
8.  Luka, Z., Pakhomova, S., Loukachevitch, L.V., Newcomer, M.E. and Wagner, C. Folate in demethylation: the crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Biochem. Biophys. Res. Commun. 449 (2014) 392–398. [DOI] [PMID: 24858690]
9.  Augustin, P., Hromic, A., Pavkov-Keller, T., Gruber, K. and Macheroux, P. Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant. FEBS J. 283 (2016) 3587–3603. [DOI] [PMID: 27486859]
[EC 1.5.8.4 created 1972 as EC 1.5.99.2, transferred 2012 to EC 1.5.8.4, modified 2017]
 
 
EC 1.5.99.1
Transferred entry: sarcosine dehydrogenase. Now EC 1.5.8.3, sarcosine dehydrogenase
[EC 1.5.99.1 created 1972, deleted 2012]
 
 
EC 1.5.99.2
Transferred entry: dimethylglycine dehydrogenase. Now EC 1.5.8.4, dimethylglycine dehydrogenase
[EC 1.5.99.2 created 1972, deleted 2012]
 
 
EC 1.13.11.13
Deleted entry: ascorbate 2,3-dioxygenase. The activity is the sum of several enzymatic and spontaneous reactions
[EC 1.13.11.13 created 1972, deleted 2012]
 
 
*EC 1.14.13.108
Transferred entry: abieta-7,13-diene hydroxylase. Now EC 1.14.14.144, abieta-7,13-diene hydroxylase
[EC 1.14.13.108 created 2009, modified 2012, deleted 2018]
 
 
*EC 1.14.13.109
Transferred entry: abieta-7,13-dien-18-ol hydroxylase. Now EC 1.14.14.145, abieta-7,13-dien-18-ol hydroxylase
[EC 1.14.13.109 created 2009, modified 2012, deleted 2018]
 
 
EC 1.14.13.137
Transferred entry: indole-2-monooxygenase. Now EC 1.14.14.153, indole-2-monooxygenase
[EC 1.14.13.137 created 2012, deleted 2018]
 
 
EC 1.14.13.138
Transferred entry: indolin-2-one monooxygenase. Now EC 1.14.14.157, indolin-2-one monooxygenase
[EC 1.14.13.138 created 2012, deleted 2018]
 
 
EC 1.14.13.139
Transferred entry: 3-hydroxyindolin-2-one monooxygenase. Now EC 1.14.14.109, 3-hydroxyindolin-2-one monooxygenase
[EC 1.14.13.139 created 2012, deleted 2018]
 
 
EC 1.14.13.140
Transferred entry: 2-hydroxy-1,4-benzoxazin-3-one monooxygenase. Now EC 1.14.14.110, 2-hydroxy-1,4-benzoxazin-3-one monooxygenase.
[EC 1.14.13.140 created 2012, deleted 2018]
 
 
EC 1.14.13.141
Transferred entry: cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]. Now EC 1.14.15.29, cholest-4-en-3-one 26-monooxygenase [(25S)-3-oxocholest-4-en-26-oate forming]..
[EC 1.14.13.141 created 2012, modified 2016, deleted 2018]
 
 
EC 1.14.13.142
Transferred entry: 3-ketosteroid 9α-monooxygenase. Now EC 1.14.15.30, 3-ketosteroid 9α-monooxygenase
[EC 1.14.13.142 created 2012, deleted 2018]
 
 
EC 1.14.13.143
Transferred entry: ent-isokaurene C2-hydroxylase. Now EC 1.14.14.76 ent-isokaurene C2/C3-hydroxylase
[EC 1.14.13.143 created 2012, deleted 2018]
 
 
EC 1.14.13.144
Transferred entry: 9β-pimara-7,15-diene oxidase. Now EC 1.14.14.111, 9β-pimara-7,15-diene oxidase.
[EC 1.14.13.144 created 2012, deleted 2018]
 
 
EC 1.14.13.145
Transferred entry: ent-cassa-12,15-diene 11-hydroxylase. Now EC 1.14.14.112, ent-cassa-12,15-diene 11-hydroxylase.
[EC 1.14.13.145 created 2012, deleted 2018]
 
 
EC 1.14.13.146
Accepted name: taxoid 14β-hydroxylase
Reaction: 10β-hydroxytaxa-4(20),11-dien-5α-yl acetate + O2 + NADPH + H+ = 10β,14β-dihydroxytaxa-4(20),11-dien-5α-yl acetate + NADP+ + H2O
For diagram of taxadiene hydroxylation, click here
Systematic name: 10β-hydroxytaxa-4(20),11-dien-5α-yl-acetate,NADPH:oxygen 14-oxidoreductase
Comments: Requires cytochrome P-450. From the yew Taxus cuspidata. Also acts on taxa-4(20),11-dien-5α-yl acetate.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Jennewein, S., Rithner, C.D., Williams, R.M. and Croteau, R. Taxoid metabolism: Taxoid 14β-hydroxylase is a cytochrome P450-dependent monooxygenase. Arch. Biochem. Biophys. 413 (2003) 262–270. [DOI] [PMID: 12729625]
[EC 1.14.13.146 created 2012]
 
 
EC 1.14.13.147
Transferred entry: taxoid 7β-hydroxylase. Now EC 1.14.14.182, taxoid 7β-hydroxylase
[EC 1.14.13.147 created 2012, deleted 2022]
 
 
EC 1.14.13.148
Accepted name: trimethylamine monooxygenase
Reaction: N,N,N-trimethylamine + NADPH + H+ + O2 = N,N,N-trimethylamine N-oxide + NADP+ + H2O
Other name(s): flavin-containing monooxygenase 3; FMO3; tmm (gene name)
Systematic name: N,N,N-trimethylamine,NADPH:oxygen oxidoreductase (N-oxide-forming)
Comments: A flavoprotein. The bacterial enzyme enables bacteria to use trimethylamine as the sole source of carbon and energy [1,4]. The mammalian enzyme is involved in detoxification of trimethylamine. Mutations in the human enzyme cause the inheritable disease known as trimethylaminuria (fish odor syndrome) [2,3].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Large, P.J., Boulton, C.A. and Crabbe, M.J. The reduced nicotinamide-adenine dinucleotide phosphate- and oxygen-dependent N-oxygenation of trimethylamine by Pseudomonas aminovorans. Biochem. J. 128 (1972) 137P–138P. [PMID: 4404764]
2.  Dolphin, C.T., Riley, J.H., Smith, R.L., Shephard, E.A. and Phillips, I.R. Structural organization of the human flavin-containing monooxygenase 3 gene (FMO3), the favored candidate for fish-odor syndrome, determined directly from genomic DNA. Genomics 46 (1997) 260–267. [DOI] [PMID: 9417913]
3.  Treacy, E.P., Akerman, B.R., Chow, L.M., Youil, R., Bibeau, C., Lin, J., Bruce, A.G., Knight, M., Danks, D.M., Cashman, J.R. and Forrest, S.M. Mutations of the flavin-containing monooxygenase gene (FMO3) cause trimethylaminuria, a defect in detoxication. Hum. Mol. Genet. 7 (1998) 839–845. [DOI] [PMID: 9536088]
4.  Chen, Y., Patel, N.A., Crombie, A., Scrivens, J.H. and Murrell, J.C. Bacterial flavin-containing monooxygenase is trimethylamine monooxygenase. Proc. Natl. Acad. Sci. USA 108 (2011) 17791–17796. [DOI] [PMID: 22006322]
[EC 1.14.13.148 created 2012]
 
 
EC 1.14.13.149
Accepted name: phenylacetyl-CoA 1,2-epoxidase
Reaction: phenylacetyl-CoA + NADPH + H+ + O2 = 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA + NADP+ + H2O
For diagram of aerobic phenylacetate catabolism, click here
Glossary: 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA = 2-{7-oxabicyclo[4.1.0]hepta-2,4-dien-1-yl}acetyl-CoA
Other name(s): ring 1,2-phenylacetyl-CoA epoxidase; phenylacetyl-CoA monooxygenase; PaaAC; PaaABC(D)E
Systematic name: phenylacetyl-CoA:oxygen oxidoreductase (1,2-epoxidizing)
Comments: Part of the aerobic pathway of phenylacetate catabolism in Escherichia coli and Pseudomonas putida.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB
References:
1.  Teufel, R., Mascaraque, V., Ismail, W., Voss, M., Perera, J., Eisenreich, W., Haehnel, W. and Fuchs, G. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. USA 107 (2010) 14390–14395. [DOI] [PMID: 20660314]
2.  Grishin, A.M., Ajamian, E., Zhang, L. and Cygler, M. Crystallization and preliminary X-ray analysis of PaaAC, the main component of the hydroxylase of the Escherichia coli phenylacetyl-coenzyme A oxygenase complex. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (2010) 1045–1049. [DOI] [PMID: 20823522]
3.  Grishin, A.M., Ajamian, E., Tao, L., Zhang, L., Menard, R. and Cygler, M. Structural and functional studies of the Escherichia coli phenylacetyl-CoA monooxygenase complex. J. Biol. Chem. 286 (2011) 10735–10743. [DOI] [PMID: 21247899]
[EC 1.14.13.149 created 2012]
 
 
EC 1.14.20.2
Transferred entry: 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase. Now EC 1.14.11.59, 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside dioxygenase
[EC 1.14.20.2 created 2012, deleted 2018]
 
 
*EC 1.16.1.9
Accepted name: ferric-chelate reductase (NADPH)
Reaction: 2 Fe(II)-siderophore + NADP+ + H+ = 2 Fe(III)-siderophore + NADPH
Other name(s): ferric chelate reductase (ambiguous); iron chelate reductase (ambiguous); NADPH:Fe3+-EDTA reductase; NADPH-dependent ferric reductase; yqjH (gene name); Fe(II):NADP+ oxidoreductase
Systematic name: Fe(II)-siderophore:NADP+ oxidoreductase
Comments: Contains FAD. The enzyme, which is widespread among bacteria, catalyses the reduction of ferric iron bound to a variety of iron chelators (siderophores), including ferric triscatecholates and ferric dicitrate, resulting in the release of ferrous iron. The enzyme from the bacterium Escherichia coli has the highest efficiency with the hydrolysed ferric enterobactin complex ferric N-(2,3-dihydroxybenzoyl)-L-serine [3]. cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.10, ferric-chelate reductase [NAD(P)H].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 120720-17-4
References:
1.  Bamford, V.A., Armour, M., Mitchell, S.A., Cartron, M., Andrews, S.C. and Watson, K.A. Preliminary X-ray diffraction analysis of YqjH from Escherichia coli: a putative cytoplasmic ferri-siderophore reductase. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 792–796. [DOI] [PMID: 18765906]
2.  Wang, S., Wu, Y. and Outten, F.W. Fur and the novel regulator YqjI control transcription of the ferric reductase gene yqjH in Escherichia coli. J. Bacteriol. 193 (2011) 563–574. [DOI] [PMID: 21097627]
3.  Miethke, M., Hou, J. and Marahiel, M.A. The siderophore-interacting protein YqjH acts as a ferric reductase in different iron assimilation pathways of Escherichia coli. Biochemistry 50 (2011) 10951–10964. [DOI] [PMID: 22098718]
[EC 1.16.1.9 created 1992 as EC 1.6.99.13, transferred 2002 to EC 1.16.1.7, transferred 2011 to EC 1.16.1.9, modified 2012, modified 2014]
 
 
EC 2.1.1.239
Accepted name: L-olivosyl-oleandolide 3-O-methyltransferase
Reaction: S-adenosyl-L-methionine + L-olivosyl-oleandolide = S-adenosyl-L-homocysteine + L-oleandrosyl-oleandolide
Other name(s): OleY
Systematic name: S-adenosyl-L-methionine:L-olivosyl-oleandolide B 3-O-methyltransferase
Comments: The enzyme is involved in the biosynthesis of the macrolide antibiotic oleandomycin in Streptomyces antibioticus. It can also act on other monoglycosylated macrolactones, including L-rhamnosyl-erythronolide B and L-mycarosyl-erythronolide B.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Rodriguez, L., Rodriguez, D., Olano, C., Brana, A.F., Mendez, C. and Salas, J.A. Functional analysis of OleY L-oleandrosyl 3-O-methyltransferase of the oleandomycin biosynthetic pathway in Streptomyces antibioticus. J. Bacteriol. 183 (2001) 5358–5363. [DOI] [PMID: 11514520]
[EC 2.1.1.239 created 2012]
 
 
EC 2.1.1.240
Accepted name: trans-resveratrol di-O-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + trans-resveratrol = 2 S-adenosyl-L-homocysteine + pterostilbene (overall reaction)
(1a) S-adenosyl-L-methionine + trans-resveratrol = S-adenosyl-L-homocysteine + 3-methoxy-4′,5-dihydroxy-trans-stilbene
(1b) S-adenosyl-L-methionine + 3-methoxy-4′,5-dihydroxy-trans-stilbene = S-adenosyl-L-homocysteine + pterostilbene
For diagram of chalcone and stilbene biosynthesis, click here
Glossary: 3-methoxy-4′,5-dihydroxy-trans-stilbene = resveratrol monomethyl ether
pterostilbene = 3,5-dimethoxy-4′-hydroxy-trans-stilbene
trans-resveratrol = 3,4′,5-trihydroxy-trans-stilbene
Other name(s): ROMT; resveratrol O-methyltransferase; pterostilbene synthase
Systematic name: S-adenosyl-L-methionine:trans-resveratrol 3,5-O-dimethyltransferase
Comments: The enzyme catalyses the biosynthesis of pterostilbene from resveratrol.
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Schmidlin, L., Poutaraud, A., Claudel, P., Mestre, P., Prado, E., Santos-Rosa, M., Wiedemann-Merdinoglu, S., Karst, F., Merdinoglu, D. and Hugueney, P. A stress-inducible resveratrol O-methyltransferase involved in the biosynthesis of pterostilbene in grapevine. Plant Physiol. 148 (2008) 1630–1639. [DOI] [PMID: 18799660]
[EC 2.1.1.240 created 2012]
 
 
EC 2.1.1.241
Accepted name: 2,4,7-trihydroxy-1,4-benzoxazin-3-one-glucoside 7-O-methyltransferase
Reaction: S-adenosyl-L-methionine + (2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = S-adenosyl-L-homocysteine + (2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside
For diagram of benzoxazinone biosynthesis, click here
Glossary: (2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = TRIMBOA β-D-glucoside
(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside = DIMBOA β-D-glucoside
Other name(s): BX7 (gene name); OMT BX7
Systematic name: S-adenosyl-L-methionine:(2R)-4,7-dihydroxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl β-D-glucopyranoside 7-O-methyltransferase
Comments: The enzyme is involved in the biosynthesis of the protective and allelophatic benzoxazinoid DIMBOA [(2R)-4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin] in some plants, most commonly from the family of Poaceae (grasses).
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Jonczyk, R., Schmidt, H., Osterrieder, A., Fiesselmann, A., Schullehner, K., Haslbeck, M., Sicker, D., Hofmann, D., Yalpani, N., Simmons, C., Frey, M. and Gierl, A. Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: characterization of Bx6 and Bx7. Plant Physiol. 146 (2008) 1053–1063. [DOI] [PMID: 18192444]
[EC 2.1.1.241 created 2012]
 
 
EC 2.1.1.242
Accepted name: 16S rRNA (guanine1516-N2)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine1516 in 16S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine1516 in 16S rRNA
Other name(s): yhiQ (gene name); rsmJ (gene name); m2G1516 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine1516-N2)-methyltransferase
Comments: The enzyme specifically methylates guanine1516 at N2 in 16S rRNA.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Basturea, G.N., Dague, D.R., Deutscher, M.P. and Rudd, K.E. YhiQ Is RsmJ, the Methyltransferase Responsible for Methylation of G1516 in 16S rRNA of E. coli. J. Mol. Biol. 415 (2012) 16–21. [DOI] [PMID: 22079366]
[EC 2.1.1.242 created 2012]
 
 
*EC 2.1.2.9
Accepted name: methionyl-tRNA formyltransferase
Reaction: 10-formyltetrahydrofolate + L-methionyl-tRNAfMet = tetrahydrofolate + N-formylmethionyl-tRNAfMet
For diagram of C1 metabolism, click here
Other name(s): N10-formyltetrahydrofolic-methionyl-transfer ribonucleic transformylase; formylmethionyl-transfer ribonucleic synthetase; methionyl ribonucleic formyltransferase; methionyl-tRNA Met formyltransferase; methionyl-tRNA transformylase; methionyl-transfer RNA transformylase; methionyl-transfer ribonucleate methyltransferase; methionyl-transfer ribonucleic transformylase
Systematic name: 10-formyltetrahydrofolate:L-methionyl-tRNA N-formyltransferase
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 9015-76-3
References:
1.  Dickerman, H.W., Steers, E., Jr., Redfield, B.G. and Weissbach, H. Methionyl soluble ribonucleic acid transformylase. I. Purification and partial characterization. J. Biol. Chem. 242 (1967) 1522–1525. [PMID: 5337045]
[EC 2.1.2.9 created 1972, modified 2002, modified 2012]
 
 
EC 2.3.1.197
Accepted name: dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose 3-N-acetyltransferase
Reaction: acetyl-CoA + dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose = CoA + dTDP-3-acetamido-3,6-dideoxy-α-D-galactopyranose
For diagram of dTDP-Fuc3NAc and dTDP-Fuc4NAc biosynthesis, click here
Other name(s): FdtC; dTDP-D-Fucp3N acetylase
Systematic name: acetyl-CoA:dTDP-3-amino-3,6-dideoxy-α-D-galactopyranose 3-N-acetyltransferase
Comments: The product, dTDP-3-acetamido-3,6-dideoxy-α-D-galactose, is a component of the glycan chain of the crystalline bacterial cell surface layer protein (S-layer glycoprotein) of Aneurinibacillus thermoaerophilus.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Pfoestl, A., Hofinger, A., Kosma, P. and Messner, P. Biosynthesis of dTDP-3-acetamido-3,6-dideoxy-α-D-galactose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 278 (2003) 26410–26417. [DOI] [PMID: 12740380]
[EC 2.3.1.197 created 2012]
 
 
EC 2.4.1.278
Accepted name: 3-α-mycarosylerythronolide B desosaminyl transferase
Reaction: dTDP-D-desosamine + 3-α-L-mycarosylerythronolide B = dTDP + erythromycin D
For diagram of erythromycin biosynthesis, click here
Glossary: dTDP-D-desosamine = dTDP-3,4,6-trideoxy-3-(dimethylamino)-α-D-xylo-hexopyranose
erythromycin D = (3R,4S,5S,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-7,12-dihydroxy-6-[3,4,6-trideoxy-3-(dimethylamino)-β-D-xylo-hexopyranosyloxy]-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione
3-O-α-mycarosylerythronolide B = (3R,4S,5R,6R,7R,9R,11R,12S,13R,14R)-4-(2,6-dideoxy-3-C-methyl-α-L-ribo-hexopyranosyloxy)-14-ethyl-6,7,12-trihydroxy-3,5,7,9,11,13-hexamethyloxacyclotetradecane-2,10-dione
Other name(s): EryCIII; dTDP-3-dimethylamino-4,6-dideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-4,6-dideoxy-α-D-glucosyltransferase
Systematic name: dTDP-3-dimethylamino-3,4,6-trideoxy-α-D-glucopyranose:3-α-mycarosylerythronolide B 3-dimethylamino-3,4,6-trideoxy-β-D-glucosyltransferase
Comments: The enzyme is involved in erythromycin biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Yuan, Y., Chung, H.S., Leimkuhler, C., Walsh, C.T., Kahne, D. and Walker, S. In vitro reconstitution of EryCIII activity for the preparation of unnatural macrolides. J. Am. Chem. Soc. 127 (2005) 14128–14129. [DOI] [PMID: 16218575]
2.  Lee, H.Y., Chung, H.S., Hang, C., Khosla, C., Walsh, C.T., Kahne, D. and Walker, S. Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway. J. Am. Chem. Soc. 126 (2004) 9924–9925. [DOI] [PMID: 15303858]
3.  Moncrieffe, M.C., Fernandez, M.J., Spiteller, D., Matsumura, H., Gay, N.J., Luisi, B.F. and Leadlay, P.F. Structure of the glycosyltransferase EryCIII in complex with its activating P450 homologue EryCII. J. Mol. Biol. 415 (2012) 92–101. [DOI] [PMID: 22056329]
[EC 2.4.1.278 created 2012, modified 2014]
 
 
*EC 2.5.1.95
Accepted name: xanthan ketal pyruvate transferase
Reaction: phosphoenolpyruvate + D-Man-β-(1→4)-D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol = 4,6-CH3(COO-)C-D-Man-β-(1→4)-D-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol + phosphate
For diagram of xanthan biosynthesis, click here
Other name(s): KPT
Systematic name: phosphoenolpyruvate:D-Man-β-(1→4)-GlcA-β-(1→2)-D-Man-α-(1→3)-D-Glc-β-(1→4)-D-Glc-α-1-diphospho-ditrans,octacis-undecaprenol 4,6-O-(1-carboxyethan-1,1-diyl)transferase
Comments: Involved in the biosynthesis of the polysaccharide xanthan. 30-40% of the terminal mannose residues of xanthan have a 4,6-O-(1-carboxyethan-1,1-diyl) ketal group. It also acts on the 6-O-acetyl derivative of the inner mannose unit.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Marzocca, M.P., Harding, N.E., Petroni, E.A., Cleary, J.M. and Ielpi, L. Location and cloning of the ketal pyruvate transferase gene of Xanthomonas campestris. J. Bacteriol. 173 (1991) 7519–7524. [DOI] [PMID: 1657892]
[EC 2.5.1.95 created 2011, modified 2012]
 
 
EC 2.5.1.98
Accepted name: Rhizobium leguminosarum exopolysaccharide glucosyl ketal-pyruvate-transferase
Reaction: phosphoenolpyruvate + [β-D-GlcA-(1→4)-2-O-Ac-β-D-GlcA-(1→4)-β-D-Glc-(1→4)-[3-O-(CH3CH(OH)CH2C(O))-4,6-CH3(COO-)C-β-D-Gal-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→6)]-2(or 3)-O-Ac-α-D-Glc-(1→6)]n = [β-D-GlcA-(1→4)-2-O-Ac-β-D-GlcA-(1→4)-β-D-Glc-(1→4)-[3-O-(CH3CH(OH)CH2C(O))-4,6-CH3(COO-)C-β-D-Gal-(1→3)-4,6-CH3(COO-)C-β-D-Glc-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→6)]-2(or 3)-O-Ac-α-D-Glc-(1→6)]n + phosphate
Other name(s): PssM; phosphoenolpyruvate:[D-GlcA-β-(1→4)-2-O-Ac-D-GlcA-β-(1→4)-D-Glc-β-(1→4)-[3-O-CH3-CH2CH(OH)C(O)-D-Gal-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→4)-D-Glc-β-(1→6)]-2(or 3)-O-Ac-D-Glc-α-(1→6)]n 4,6-O-(1-carboxyethan-1,1-diyl)transferase
Systematic name: phosphoenolpyruvate:[β-D-GlcA-(1→4)-2-O-Ac-β-D-GlcA-(1→4)-β-D-Glc-(1→4)-[3-O-CH3-CH2CH(OH)C(O)-4,6-CH3(COO-)C-β-D-Gal-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→4)-β-D-Glc-(1→6)]-2(or 3)-O-Ac-α-D-Glc-(1→6)]n 4,6-O-(1-carboxyethan-1,1-diyl)transferase
Comments: The enzyme is responsible for pyruvylation of the subterminal glucose in the acidic octasaccharide repeating unit of the exopolysaccharide of Rhizobium leguminosarum (bv. viciae strain VF39) which is necessary to establish nitrogen-fixing symbiosis with Pisum sativum, Vicia faba, and Vicia sativa.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Ivashina, T.V., Fedorova, E.E., Ashina, N.P., Kalinchuk, N.A., Druzhinina, T.N., Shashkov, A.S., Shibaev, V.N. and Ksenzenko, V.N. Mutation in the pssM gene encoding ketal pyruvate transferase leads to disruption of Rhizobium leguminosarum bv. viciae—Pisum sativum symbiosis. J. Appl. Microbiol. 109 (2010) 731–742. [DOI] [PMID: 20233262]
[EC 2.5.1.98 created 2012, modified 2018]
 
 
EC 2.7.7.81
Accepted name: pseudaminic acid cytidylyltransferase
Reaction: CTP + 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid = diphosphate + CMP-5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid
Glossary: 5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid = pseudaminic acid
Other name(s): PseF
Systematic name: CTP:5,7-diacetamido-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-nonulosonic acid cytidylyltransferase
Comments: Mg2+ is required for activity.
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C–14C. [DOI] [PMID: 16751642]
[EC 2.7.7.81 created 2012]
 
 
EC 3.1.7.10
Accepted name: (13E)-labda-7,13-dien-15-ol synthase
Reaction: geranylgeranyl diphosphate + H2O = (13E)-labda-7,13-dien-15-ol + diphosphate
For diagram of abietadiene, abietate, isopimaradiene, labdadienol and sclareol biosynthesis, click here and for diagram of sclareol and (13e)-labda-7,13-dien-15-ol biosynthesis, click here
Other name(s): labda-7,13E-dien-15-ol synthase
Systematic name: geranylgeranyl-diphosphate diphosphohydrolase [(13E)-labda-7,13-dien-15-ol-forming]
Comments: The enzyme from the lycophyte Selaginella moellendorffii is bifunctional, initially forming (13E)-labda-7,13-dien-15-yl diphosphate, which is hydrolysed to the alcohol.
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Mafu, S., Hillwig, M.L. and Peters, R.J. A novel labda-7,13E-dien-15-ol-producing bifunctional diterpene synthase from Selaginella moellendorffii. ChemBioChem 12 (2011) 1984–1987. [DOI] [PMID: 21751328]
[EC 3.1.7.10 created 2012]
 
 
*EC 3.2.1.172
Accepted name: unsaturated rhamnogalacturonyl hydrolase
Reaction: 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose + H2O = 5-dehydro-4-deoxy-D-glucuronate + L-rhamnopyranose
For diagram of ramnosylgalacturan degradation, click here
Glossary: 6-deoxy-2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-mannopyranose = 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose
5-dehydro-4-deoxy-D-glucuronate = (4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate
Other name(s): YteR; YesR
Systematic name: 2-O-(4-deoxy-β-L-threo-hex-4-enopyranuronosyl)-α-L-rhamnopyranose hydrolase
Comments: The enzyme is part of the degradation system for rhamnogalacturonan I in Bacillus subtilis strain 168.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K. A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J. Mol. Biol. 360 (2006) 573–585. [DOI] [PMID: 16781735]
2.  Zhang, R., Minh, T., Lezondra, L., Korolev, S., Moy, S.F., Collart, F. and Joachimiak, A. 1.6 Å crystal structure of YteR protein from Bacillus subtilis, a predicted lyase. Proteins 60 (2005) 561–565. [DOI] [PMID: 15906318]
3.  Itoh, T., Ochiai, A., Mikami, B., Hashimoto, W. and Murata, K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem. Biophys. Res. Commun. 347 (2006) 1021–1029. [DOI] [PMID: 16870154]
[EC 3.2.1.172 created 2011, modified 2012]
 
 
EC 3.4.19.14
Accepted name: leukotriene-C4 hydrolase
Reaction: leukotriene C4 + H2O = leukotriene D4 + L-glutamate
Other name(s): γ-glutamyl leukotrienase; GGT5
Comments: The mouse enzyme is specific for leukotriene C4, while the human enzyme also has considerable activity towards glutathione and oxidized glutathione (cf. EC 3.4.19.13, glutathione hydrolase) [3-4].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Carter, B.Z., Wiseman, A.L., Orkiszewski, R., Ballard, K.D., Ou, C.N. and Lieberman, M.W. Metabolism of leukotriene C4 in γ-glutamyl transpeptidase-deficient mice. J. Biol. Chem. 272 (1997) 12305–12310. [DOI] [PMID: 9139674]
2.  Shi, Z.Z., Han, B., Habib, G.M., Matzuk, M.M. and Lieberman, M.W. Disruption of γ-glutamyl leukotrienase results in disruption of leukotriene D4 synthesis in vivo and attenuation of the acute inflammatory response. Mol. Cell Biol. 21 (2001) 5389–5395. [DOI] [PMID: 11463821]
3.  Han, B., Luo, G., Shi, Z.Z., Barrios, R., Atwood, D., Liu, W., Habib, G.M., Sifers, R.N., Corry, D.B. and Lieberman, M.W. γ-glutamyl leukotrienase, a novel endothelial membrane protein, is specifically responsible for leukotriene D4 formation in vivo. Am J Pathol 161 (2002) 481–490. [DOI] [PMID: 12163373]
4.  Wickham, S., West, M.B., Cook, P.F. and Hanigan, M.H. Gamma-glutamyl compounds: substrate specificity of γ-glutamyl transpeptidase enzymes. Anal. Biochem. 414 (2011) 208–214. [DOI] [PMID: 21447318]
[EC 3.4.19.14 created 2012]
 
 
EC 3.5.4.32
Accepted name: 8-oxoguanine deaminase
Reaction: 8-oxoguanine + H2O = urate + NH3
Glossary: 8-oxoguanine = 2-amino-7,9-dihydro-1H-purine-6,8-dione
Other name(s): 8-OGD
Systematic name: 8-oxoguanine aminohydrolase
Comments: Zn2+ is bound in the active site. 8-Oxoguanine is formed via the oxidation of guanine within DNA by reactive oxygen species. If uncorrected, this modification leads to the incorporation of 8-oxoG:A mismatches and eventually to G:C to T:A transversions.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Hall, R.S., Fedorov, A.A., Marti-Arbona, R., Fedorov, E.V., Kolb, P., Sauder, J.M., Burley, S.K., Shoichet, B.K., Almo, S.C. and Raushel, F.M. The hunt for 8-oxoguanine deaminase. J. Am. Chem. Soc. 132 (2010) 1762–1763. [DOI] [PMID: 20088583]
[EC 3.5.4.32 created 2012]
 
 
EC 3.6.1.30
Deleted entry: m7G(5′)pppN diphosphatase. Now covered by EC 3.6.1.59 [m7GpppX diphosphatase] and EC 3.6.1.62 [m7GpppN-mRNA hydrolase].
[EC 3.6.1.30 created 1978, deleted 2012]
 
 
EC 3.6.1.58
Accepted name: 8-oxo-dGDP phosphatase
Reaction: (1) 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate
(2) 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate
Glossary: 8-oxo-dGDP = 8-oxo-7,8-dihydro-2′-deoxyguanosine 5′-diphosphate
Other name(s): NUDT5; MTH3 (gene name); NUDT18
Systematic name: 8-oxo-dGDP phosphohydrolase
Comments: The enzyme catalyses the hydrolysis of both 8-oxo-dGDP and 8-oxo-GDP thereby preventing translational errors caused by oxidative damage. The preferred in vivo substrate is not known. The enzyme does not degrade 8-oxo-dGTP and 8-oxo-GTP to the monophosphates (cf. EC 3.6.1.55, 8-oxo-dGTP diphosphatase) [1,2]. Ribonucleotide diphosphates and deoxyribonucleotide diphosphates are hydrolysed with broad specificity. The bifunctional enzyme NUDT5 also hydrolyses ADP-ribose to AMP and D-ribose 5-phosphate (cf. EC 3.6.1.13, ADP-ribose diphosphatase) [4]. The human enzyme NUDT18 also hydrolyses 8-oxo-dADP and 2-hydroxy-dADP, the latter at a slower rate [6].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Ishibashi, T., Hayakawa, H., Ito, R., Miyazawa, M., Yamagata, Y. and Sekiguchi, M. Mammalian enzymes for preventing transcriptional errors caused by oxidative damage. Nucleic Acids Res. 33 (2005) 3779–3784. [DOI] [PMID: 16002790]
2.  Ishibashi, T., Hayakawa, H. and Sekiguchi, M. A novel mechanism for preventing mutations caused by oxidation of guanine nucleotides. EMBO Rep. 4 (2003) 479–483. [DOI] [PMID: 12717453]
3.  Kamiya, H., Hori, M., Arimori, T., Sekiguchi, M., Yamagata, Y. and Harashima, H. NUDT5 hydrolyzes oxidized deoxyribonucleoside diphosphates with broad substrate specificity. DNA Repair (Amst) 8 (2009) 1250–1254. [DOI] [PMID: 19699693]
4.  Ito, R., Sekiguchi, M., Setoyama, D., Nakatsu, Y., Yamagata, Y. and Hayakawa, H. Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein. J. Biochem. 149 (2011) 731–738. [DOI] [PMID: 21389046]
5.  Zha, M., Zhong, C., Peng, Y., Hu, H. and Ding, J. Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity. J. Mol. Biol. 364 (2006) 1021–1033. [DOI] [PMID: 17052728]
6.  Takagi, Y., Setoyama, D., Ito, R., Kamiya, H., Yamagata, Y. and Sekiguchi, M. Human MTH3 (NUDT18) protein hydrolyzes oxidized forms of guanosine and deoxyguanosine diphosphates: comparison with MTH1 and MTH2. J. Biol. Chem. 287 (2012) 21541–21549. [DOI] [PMID: 22556419]
[EC 3.6.1.58 created 2012]
 
 
EC 3.6.1.59
Accepted name: 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] diphosphatase
Reaction: a 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] + H2O = N7-methylguanosine 5′-phosphate + a 5′-diphospho-[mRNA]
Other name(s): DcpS; m7GpppX pyrophosphatase; m7GpppN m7GMP phosphohydrolase; m7GpppX diphosphatase; m7G5′ppp5’N m7GMP phosphohydrolase
Systematic name: 5′-(N7-methyl 5′-triphosphoguanosine)-[mRNA] N7-methylguanosine 5′-phosphate phosphohydrolase
Comments: The enzyme removes (decaps) the N7-methylguanosine 5-phosphate cap from an mRNA degraded to a maximal length of 10 nucleotides [3,6]. Decapping is an important process in the control of eukaryotic mRNA degradation. The enzyme functions to clear the cell of cap structure following decay of the RNA body [2]. The nematode enzyme can also decap triply methylated substrates, 5′-(N2,N2,N7-trimethyl 5′-triphosphoguanosine)-[mRNA] [4].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Malys, N. and McCarthy, J.E. Dcs2, a novel stress-induced modulator of m7GpppX pyrophosphatase activity that locates to P bodies. J. Mol. Biol. 363 (2006) 370–382. [DOI] [PMID: 16963086]
2.  Liu, S.W., Rajagopal, V., Patel, S.S. and Kiledjian, M. Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme. J. Biol. Chem. 283 (2008) 16427–16436. [DOI] [PMID: 18441014]
3.  Liu, H., Rodgers, N.D., Jiao, X. and Kiledjian, M. The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J. 21 (2002) 4699–4708. [DOI] [PMID: 12198172]
4.  van Dijk, E., Le Hir, H. and Seraphin, B. DcpS can act in the 5′-3′ mRNA decay pathway in addition to the 3′-5′ pathway. Proc. Natl. Acad. Sci. USA 100 (2003) 12081–12086. [DOI] [PMID: 14523240]
5.  Chen, N., Walsh, M.A., Liu, Y., Parker, R. and Song, H. Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. J. Mol. Biol. 347 (2005) 707–718. [DOI] [PMID: 15769464]
6.  Cohen, L.S., Mikhli, C., Friedman, C., Jankowska-Anyszka, M., Stepinski, J., Darzynkiewicz, E. and Davis, R.E. Nematode m7GpppG and m3(2,2,7)GpppG decapping: activities in Ascaris embryos and characterization of C. elegans scavenger DcpS. RNA 10 (2004) 1609–1624. [DOI] [PMID: 15383679]
7.  Wypijewska, A., Bojarska, E., Lukaszewicz, M., Stepinski, J., Jemielity, J., Davis, R.E. and Darzynkiewicz, E. 7-Methylguanosine diphosphate (m7GDP) is not hydrolyzed but strongly bound by decapping scavenger (DcpS) enzymes and potently inhibits their activity. Biochemistry 51 (2012) 8003–8013. [DOI] [PMID: 22985415]
[EC 3.6.1.59 created 2012, modified 2013]
 
 
EC 3.6.1.60
Accepted name: diadenosine hexaphosphate hydrolase (AMP-forming)
Reaction: (1) P1,P6-bis(5′-adenosyl)hexaphosphate + H2O = adenosine 5′-pentaphosphate + AMP
(2) P1,P5-bis(5′-adenosyl)pentaphosphate + H2O = adenosine 5′-tetraphosphate + AMP
Other name(s): hAps1; NUDT11 (gene name); hAps2; NUDT10 (gene name)
Systematic name: P1,P6-bis(5′-adenosyl)hexaphosphate nucleotidohydrolase (AMP-forming)
Comments: A divalent cation is essential for activity. Mn2+ (2–6 mM) is most effective. The enzyme controls intracellular levels of P1,P5-bis(5′-adenosyl)pentaphosphate and P1,P6-bis(5′-adenosyl)hexaphosphate. Weak activity with P1,P4-bis(5′-adenosyl)tetraphosphate. Marked preference for adenine over guanine nucleotides.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Leslie, N.R., McLennan, A.G. and Safrany, S.T. Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases. BMC Biochem. 3:20 (2002). [DOI] [PMID: 12121577]
2.  Safrany, S.T., Ingram, S.W., Cartwright, J.L., Falck, J.R., McLennan, A.G., Barnes, L.D. and Shears, S.B. The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT-type protein. J. Biol. Chem. 274 (1999) 21735–21740. [DOI] [PMID: 10419486]
[EC 3.6.1.60 created 2012]
 
 
EC 3.6.1.61
Accepted name: diadenosine hexaphosphate hydrolase (ATP-forming)
Reaction: (1) P1,P6-bis(5′-adenosyl)hexaphosphate + H2O = 2 ATP
(2) P1,P5-bis(5′-adenosyl)pentaphosphate + H2O = ATP + ADP
(3) P1,P4-bis(5′-adenosyl)tetraphosphate + H2O = ATP + AMP
Other name(s): Ndx1
Systematic name: P1,P6-bis(5′-adenosyl)hexaphosphate nucleotidohydrolase (ATP-forming)
Comments: The enzyme requires the presence of the divalent cations (Mn2+, Mg2+, Zn2+, and Co2+). It hydrolyses P1,P4-bis(5′-guanosyl) tetraphosphate very slowly [cf. EC 3.6.1.17, bis(5′-nucleosyl)-tetraphosphatase (asymmetrical)].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Iwai, T., Kuramitsu, S. and Masui, R. The Nudix hydrolase Ndx1 from Thermus thermophilus HB8 is a diadenosine hexaphosphate hydrolase with a novel activity. J. Biol. Chem. 279 (2004) 21732–21739. [DOI] [PMID: 15024014]
[EC 3.6.1.61 created 2012]
 
 
EC 3.6.1.62
Accepted name: 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] hydrolase
Reaction: a 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] + H2O = N7-methylguanosine 5′-diphosphate + a 5′-phospho-[mRNA]
Glossary: N7-methylguanosine 5′-diphosphate = m7GDP
Other name(s): Dcp2; NUDT16; D10 protein; D9 protein; D10 decapping enzyme; decapping enzyme; m7GpppN-mRNA hydrolase; m7GpppN-mRNA m7GDP phosphohydrolase
Systematic name: 5′-(N7-methylguanosine 5′-triphospho)-[mRNA] N7-methylguanosine-5′-diphosphate phosphohydrolase
Comments: Decapping of mRNA is a critical step in eukaryotic mRNA turnover. The enzyme is unable to cleave a free cap structure (m7GpppG) [3]. The enzyme from Vaccinia virus is synergistically activated in the presence of Mg2+ and Mn2+ [5].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Xu, J., Yang, J.Y., Niu, Q.W. and Chua, N.H. Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development. Plant Cell 18 (2006) 3386–3398. [DOI] [PMID: 17158604]
2.  Lu, G., Zhang, J., Li, Y., Li, Z., Zhang, N., Xu, X., Wang, T., Guan, Z., Gao, G.F. and Yan, J. hNUDT16: a universal decapping enzyme for small nucleolar RNA and cytoplasmic mRNA. Protein Cell 2 (2011) 64–73. [DOI] [PMID: 21337011]
3.  van Dijk, E., Cougot, N., Meyer, S., Babajko, S., Wahle, E. and Seraphin, B. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J. 21 (2002) 6915–6924. [DOI] [PMID: 12486012]
4.  Parrish, S., Resch, W. and Moss, B. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proc. Natl. Acad. Sci. USA 104 (2007) 2139–2144. [DOI] [PMID: 17283339]
5.  Souliere, M.F., Perreault, J.P. and Bisaillon, M. Characterization of the vaccinia virus D10 decapping enzyme provides evidence for a two-metal-ion mechanism. Biochem. J. 420 (2009) 27–35. [DOI] [PMID: 19210265]
6.  Parrish, S. and Moss, B. Characterization of a second vaccinia virus mRNA-decapping enzyme conserved in poxviruses. J. Virol. 81 (2007) 12973–12978. [DOI] [PMID: 17881455]
7.  Song, M.G., Li, Y. and Kiledjian, M. Multiple mRNA decapping enzymes in mammalian cells. Mol. Cell 40 (2010) 423–432. [DOI] [PMID: 21070968]
[EC 3.6.1.62 created 2012, modified 2013]
 
 
EC 3.7.1.17
Accepted name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Reaction: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H2O = 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + (2Z,4Z)-2-hydroxyhexa-2,4-dienoate
Other name(s): tesD (gene name); hsaD (gene name)
Systematic name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase ( (2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming)
Comments: The enzyme is involved in the bacterial degradation of the steroid ring structure, and is involved in degradation of multiple steroids, such as testosterone [1], cholesterol [2], and sitosterol.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, Gene, KEGG, PDB
References:
1.  Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275–5281. [DOI] [PMID: 16151114]
2.  Van der Geize, R., Yam, K., Heuser, T., Wilbrink, M.H., Hara, H., Anderton, M.C., Sim, E., Dijkhuizen, L., Davies, J.E., Mohn, W.W. and Eltis, L.D. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. USA 104 (2007) 1947–1952. [DOI] [PMID: 17264217]
3.  Lack, N., Lowe, E.D., Liu, J., Eltis, L.D., Noble, M.E., Sim, E. and Westwood, I.M. Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 2–7. [DOI] [PMID: 18097091]
4.  Lack, N.A., Yam, K.C., Lowe, E.D., Horsman, G.P., Owen, R.L., Sim, E. and Eltis, L.D. Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 285 (2010) 434–443. [DOI] [PMID: 19875455]
[EC 3.7.1.17 created 2012]
 
 
*EC 4.2.1.88
Accepted name: synephrine dehydratase
Reaction: (R)-synephrine = (4-hydroxyphenyl)acetaldehyde + methylamine
Glossary: (R)-synephrine = D-(-)-synephrine = 4-[(1R)-1-hydroxy-2-(methylamino)ethyl]phenol
Other name(s): syringinase
Systematic name: (R)-synephrine hydro-lyase (methylamine-forming)
Comments: Removal of H2O from (R)-synephrine produces a 2,3-enamine, which hydrolyses to the products shown in the reaction above. The enzyme from Arthrobacter synephrinum is highly specific [1].
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 104118-54-9
References:
1.  Veeraswamy, M., Devi, N.A., Krishnan Kutty, R. and Subba Rao, P.V. Conversion of (±) synephrine into p-hydroxyphenylacetaldehyde by Arthrobacter synephrinum. A novel enzymic reaction. Biochem. J. 159 (1976) 807–809. [PMID: 1008837]
2.  Manne, V., Kutty, K.R. and Pillarisetti, S.R. Purification and properties of synephrinase from Arthrobacter synephrinum. Arch. Biochem. Biophys. 248 (1986) 324–334. [DOI] [PMID: 3729420]
[EC 4.2.1.88 created 1989, modified 2012]
 
 
*EC 4.2.3.18
Accepted name: abieta-7,13-diene synthase
Reaction: (+)-copalyl diphosphate = abieta-7,13-diene + diphosphate
For diagram of abietadiene, abietate, isopimaradiene, phyllocladan-16alpha-ol and sclareol biosynthesis, click here and for diagram of reaction, click here
Glossary: (+)-copalyl diphosphate = (2E)-3-methyl-5-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate
abieta-7,13-diene = (4aS,4bR,10aS)-7-isopropyl-1,1,4a-trimethyl-1,2,3,4,4a,4b,5,6,10,10a-decahydrophenanthrene
Other name(s): copalyl-diphosphate diphosphate-lyase (cyclizing) (ambiguous); abietadiene synthase (ambiguous)
Systematic name: (+)-copalyl-diphosphate diphosphate-lyase [cyclizing, abieta-7,13-diene-forming]
Comments: Part of a bifunctional enzyme involved in the biosynthesis of abietadiene. See also EC 5.5.1.12, copalyl diphosphate synthase. Requires Mg2+.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 157972-08-2
References:
1.  Peters, R.J., Flory, J.E., Jetter, R., Ravn, M.M., Lee, H.J., Coates, R.M. and Croteau, R.B. Abietadiene synthase from grand fir (Abies grandis): characterization and mechanism of action of the "pseudomature" recombinant enzyme. Biochemistry 39 (2000) 15592–15602. [DOI] [PMID: 11112547]
2.  Peters, R.J., Ravn, M.M., Coates, R.M. and Croteau, R.B. Bifunctional abietadiene synthase: free diffusive transfer of the (+)-copalyl diphosphate intermediate between two distinct active sites. J. Am. Chem. Soc. 123 (2001) 8974–8978. [DOI] [PMID: 11552804]
3.  Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: mutational analysis of a prenyl diphosphate ionization-initiated cyclization and rearrangement. Proc. Natl. Acad. Sci. USA 99 (2002) 580–584. [DOI] [PMID: 11805316]
4.  Peters, R.J. and Croteau, R.B. Abietadiene synthase catalysis: conserved residues involved in protonation-initiated cyclization of geranylgeranyl diphosphate to (+)-copalyl diphosphate. Biochemistry 41 (2002) 1836–1842. [DOI] [PMID: 11827528]
5.  Ravn, M.M., Peters, R.J., Coates, R.M. and Croteau, R. Mechanism of abietadiene synthase catalysis: stereochemistry and stabilization of the cryptic pimarenyl carbocation intermediates. J. Am. Chem. Soc. 124 (2002) 6998–7006. [DOI] [PMID: 12059223]
[EC 4.2.3.18 created 2002, modified 2012]
 
 
*EC 4.2.3.68
Accepted name: β-eudesmol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = β-eudesmol + diphosphate
For diagram of eudesmol and selinene biosynthesis, click here and for diagram of eudesmol biosynthesis, click here
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (β-eudesmol-forming)
Comments: The recombinant enzyme from ginger (Zingiber zerumbet) gives 62.6% β-eudesmol, 16.8% 10-epi-γ-eudesmol (cf. EC 4.2.3.84, 10-epi-γ-eudesmol synthase), 10% α-eudesmol (cf. EC 4.2.3.85, α-eudesmol synthase), and 5.6% aristolene.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Yu, F., Harada, H., Yamasaki, K., Okamoto, S., Hirase, S., Tanaka, Y., Misawa, N. and Utsumi, R. Isolation and functional characterization of a β-eudesmol synthase, a new sesquiterpene synthase from Zingiber zerumbet Smith. FEBS Lett. 582 (2008) 565–572. [DOI] [PMID: 18242187]
[EC 4.2.3.68 created 2011, modified 2011, modified 2012]
 
 
*EC 4.2.3.69
Accepted name: (+)-α-barbatene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (+)-α-barbatene + diphosphate
For diagram of barbatene biosynthesis, click here and for diagram of biosynthesis of tricyclic sesquiterpenoids derived from bisabolyl cation, click here
Other name(s): AtBS
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-α-barbatene-forming]
Comments: The recombinant enzyme from the plant Arabidopsis thaliana produces 27.3% α-barbatene, 17.8% thujopsene (cf. EC 4.2.3.79, thujopsene synthase) and 9.9% β-chamigrene (cf. EC 4.2.3.78, β-chamigrene synthase) [1] plus traces of other sesquiterpenoids [2].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Wu, S., Schoenbeck, M.A., Greenhagen, B.T., Takahashi, S., Lee, S., Coates, R.M. and Chappell, J. Surrogate splicing for functional analysis of sesquiterpene synthase genes. Plant Physiol. 138 (2005) 1322–1333. [DOI] [PMID: 15965019]
2.  Tholl, D., Chen, F., Petri, J., Gershenzon, J. and Pichersky, E. Two sesquiterpene synthases are responsible for the complex mixture of sesquiterpenes emitted from Arabidopsis flowers. Plant J. 42 (2005) 757–771. [DOI] [PMID: 15918888]
[EC 4.2.3.69 created 2011, modified 2012]
 
 
EC 4.2.3.94
Accepted name: γ-curcumene synthase
Reaction: (2E,6E)-farnesyl diphosphate = γ-curcumene + diphosphate
For diagram of bisabolene biosynthesis, click here and for diagram of γ-curcumene, β-sesquiphellandrene and zingiberene biosynthesis, click here
Other name(s): PatTpsA (gene name)
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, γ-curcumene-forming)
Comments: One of five sesquiterpenoid synthases in Pogostemon cablin (patchouli).
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Deguerry, F., Pastore, L., Wu, S., Clark, A., Chappell, J. and Schalk, M. The diverse sesquiterpene profile of patchouli, Pogostemon cablin, is correlated with a limited number of sesquiterpene synthases. Arch. Biochem. Biophys. 454 (2006) 123–136. [DOI] [PMID: 16970904]
[EC 4.2.3.94 created 2012]
 
 
EC 4.2.3.95
Accepted name: (-)-α-cuprenene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-α-cuprenene + diphosphate
For diagram of biosynthesis of bicyclic sesquiterpenoids derived from bisabolyl cation, click here and for diagram of trichodiene and (–)-α-cuprenene biosynthesis, click here
Other name(s): Cop6
Systematic name: (-)-α-cuprenene hydrolase [cyclizing, (-)-α-cuprenene-forming]
Comments: The enzyme from the fungus Coprinopsis cinerea produces (-)-α-cuprenene with high selectivity.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Lopez-Gallego, F., Agger, S.A., Abate-Pella, D., Distefano, M.D. and Schmidt-Dannert, C. Sesquiterpene synthases Cop4 and Cop6 from Coprinus cinereus: catalytic promiscuity and cyclization of farnesyl pyrophosphate geometric isomers. ChemBioChem 11 (2010) 1093–1106. [DOI] [PMID: 20419721]
[EC 4.2.3.95 created 2012]
 
 
EC 4.2.3.96
Accepted name: avermitilol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = avermitilol + diphosphate
For diagram of bicyclogermacrene and avermitilol biosynthesis, click here
Systematic name: avermitilol hydrolase (cyclizing, avermitilol-forming)
Comments: Requires Mg2+. The recombinent enzyme gives avermitilol (85%) plus traces of germacrene A, germacrene B and viridiflorol. The (1S)-hydrogen of farnesyl diphosphate is retained.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Chou, W.K., Fanizza, I., Uchiyama, T., Komatsu, M., Ikeda, H. and Cane, D.E. Genome mining in Streptomyces avermitilis: cloning and characterization of SAV_76, the synthase for a new sesquiterpene, avermitilol. J. Am. Chem. Soc. 132 (2010) 8850–8851. [DOI] [PMID: 20536237]
[EC 4.2.3.96 created 2012]
 
 
EC 4.2.3.97
Accepted name: (-)-δ-cadinene synthase
Reaction: (2E,6E)-farnesyl diphosphate = (-)-δ-cadinene + diphosphate
For diagram of ent-cadinane sesquiterpenoid biosynthesis, click here
Glossary: (-)-δ-cadinene = (1R,8aS)-4,7-dimethyl-1-(propan-2-yl)-1,2,3,5,6,8a-hexahydronaphthalene
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, (-)-δ-cadinene-forming)
Comments: The cyclization mechanism involves an intermediate nerolidyl diphosphate leading to a helminthogermacradienyl cation. Following a 1,3-hydride shift of the original 1-pro-S hydrogen of (2E,6E)-farnesyl diphosphate, cyclization and deprotonation gives (-)-δ-cadinene.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Hu, Y., Chou, W.K., Hopson, R. and Cane, D.E. Genome mining in Streptomyces clavuligerus: expression and biochemical characterization of two new cryptic sesquiterpene synthases. Chem. Biol. 18 (2011) 32–37. [DOI] [PMID: 21276937]
[EC 4.2.3.97 created 2012]
 
 
EC 4.2.3.98
Accepted name: (+)-T-muurolol synthase
Reaction: (2E,6E)-farnesyl diphosphate + H2O = (+)-T-muurolol + diphosphate
For diagram of ent-cadinane sesquiterpenoid biosynthesis, click here
Glossary: (+)-T-muurolol = (1R,4R,4aS,8aR)-1,6-dimethyl-4-(propan-2-yl)-1,2,3,4,4a,7,8,8a-octahydronaphthalen-1-ol
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, (+)-T-muurolol-forming)
Comments: The cyclization mechanism involves an intermediate nerolidyl diphosphate leading to a helminthogermacradienyl cation. After a 1,3-hydride shift of the original 1-pro-S hydrogen of farnesyl diphosphate, cyclization and deprotonation result in (+)-T-muurolol.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Hu, Y., Chou, W.K., Hopson, R. and Cane, D.E. Genome mining in Streptomyces clavuligerus: expression and biochemical characterization of two new cryptic sesquiterpene synthases. Chem. Biol. 18 (2011) 32–37. [DOI] [PMID: 21276937]
[EC 4.2.3.98 created 2012]
 
 
EC 4.2.3.99
Accepted name: labdatriene synthase
Reaction: 9α-copalyl diphosphate = (12E)-9α-labda-8(17),12,14-triene + diphosphate
For diagram of diterpenoids from 9α-copalyl diphosphate, click here
Glossary: 9α-copalyl diphosphate = syn-copalyl diphosphate = (2E)-3-methyl-5-[(1R,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]pent-2-en-1-yl trihydrogen diphosphate
(12E)-9α-labda-8(17),12,14-triene = (4aS,5R,8aS)-1,1,4a-trimethyl-6-methylidene-5-[(2E)-3-methylpenta-2,4-dien-1-yl]decahydronaphthalene
Other name(s): OsKSL10 (gene name)
Systematic name: 9α-copalyl-diphosphate diphosphate-lyase [(12E)-9α-labda-8(17),12,14-triene-forming]
Comments: The enzyme from rice (Oryza sativa), expressed in Escherichia coli, also produces ent-sandaracopimara-8(14),15-diene from ent-copalyl diphosphate, another naturally occuring copalyl isomer in rice (cf. ent-sandaracopimaradiene synthase, EC 4.2.3.29).
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Morrone, D., Hillwig, M.L., Mead, M.E., Lowry, L., Fulton, D.B. and Peters, R.J. Evident and latent plasticity across the rice diterpene synthase family with potential implications for the evolution of diterpenoid metabolism in the cereals. Biochem. J. 435 (2011) 589–595. [DOI] [PMID: 21323642]
[EC 4.2.3.99 created 2012]
 
 
EC 4.2.3.100
Accepted name: bicyclogermacrene synthase
Reaction: (2E,6E)-farnesyl diphosphate = bicyclogermacrene + diphosphate
For diagram of bicyclogermacrene and avermitilol biosynthesis, click here
Other name(s): Ov-TPS4
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (bicyclogermacrene-forming)
Comments: The enzyme from oregano (Origanum vulgare) gives mainly bicyclogermacrene with Mn2+ as a cofactor. With Mg2+ a more complex mixture is produced.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Crocoll, C., Asbach, J., Novak, J., Gershenzon, J. and Degenhardt, J. Terpene synthases of oregano (Origanum vulgare L.) and their roles in the pathway and regulation of terpene biosynthesis. Plant Mol. Biol. 73 (2010) 587–603. [DOI] [PMID: 20419468]
[EC 4.2.3.100 created 2012]
 
 
EC 4.2.3.101
Accepted name: 7-epi-sesquithujene synthase
Reaction: (2E,6E)-farnesyl diphosphate = 7-epi-sesquithujene + diphosphate
For diagram of biosynthesis of bicyclic sesquiterpenoids derived from bisabolyl cation, click here and for diagram of mechanism, click here
Other name(s): TPS4-B73
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (7-epi-sesquithujene-forming)
Comments: The enzyme from Zea mays, variety B73, gives mainly 7-epi-sesquithujene with (S)-β-bisabolene and traces of other sesquiterpenoids, cf. EC 4.2.3.55 (S)-β-bisabolene synthase. It requires Mg2+ or Mn2+. The product ratio is dependent on which metal ion is present. 7-epi-Sesquithujene is an attractant for the emerald ash borer beetle.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Köllner, T.G., Schnee, C., Gershenzon, J. and Degenhardt, J. The variability of sesquiterpenes emitted from two Zea mays cultivars is controlled by allelic variation of two terpene synthase genes encoding stereoselective multiple product enzymes. Plant Cell 16 (2004) 1115–1131. [DOI] [PMID: 15075399]
[EC 4.2.3.101 created 2012]
 
 
EC 4.2.3.102
Accepted name: sesquithujene synthase
Reaction: (2E,6E)-farnesyl diphosphate = sesquithujene + diphosphate
For diagram of biosynthesis of bicyclic sesquiterpenoids derived from bisabolyl cation, click here and for diagram of mechanism, click here
Other name(s): TPS5-Del1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (sesquithujene-forming)
Comments: The enzyme from Zea mays, variety Delprim, gives mainly sesquithujene with (S)-β-bisabolene and (E)-β-farnesene plus traces of other sesquiterpenoids, cf. EC 4.2.3.55 [(S)-β-bisabolene synthase] and EC 4.2.3.47 (β-farnesene synthase). It requires Mg2+ or Mn2+. The exact product ratio is dependent on which metal ion is present.
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Köllner, T.G., Schnee, C., Gershenzon, J. and Degenhardt, J. The variability of sesquiterpenes emitted from two Zea mays cultivars is controlled by allelic variation of two terpene synthase genes encoding stereoselective multiple product enzymes. Plant Cell 16 (2004) 1115–1131. [DOI] [PMID: 15075399]
[EC 4.2.3.102 created 2012]
 
 
EC 4.2.3.103
Accepted name: ent-isokaurene synthase
Reaction: ent-copalyl diphosphate = ent-isokaurene + diphosphate
For diagram of biosynthesis of diterpenoids from ent-copalyl diphosphate, click here and for diagram of ent-kaurene and ent-isokaurene, click here
Other name(s): OsKSL5i; OsKSL6
Systematic name: ent-copalyl-diphosphate diphosphate-lyase (cyclizing, ent-isokaurene-forming)
Comments: Two enzymes of the rice sub-species Oryza sativa ssp. indica, OsKSL5 and OsKSL6, produce ent-isokaurene. A variant of OsKSL5 from the sub-species Oryza sativa ssp. japonica produces ent-pimara-8(14),15-diene instead [cf. EC 4.2.3.30, ent-pimara-8(14),15-diene synthase].
Links to other databases: BRENDA, EXPASY, Gene, KEGG
References:
1.  Xu, M., Wilderman, P.R., Morrone, D., Xu, J., Roy, A., Margis-Pinheiro, M., Upadhyaya, N.M., Coates, R.M. and Peters, R.J. Functional characterization of the rice kaurene synthase-like gene family. Phytochemistry 68 (2007) 312–326. [DOI] [PMID: 17141283]
2.  Xu, M., Wilderman, P.R. and Peters, R.J. Following evolution’s lead to a single residue switch for diterpene synthase product outcome. Proc. Natl. Acad. Sci. USA 104 (2007) 7397–7401. [DOI] [PMID: 17456599]
[EC 4.2.3.103 created 2012]
 
 
EC 4.2.3.104
Accepted name: α-humulene synthase
Reaction: (2E,6E)-farnesyl diphosphate = α-humulene + diphosphate
For diagram of sesquiterpenoid biosynthesis based on humulene, click here
Other name(s): ZSS1
Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase (α-humulene-forming)
Comments: The enzyme from Zingiber zerumbet, shampoo ginger, also gives traces of β-caryophyllene.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB
References:
1.  Yu, F., Okamto, S., Nakasone, K., Adachi, K., Matsuda, S., Harada, H., Misawa, N. and Utsumi, R. Molecular cloning and functional characterization of α-humulene synthase, a possible key enzyme of zerumbone biosynthesis in shampoo ginger (Zingiber zerumbet Smith). Planta 227 (2008) 1291–1299. [DOI] [PMID: 18273640]
[EC 4.2.3.104 created 2012]
 
 
*EC 5.3.1.17
Accepted name: 5-dehydro-4-deoxy-D-glucuronate isomerase
Reaction: 5-dehydro-4-deoxy-D-glucuronate = 3-deoxy-D-glycero-2,5-hexodiulosonate
Glossary: 5-dehydro-4-deoxy-D-glucuronate = (4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate
3-deoxy-D-glycero-2,5-hexodiulosonate = (4S)-4,6-dihydroxy-2,5-dioxohexanoate
Other name(s): 4-deoxy-L-threo-5-hexulose uronate isomerase; 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase; kduI (gene name)
Systematic name: 5-dehydro-4-deoxy-D-glucuronate aldose-ketose-isomerase
Comments: The enzyme is involved in the degradation of polygalacturonate, a later stage in the degradation of pectin by many microorganisms.
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37318-44-8
References:
1.  Preiss, J. 4-Deoxy-L-threo-5-hexosulose uronic acid isomerase. Methods Enzymol. 9 (1966) 602–604.
2.  Condemine, G. and Robert-Baudouy, J. Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation. Mol. Microbiol. 5 (1991) 2191–2202. [DOI] [PMID: 1766386]
3.  Dunten, P., Jaffe, H. and Aksamit, R.R. Crystallization of 5-keto-4-deoxyuronate isomerase from Escherichia coli. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 678–680. [PMID: 9761873]
4.  Crowther, R.L. and Georgiadis, M.M. The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli. Proteins 61 (2005) 680–684. [DOI] [PMID: 16152643]
[EC 5.3.1.17 created 1972, modified 2012]
 
 
*EC 5.4.4.4
Accepted name: geraniol isomerase
Reaction: geraniol = (3S)-linalool
For diagram of acyclic monoterpenoid biosynthesis, click here
Systematic name: geraniol hydroxymutase
Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the isomerization of (3S)-linalool to geraniol and the hydration of myrcene to (3S)-linalool, the latter activity being classified as EC 4.2.1.127, linalool dehydratase.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Brodkorb, D., Gottschall, M., Marmulla, R., Lüddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436–30442. [DOI] [PMID: 20663876]
2.  Lüddeke, F. and Harder, J. Enantiospecific (S)-(+)-linalool formation from β-myrcene by linalool dehydratase-isomerase. Z. Naturforsch. C 66 (2011) 409–412. [PMID: 21950166]
[EC 5.4.4.4 created 2011, modified 2012]
 
 
EC 5.4.99.57
Accepted name: baruol synthase
Reaction: (3S)-2,3-epoxy-2,3-dihydrosqualene = baruol
For diagram of baccharis oxide, baruol and shionone biosynthesis, click here
Other name(s): BARS1
Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene mutase (cyclizing, baruol-forming)
Comments: The enzyme from Arabidopsis thaliana also produces traces of 22 other triterpenoids.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Lodeiro, S., Xiong, Q., Wilson, W.K., Kolesnikova, M.D., Onak, C.S. and Matsuda, S.P. An oxidosqualene cyclase makes numerous products by diverse mechanisms: a challenge to prevailing concepts of triterpene biosynthesis. J. Am. Chem. Soc. 129 (2007) 11213–11222. [DOI] [PMID: 17705488]
[EC 5.4.99.57 created 2012]
 
 
*EC 5.5.1.16
Accepted name: halimadienyl-diphosphate synthase
Reaction: geranylgeranyl diphosphate = tuberculosinyl diphosphate
For diagram of diterpenoid biosynthesis, click here
Glossary: tuberculosinyl diphosphate = halima-5,13-dien-15-yl diphosphate
Other name(s): Rv3377c; halimadienyl diphosphate synthase; tuberculosinol diphosphate synthase; halima-5(6),13-dien-15-yl-diphosphate lyase (cyclizing); halima-5,13-dien-15-yl-diphosphate lyase (decyclizing)
Systematic name: halima-5,13-dien-15-yl-diphosphate lyase (ring-opening)
Comments: Requires Mg2+ for activity. This enzyme is found in pathogenic prokaryotes such as Mycobacterium tuberculosis but not in non-pathogens such as Mycobacterium smegmatis so may play a role in pathogenicity. The product of the reaction is subsequently dephosphorylated yielding tuberculosinol (halima-5,13-dien-15-ol).
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Nakano, C., Okamura, T., Sato, T., Dairi, T. and Hoshino, T. Mycobacterium tuberculosis H37Rv3377c encodes the diterpene cyclase for producing the halimane skeleton. Chem. Commun. (Camb.) (2005) 1016–1018. [DOI] [PMID: 15719101]
[EC 5.5.1.16 created 2008, modified 2012]
 
 
*EC 6.3.2.14
Accepted name: enterobactin synthase
Reaction: 6 ATP + 3 2,3-dihydroxybenzoate + 3 L-serine = enterobactin + 6 AMP + 6 diphosphate
For diagram of enterobactin biosynthesis, click here
Other name(s): N-(2,3-dihydroxybenzoyl)-serine synthetase; 2,3-dihydroxybenzoylserine synthetase; 2,3-dihydroxybenzoate—serine ligase
Systematic name: 2,3-dihydroxybenzoate:L-serine ligase
Comments: This enzyme complex catalyses the conversion of three molecules each of 2,3-dihydroxybenzoate and L-serine to form the siderophore enterobactin. In Escherichia coli the complex is formed by EntB (an aryl carrier protein that has to be activated by 4′-phosphopantetheine), EntD (a phosphopantetheinyl transferase that activates EntB), EntE (catalyses the ATP-dependent condensation of 2,3-dihydroxybenzoate and holo-EntB to form the covalently arylated form of EntB), and EntF (a four domain protein that catalyses the activation of L-serine by ATP, the condensation of the activated L-serine with the activated 2,3-dihydroxybenzoate, and the trimerization of three such moieties to a single enterobactin molecule).
Links to other databases: BRENDA, EXPASY, Gene, KEGG, PDB, CAS registry number: 37318-63-1
References:
1.  Brot, N. and Goodwin, J. Regulation of 2,3-dihydroxybenzoylserine synthetase by iron. J. Biol. Chem. 243 (1968) 510–513. [PMID: 4966114]
2.  Rusnak, F., Faraci, W.S. and Walsh, C.T. Subcloning, expression, and purification of the enterobactin biosynthetic enzyme 2,3-dihydroxybenzoate-AMP ligase: demonstration of enzyme-bound (2,3-dihydroxybenzoyl)adenylate product. Biochemistry 28 (1989) 6827–6835. [PMID: 2531000]
3.  Rusnak, F., Liu, J., Quinn, N., Berchtold, G.A. and Walsh, C.T. Subcloning of the enterobactin biosynthetic gene entB: expression, purification, characterization, and substrate specificity of isochorismatase. Biochemistry 29 (1990) 1425–1435. [PMID: 2139796]
4.  Rusnak, F., Sakaitani, M., Drueckhammer, D., Reichert, J. and Walsh, C.T. Biosynthesis of the Escherichia coli siderophore enterobactin: sequence of the entF gene, expression and purification of EntF, and analysis of covalent phosphopantetheine. Biochemistry 30 (1991) 2916–2927. [PMID: 1826089]
5.  Gehring, A.M., Mori, I. and Walsh, C.T. Reconstitution and characterization of the Escherichia coli enterobactin synthetase from EntB, EntE, and EntF. Biochemistry 37 (1998) 2648–2659. [DOI] [PMID: 9485415]
6.  Shaw-Reid, C.A., Kelleher, N.L., Losey, H.C., Gehring, A.M., Berg, C. and Walsh, C.T. Assembly line enzymology by multimodular nonribosomal peptide synthetases: the thioesterase domain of E. coli EntF catalyzes both elongation and cyclolactonization. Chem. Biol. 6 (1999) 385–400. [DOI] [PMID: 10375542]
[EC 6.3.2.14 created 1972, modified 2012]
 
 
*EC 6.3.5.6
Accepted name: asparaginyl-tRNA synthase (glutamine-hydrolysing)
Reaction: ATP + L-aspartyl-tRNAAsn + L-glutamine + H2O = ADP + phosphate + L-asparaginyl-tRNAAsn + L-glutamate
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + L-aspartyl-tRNAAsn = ADP + 4-phosphooxy-L-aspartyl-tRNAAsn
(1c) 4-phosphooxy-L-aspartyl-tRNAAsn + NH3 = L-asparaginyl-tRNAAsn + phosphate
Other name(s): Asp-AdT; Asp-tRNAAsn amidotransferase; aspartyl-tRNAAsn amidotransferase; Asn-tRNAAsn:L-glutamine amido-ligase (ADP-forming); aspartyl-tRNAAsn:L-glutamine amido-ligase (ADP-forming); GatCAB
Systematic name: L-aspartyl-tRNAAsn:L-glutamine amido-ligase (ADP-forming)
Comments: This reaction forms part of a two-reaction system for producing asparaginyl-tRNA in Deinococcus radiodurans and other organisms lacking a specific enzyme for asparagine synthesis. In the first step, a non-discriminating ligase (EC 6.1.1.23, aspartate—tRNAAsn ligase) mischarges tRNAAsn with aspartate, leading to the formation of aspartyl-tRNAAsn. The aspartyl-tRNAAsn is not used in protein synthesis until the present enzyme converts it into asparaginyl-tRNAAsn (aspartyl-tRNAAsp is not a substrate for this enzyme). A glutaminase subunit (cf. EC 3.5.1.2, glutaminase) produces an ammonia molecule that is transferred by a 30 Å tunnel to a synthase subunit, where it is ligated to the carboxy group that has been activated by phosphorylation. Bacterial GatCAB complexes also has the activity of EC 6.3.5.7 [glutaminyl-tRNA synthase (glutamine-hydrolysing)].
Links to other databases: BRENDA, EXPASY, Gene, KEGG, CAS registry number: 37211-76-0
References:
1.  Curnow, A.W., Tumbula, D.L., Pelaschier, J.T., Min, B. and Söll, D. Glutamyl-tRNAGln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95 (1998) 12838–12843. [DOI] [PMID: 9789001]
2.  Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617–650. [DOI] [PMID: 10966471]
3.  Min, B., Pelaschier, J.T., Graham, D.E., Tumbula-Hansen, D. and Söll, D. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. USA 99 (2002) 2678–2683. [DOI] [PMID: 11880622]
[EC 6.3.5.6 created 2002, modified 2012, modified 2019]
 
 


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