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. The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Richard Cammack, Ron Caspi, Masaaki Kotera, Andrew McDonald, Gerry Moss, Dietmar Schomburg, 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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.2.1.30 carboxylate reductase (NADP+) (27 March 2019)
*EC 1.3.8.6 glutaryl-CoA dehydrogenase (ETF) (27 March 2019)
*EC 1.4.1.14 glutamate synthase (NADH) (27 March 2019)
*EC 1.8.5.3 respiratory dimethylsulfoxide reductase (27 March 2019)
EC 1.13.11.88 isoeugenol monooxygenase (27 March 2019)
EC 1.14.11.61 feruloyl-CoA 6-hydroxylase (27 March 2019)
EC 1.14.11.62 trans-4-coumaroyl-CoA 2-hydroxylase (27 March 2019)
EC 1.14.11.63 peptidyl-lysine (3S)-dioxygenase (27 March 2019)
EC 1.14.13.243 toluene 2-monooxygenase (27 March 2019)
EC 1.14.13.244 phenol 2-monooxygenase (NADH) (27 March 2019)
EC 1.14.13.245 assimilatory dimethylsulfide S-monooxygenase (27 March 2019)
EC 1.14.15.36 sterol 14α-demethylase (ferredoxin) (27 March 2019)
EC 1.14.15.37 luteothin monooxygenase (27 March 2019)
EC 1.14.99.65 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase (27 March 2019)
EC 2.1.1.353 demethylluteothin O-methyltransferase (27 March 2019)
*EC 2.3.1.85 fatty-acid synthase system (27 March 2019)
*EC 2.3.1.86 fatty-acyl-CoA synthase system (27 March 2019)
*EC 2.3.1.161 lovastatin nonaketide synthase (27 March 2019)
EC 2.3.1.281 5-hydroxydodecatetraenal polyketide synthase (27 March 2019)
EC 2.3.1.282 phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase (27 March 2019)
EC 2.3.1.283 2'-acyl-2-O-sulfo-trehalose (hydroxy)phthioceranyltransferase (27 March 2019)
EC 2.3.1.284 3'-(hydroxy)phthioceranyl-2'-palmitoyl(stearoyl)-2-O-sulfo-trehalose (hydroxy)phthioceranyltransferase (27 March 2019)
EC 2.3.1.285 (13S,14R)-1,13-dihydroxy-N-methylcanadine 13-O-acetyltransferase (27 March 2019)
EC 2.4.1.361 GDP-mannose:di-myo-inositol-1,3'-phosphate β-1,2-mannosyltransferase (27 March 2019)
EC 2.4.1.362 α-(1→3) branching sucrase (27 March 2019)
EC 2.5.1.152 D-histidine 2-aminobutanoyltransferase (27 March 2019)
EC 2.6.1.115 5-hydroxydodecatetraenal 1-aminotransferase (27 March 2019)
EC 2.7.1.225 L-serine kinase (ATP) (27 March 2019)
EC 2.7.1.226 L-serine kinase (ADP) (27 March 2019)
EC 3.1.1.105 3-O-acetylpapaveroxine carboxylesterase (27 March 2019)
EC 3.1.4.59 cyclic-di-AMP phosphodiesterase (27 March 2019)
EC 3.1.4.60 pApA phosphodiesterase (27 March 2019)
*EC 3.2.1.15 endo-polygalacturonase (27 March 2019)
*EC 3.2.1.67 galacturonan 1,4-α-galacturonidase (27 March 2019)
*EC 3.2.1.82 exo-poly-α-digalacturonosidase (27 March 2019)
*EC 3.4.19.13 glutathione γ-glutamate hydrolase (27 March 2019)
*EC 3.5.1.84 biuret amidohydrolase (27 March 2019)
EC 3.5.1.130 [lysine-biosynthesis-protein LysW]-lysine/ornithine hydrolase (27 March 2019)
EC 3.5.1.131 1-carboxybiuret hydrolase (27 March 2019)
EC 3.5.1.132 [amino group carrier protein]-ornithine hydrolase (5 April 2019)
*EC 3.5.2.15 cyanuric acid amidohydrolase (27 March 2019)
EC 4.1.1.70 transferred now EC 7.2.4.5 (27 March 2019)
EC 4.1.1.115 indoleacetate decarboxylase (27 March 2019)
EC 4.1.1.116 D-ornithine/D-lysine decarboxylase (27 March 2019)
EC 4.1.1.117 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate decarboxylase (27 March 2019)
*EC 4.2.1.139 pterocarpan synthase (27 March 2019)
EC 4.2.99.24 thebaine synthase (27 March 2019)
EC 5.1.1.24 histidine racemase (27 March 2019)
EC 5.1.3.43 sulfoquinovose mutarotase (27 March 2019)
*EC 6.2.1.40 4-hydroxybutyrate—CoA ligase (AMP-forming) (27 March 2019)
EC 6.2.1.56 4-hydroxybutyrate—CoA ligase (ADP-forming) (27 March 2019)
*EC 6.3.2.39 aerobactin synthase (27 March 2019)
EC 6.3.2.54 L-2,3-diaminopropanoate—citrate ligase (27 March 2019)
EC 6.3.2.55 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate synthase (27 March 2019)
EC 6.3.2.56 staphyloferrin B synthase (27 March 2019)
*EC 6.3.5.6 asparaginyl-tRNA synthase (glutamine-hydrolysing) (27 March 2019)
*EC 6.3.5.7 glutaminyl-tRNA synthase (glutamine-hydrolysing) (27 March 2019)
EC 6.3.5.13 lipid II isoglutaminyl synthase (glutamine-hydrolysing) (27 March 2019)
EC 7.2.4.5 glutaconyl-CoA decarboxylase (27 March 2019)

*EC 1.2.1.30

Accepted name: carboxylate reductase (NADP+)

Reaction: an aromatic aldehyde + NADP+ + AMP + diphosphate = an aromatic acid + NADPH + H+ + ATP

Other name(s): aromatic acid reductase; aryl-aldehyde dehydrogenase (NADP+)

Systematic name: aryl-aldehyde:NADP+ oxidoreductase (ATP-forming)

Comments: The enzyme contains an adenylation domain, a phosphopantetheinyl binding domain, and a reductase domain, and requires activation by attachment of a phosphopantetheinyl group. The enzyme activates its substrate to an adenylate form, followed by a transfer to the phosphopantetheinyl binding domain. The resulting thioester is subsequently transferred to the reductase domain, where it is reduced to an aldehyde and released.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 9074-94-6

References:

1. Gross, G.G. and Zenk, M.H. Reduktion aromatischer Säuer zu Aldehyden und Alkoholen im zellfreien System. 1. Reinigung und Eigenschaften von Aryl-Aldehyd:NADP-Oxidoreduktase aus Neurospora crassa. Eur. J. Biochem. 8 (1969) 413-419. [PMID: 4389863]

2. Gross, G.G. Formation and reduction of intermediate acyladenylate by aryl-aldehyde. NADP oxidoreductase from Neurospora crassa. Eur. J. Biochem. 31 (1972) 585-592. [PMID: 4405494]

3. Venkitasubramanian, P., Daniels, L. and Rosazza, J.P. Reduction of carboxylic acids by Nocardia aldehyde oxidoreductase requires a phosphopantetheinylated enzyme. J. Biol. Chem 282 (2007) 478-485. [PMID: 17102130]

4. Stolterfoht, H., Schwendenwein, D., Sensen, C.W., Rudroff, F. and Winkler, M. Four distinct types of E.C. 1.2.1.30 enzymes can catalyze the reduction of carboxylic acids to aldehydes. J. Biotechnol. 257 (2017) 222-232. [PMID: 28223183]

[EC 1.2.1.30 created 1972, modified 2019]

*EC 1.3.8.6

Accepted name: glutaryl-CoA dehydrogenase (ETF)

Reaction: glutaryl-CoA + electron-transfer flavoprotein = crotonyl-CoA + CO2 + reduced electron-transfer flavoprotein (overall reaction)
(1a) glutaryl-CoA + electron-transfer flavoprotein = (E)-glutaconyl-CoA + reduced electron-transfer flavoprotein
(1b) (E)-glutaconyl-CoA = crotonyl-CoA + CO2

For diagram of reaction click here.

Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA
crotonyl-CoA = (E)-but-2-enoyl-CoA

Other name(s): glutaryl coenzyme A dehydrogenase; glutaryl-CoA:(acceptor) 2,3-oxidoreductase (decarboxylating); glutaryl-CoA dehydrogenase

Systematic name: glutaryl-CoA:electron-transfer flavoprotein 2,3-oxidoreductase (decarboxylating)

Comments: Contains FAD. The enzyme catalyses the oxidation of glutaryl-CoA to glutaconyl-CoA (which remains bound to the enzyme), and the decarboxylation of the latter to crotonyl-CoA (cf. EC 7.2.4.5, glutaconyl-CoA decarboxylase). FAD is the electron acceptor in the oxidation of the substrate, and its reoxidation by electron-transfer flavoprotein completes the catalytic cycle. The anaerobic, sulfate-reducing bacterium Desulfococcus multivorans contains two glutaryl-CoA dehydrogenases: a decarboxylating enzyme (this entry), and a non-decarboxylating enzyme that only catalyses the oxidation to glutaconyl-CoA [EC 1.3.99.32, glutaryl-CoA dehydrogenase (acceptor)].

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, UM-BBD, CAS registry number: 37255-38-2

References:

1. Besrat, A., Polan, C.E. and Henderson, L.M. Mammalian metabolism of glutaric acid. J. Biol. Chem. 244 (1969) 1461-1467. [PMID: 4304226]

2. Hartel, U., Eckel, E., Koch, J., Fuchs, G., Linder, D. and Buckel, W. Purification of glutaryl-CoA dehydrogenase from Pseudomonas sp., an enzyme involved in the anaerobic degradation of benzoate. Arch. Microbiol. 159 (1993) 174-181. [PMID: 8439237]

3. Dwyer, T.M., Zhang, L., Muller, M., Marrugo, F. and Frerman, F. The functions of the flavin contact residues, αArg249 and βTyr16, in human electron transfer flavoprotein. Biochim. Biophys. Acta 1433 (1999) 139-152. [PMID: 10446367]

4. Rao, K.S., Albro, M., Dwyer, T.M. and Frerman, F.E. Kinetic mechanism of glutaryl-CoA dehydrogenase. Biochemistry 45 (2006) 15853-15861. [PMID: 17176108]

[EC 1.3.8.6 created 1972 as EC 1.3.99.7, transferred 2012 to EC 1.3.8.6, modified 2013, modified 2019]

*EC 1.4.1.14

Accepted name: glutamate synthase (NADH)

Reaction: 2 L-glutamate + NAD+ = L-glutamine + 2-oxoglutarate + NADH + H+
(1a) L-glutamate + NH3 = L-glutamine + H2O
(1b) L-glutamate + NAD+ + H2O = NH3 + 2-oxoglutarate + NADH + H+

For diagram of reaction click here.

Other name(s): glutamate (reduced nicotinamide adenine dinucleotide) synthase; NADH: GOGAT; L-glutamate synthase (NADH); L-glutamate synthetase; NADH-glutamate synthase; NADH-dependent glutamate synthase

Systematic name: L-glutamate:NAD+ oxidoreductase (transaminating)

Comments: A flavoprotein (FMN). The reaction takes place in the direction of L-glutamate production. 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 (cf. EC 1.4.1.2, glutamate dehydrogenase).

Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, CAS registry number: 65589-88-0

References:

1. Roon, R.J., Even, H.L. and Larimore, F. Glutamate synthase: properties of the reduced nicotinamide adenine dinucleotide-dependent enzyme from Saccharomyces cerevisiae. J. Bacteriol. 118 (1974) 89-95. [PMID: 4362465]

2. Boland, M.J. and Benny, A.G. Enzymes of nitrogen metabolism in legume nodules. Purification and properties of NADH-dependent glutamate synthase from lupin nodules. Eur. J. Biochem. 79 (1977) 355-362. [PMID: 21790]

3. Masters, D.S., Jr. and Meister, A. Inhibition of homocysteine sulfonamide of glutamate synthase purified from Saccharomyces cerevisiae. J. Biol. Chem 257 (1982) 8711-8715. [PMID: 7047525]

4. Anderson, M.P., Vance, C.P., Heichel, G.H. and Miller, S.S. Purification and characterization of NADH-glutamate synthase from alfalfa root nodules. Plant Physiol. 90 (1989) 351-358. [PMID: 16666762]

5. Blanco, L., Reddy, P.M., Silvente, S., Bucciarelli, B., Khandual, S., Alvarado-Affantranger, X., Sanchez, F., Miller, S., Vance, C. and Lara-Flores, M. Molecular cloning, characterization and regulation of two different NADH-glutamate synthase cDNAs in bean nodules. Plant Cell Environ 31 (2008) 454-472. [PMID: 18182018]

[EC 1.4.1.14 created 1978, modified 2019]

*EC 1.8.5.3

Accepted name: respiratory dimethylsulfoxide reductase

Reaction: dimethylsulfide + menaquinone + H2O = dimethylsulfoxide + menaquinol

For diagram of reaction click here.

Other name(s): dmsABC (gene names); DMSO reductase (ambiguous); dimethylsulfoxide reductase (ambiguous)

Systematic name: dimethyl sulfide:menaquinone oxidoreductase

Comments: The enzyme participates in bacterial electron transfer pathways in which dimethylsulfoxide (DMSO) is the terminal electron acceptor. It is composed of three subunits - DmsA contains a bis(guanylyl molybdopterin) cofactor and a [4Fe-4S] cluster, DmsB is an iron-sulfur protein, and DmsC is a transmembrane protein that anchors the enzyme and accepts electrons from the quinol pool. The electrons are passed through DmsB to DmsA and on to DMSO. The enzyme can also reduce pyridine-N-oxide and trimethylamine N-oxide to the corresponding amines with lower activity.

Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, CAS registry number:

References:

1. Daruwala, R. and Meganathan, R. Dimethyl sulfoxide reductase is not required for trimethylamine N-oxide reduction in Escherichia coli. FEMS Microbiol. Lett. 67 (1991) 255-259. [PMID: 1769531]

2. Miguel, L. and Meganthan, R. Electron donors and the quinone involved in dimethyl sulfoxide reduction in Escherichia coli. Curr. Microbiol. 22 (1991) 109-115.

3. Simala-Grant, J.L. and Weiner, J.H. Kinetic analysis and substrate specificity of Escherichia coli dimethyl sulfoxide reductase. Microbiology 142 (1996) 3231-3239. [PMID: 8969520]

4. Rothery, R.A., Trieber, C.A. and Weiner, J.H. Interactions between the molybdenum cofactor and iron-sulfur clusters of Escherichia coli dimethylsulfoxide reductase. J. Biol. Chem. 274 (1999) 13002-13009. [PMID: 10224050]

[EC 1.8.5.3 created 2011, modified 2019]

EC 1.13.11.88

Accepted name: isoeugenol monooxygenase

Reaction: isoeugenol + O2 = vanillin + acetaldehyde

For diagram of reaction click here.

Glossary: isoeugenol = 2-methoxy-4-(prop-1-en-1-yl)phenol

Other name(s): iem (gene name)

Systematic name: isoeugenol:oxygen 7,8-oxidoreductase (bond-cleaving)

Comments: Contains Fe(II). The enzyme, charcterised from the bacteria Pseudomonas putida and Pseudomonas nitroreducens, catalyses the epoxidation of the double bond in the side chain of isoeugenol, followed by a second oxygenation and cleavage of the side chain in the form of acetaldehyde.

References:

1. Shimoni, E., Ravid, U. and Shoham, Y. Isolation of a Bacillus sp. capable of transforming isoeugenol to vanillin. J. Biotechnol. 78 (2000) 1-9. [PMID: 10702906]

2. Yamada, M., Okada, Y., Yoshida, T. and Nagasawa, T. Biotransformation of isoeugenol to vanillin by Pseudomonas putida IE27 cells. Appl. Microbiol. Biotechnol. 73 (2007) 1025-1030. [PMID: 16944125]

3. Yamada, M., Okada, Y., Yoshida, T. and Nagasawa, T. Purification, characterization and gene cloning of isoeugenol-degrading enzyme from Pseudomonas putida IE27. Arch. Microbiol. 187 (2007) 511-517. [PMID: 17516050]

4. Ryu, J.Y., Seo, J., Unno, T., Ahn, J.H., Yan, T., Sadowsky, M.J. and Hur, H.G. Isoeugenol monooxygenase and its putative regulatory gene are located in the eugenol metabolic gene cluster in Pseudomonas nitroreducens Jin1. Arch. Microbiol. 192 (2010) 201-209. [PMID: 20091296]

5. Ryu, J.Y., Seo, J., Park, S., Ahn, J.H., Chong, Y., Sadowsky, M.J. and Hur, H.G. Characterization of an isoeugenol monooxygenase (iem) from Pseudomonas nitroreducens Jin1 that transforms isoeugenol to vanillin. Biosci. Biotechnol. Biochem. 77 (2013) 289-294. [PMID: 23391906]

[EC 1.13.11.88 created 2019]

EC 1.14.11.61

Accepted name: feruloyl-CoA 6-hydroxylase

Reaction: trans-feruloyl-CoA + 2-oxoglutarate + O2 = trans-6-hydroxyferuloyl-CoA + succinate + CO2

Glossary: trans-feruloyl-CoA = 4-hydroxy-3-methoxycinnamoyl-CoA = (E)-3-(4-hydroxy-3-methoxyphenyl)propenoyl-CoA

Systematic name: feruloyl-CoA,2-oxoglutarate:oxygen oxidoreductase (6-hydroxylating)

Comments: Requires iron(II) and ascorbate. The product spontaneously undergoes trans-cis isomerization and lactonization to form scopoletin, liberating CoA in the process. The enzymes from the plants Ruta graveolens and Ipomoea batatas also act on trans-4-coumaroyl-CoA. cf. EC 1.14.11.62, trans-4-coumaroyl-CoA 2-hydroxylase.

References:

1. Kai, K., Mizutani, M., Kawamura, N., Yamamoto, R., Tamai, M., Yamaguchi, H., Sakata, K. and Shimizu, B. Scopoletin is biosynthesized via ortho-hydroxylation of feruloyl CoA by a 2-oxoglutarate-dependent dioxygenase in Arabidopsis thaliana. Plant J. 55 (2008) 989-999. [PMID: 18547395]

2. Bayoumi, S.A., Rowan, M.G., Blagbrough, I.S. and Beeching, J.R. Biosynthesis of scopoletin and scopolin in cassava roots during post-harvest physiological deterioration: the E-Z-isomerisation stage. Phytochemistry 69 (2008) 2928-2936. [PMID: 19004461]

3. Vialart, G., Hehn, A., Olry, A., Ito, K., Krieger, C., Larbat, R., Paris, C., Shimizu, B., Sugimoto, Y., Mizutani, M. and Bourgaud, F. A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2'-hydroxylase activity (C2’H): a missing step in the synthesis of umbelliferone in plants. Plant J. 70 (2012) 460-470. [PMID: 22168819]

4. Matsumoto, S., Mizutani, M., Sakata, K. and Shimizu, B. Molecular cloning and functional analysis of the ortho-hydroxylases of p-coumaroyl coenzyme A/feruloyl coenzyme A involved in formation of umbelliferone and scopoletin in sweet potato, Ipomoea batatas (L.) Lam. Phytochemistry 74 (2012) 49-57. [PMID: 22169019]

[EC 1.14.11.61 created 2019]

EC 1.14.11.62

Accepted name: trans-4-coumaroyl-CoA 2-hydroxylase

Reaction: trans-4-coumaroyl-CoA + 2-oxoglutarate + O2 = 2,4-dihydroxycinnamoyl-CoA + succinate + CO2

Glossary: trans-4-coumaroyl-CoA = (2E)-3-(4-hydroxyphenyl)prop-2-enoyl-CoA
2,4-dihydroxycinnamoyl-CoA = (2E)-3-(2,4-dihydroxyphenyl)prop-2-enoyl-CoA
umbelliferone = 7-hydroxycoumarin

Other name(s): Diox4 (gene name); C2'H (gene name)

Systematic name: (2E)-3-(4-hydroxyphenyl)prop-2-enoyl-CoA,2-oxoglutarate:oxygen oxidoreductase (2-hydroxylating)

Comments: Requires iron(II) and ascorbate. The product spontaneously undergoes trans-cis isomerization followed by lactonization and cyclization, liberating CoA and forming umbelliferone. The enzymes from the plants Ruta graveolens and Ipomoea batatas also act on trans-feruloyl-CoA (cf. EC 1.14.11.61, feruloyl-CoA 6-hydroxylase).

References:

1. Vialart, G., Hehn, A., Olry, A., Ito, K., Krieger, C., Larbat, R., Paris, C., Shimizu, B., Sugimoto, Y., Mizutani, M. and Bourgaud, F. A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2'-hydroxylase activity (C2'H): a missing step in the synthesis of umbelliferone in plants. Plant J. 70 (2012) 460-470. [PMID: 22168819]

2. Matsumoto, S., Mizutani, M., Sakata, K. and Shimizu, B. Molecular cloning and functional analysis of the ortho-hydroxylases of p-coumaroyl coenzyme A/feruloyl coenzyme A involved in formation of umbelliferone and scopoletin in sweet potato, Ipomoea batatas (L.) Lam. Phytochemistry 74 (2012) 49-57. [PMID: 22169019]

[EC 1.14.11.62 created 2019]

EC 1.14.11.63

Accepted name: peptidyl-lysine (3S)-dioxygenase

Reaction: a [protein]-L-lysine + 2-oxoglutarate + O2 = a [protein]-(3S)-3-hydroxy-L-lysine + succinate + CO2

Other name(s): JMJD7 (gene name); Jumonji domain-containing protein 7; JmjC domain-containing protein 7

Systematic name: [protein]-L-lysine,2-oxoglutarate:oxygen oxidoreductase (3S-hydroxylating)

Comments: Requires iron(II). The enzyme acts on specific lysine residues in its substrates, and is stereo-specific. The enzyme encoded by the human JMJD7 gene acts specifically on two related members of the translation factor family of GTPases, DRG1 and DRG2.

References:

1. Markolovic, S., Zhuang, Q., Wilkins, S.E., Eaton, C.D., Abboud, M.I., Katz, M.J., McNeil, H.E., Lesniak, R.K., Hall, C., Struwe, W.B., Konietzny, R., Davis, S., Yang, M., Ge, W., Benesch, J.LP., Kessler, B.M., Ratcliffe, P.J., Cockman, M.E., Fischer, R., Wappner, P., Chowdhury, R., Coleman, M.L. and Schofield, C.J. The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases. Nat. Chem. Biol. 14 (2018) 688-695. [PMID: 29915238]

[EC 1.14.11.63 created 2019]

EC 1.14.13.243

Accepted name: toluene 2-monooxygenase

Reaction: (1) toluene + NADH + H+ + O2 = 2-methylphenol + NAD+ + H2O
(2) 2-methylphenol + NADH + H+ + O2 = 3-methylcatechol + NAD+ + H2O

Other name(s): tomA1/2/3/4/5 (gene names); toluene ortho-monooxygenase

Systematic name: toluene,NADH:oxygen oxidoreductase (2,3-dihydroxylating)

Comments: The enzyme, characterized from the bacterium Burkholderia cepacia, belongs to a class of nonheme, oxygen-dependent diiron enzymes. It contains a hydroxylase component with two binuclear iron centers, an NADH-oxidoreductase component containing FAD and a [2Fe-2S] iron-sulfur cluster, and a third component involved in electron transfer between the hydroxylase and the reductase. The enzyme dihydroxylates its substrate in two sequential hydroxylations, initially forming 2-methylphenol, which is hydroxylated to 3-methylcatechol.

References:

1. Newman, L.M. and Wackett, L.P. Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry 34 (1995) 14066-14076. [PMID: 7578004]

2. Yeager, C.M., Bottomley, P.J., Arp, D.J. and Hyman, M.R. Inactivation of toluene 2-monooxygenase in Burkholderia cepacia G4 by alkynes. Appl. Environ. Microbiol. 65 (1999) 632-639. [PMID: 9925593]

3. Canada, K.A., Iwashita, S., Shim, H. and Wood, T.K. Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation. J. Bacteriol. 184 (2002) 344-349. [PMID: 11751810]

[EC 1.14.13.243 created 2019]

EC 1.14.13.244

Accepted name: phenol 2-monooxygenase (NADH)

Reaction: phenol + NADH + H+ + O2 = catechol + NAD+ + H2O

For diagram of reaction click here.

Other name(s): dmpLMNOP (gene names)

Systematic name: phenol,NADH:oxygen oxidoreductase (2-hydroxylating)

Comments: The enzyme, characterized from the bacteria Pseudomonas sp. CF600 and Acinetobacter radioresistens, consists of a multisubunit oxygenease component that contains the active site and a dinuclear iron center, a reductase component that contains FAD and one iron-sulfur cluster, and a regulatory component. The reductase component is responsible for transferring electrons from NADH to the dinuclear iron center.

References:

1. Nordlund, I., Powlowski, J. and Shingler, V. Complete nucleotide sequence and polypeptide analysis of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J. Bacteriol. 172 (1990) 6826-6833. [PMID: 2254258]

2. Powlowski, J. and Shingler, V. In vitro analysis of polypeptide requirements of multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J. Bacteriol. 172 (1990) 6834-6840. [PMID: 2254259]

3. Powlowski, J., Sealy, J., Shingler, V. and Cadieux, E. On the role of DmpK, an auxiliary protein associated with multicomponent phenol hydroxylase from Pseudomonas sp. strain CF600. J. Biol. Chem 272 (1997) 945-951. [PMID: 8995386]

4. Qian, H., Edlund, U., Powlowski, J., Shingler, V. and Sethson, I. Solution structure of phenol hydroxylase protein component P2 determined by NMR spectroscopy. Biochemistry 36 (1997) 495-504. [PMID: 9012665]

5. Cadieux, E., Vrajmasu, V., Achim, C., Powlowski, J. and Munck, E. Biochemical, Mossbauer, and EPR studies of the diiron cluster of phenol hydroxylase from Pseudomonas sp. strain CF 600. Biochemistry 41 (2002) 10680-10691. [PMID: 12186554]

[EC 1.14.13.244 created 2019]

EC 1.14.13.245

Accepted name: assimilatory dimethylsulfide S-monooxygenase

Reaction: (1) dimethyl sulfide + NADH + H+ + O2 = dimethyl sulfoxide + NAD+ + H2O
(2) dimethyl sulfoxide + NADH + H+ + O2 = dimethyl sulfone + NAD+ + H2O

For diagram of reaction click here.

Other name(s): dsoBCDEF (gene names)

Systematic name: dimethyl sulfide,NADH:oxygen oxidoreductase (S-oxidizing)

Comments: The enzyme, studied from the bacterium Acinetobacter sp. strain 20B, is very similar to EC 1.14.13.244, phenol 2-monooxygenase (NADH). It consists of a multisubunit oxygenease component that contains the active site and a dinuclear iron center, a reductase component that contains FAD and one iron-sulfur cluster, and a regulatory component. The three components comprise five different polypeptides. The enzyme catalyses the first two steps of a dimethyl sulfide oxidation pathway in this organism.

References:

1. Horinouchi, M., Kasuga, K., Nojiri, H., Yamane, H. and Omori, T. Cloning and characterization of genes encoding an enzyme which oxidizes dimethyl sulfide in Acinetobacter sp. strain 20B. FEMS Microbiol. Lett. 155 (1997) 99-105. [PMID: 9345770]

2. Horinouchi, M., Yoshida, T., Nojiri, H., Yamane, H. and Omori, T. Polypeptide requirement of multicomponent monooxygenase DsoABCDEF for dimethyl sulfide oxidizing activity. Biosci. Biotechnol. Biochem. 63 (1999) 1765-1771. [PMID: 26300166]

[EC 1.14.13.245 created 2019]

EC 1.14.15.36

Accepted name: sterol 14α-demethylase (ferredoxin)

Reaction: a 14α-methylsteroid + 6 reduced ferredoxin [iron-sulfur] cluster + 6 H+ + 3 O2 = a Δ14-steroid + formate + 6 oxidized ferredoxin [iron-sulfur] cluster + 4 H2O (overall reaction)
(1a) a 14α-methylsteroid + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = a 14α-hydroxymethylsteroid + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O
(1b) a 14α-hydroxymethylsteroid + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = a 14α-formylsteroid + 2 oxidized ferredoxin [iron-sulfur] cluster + 2 H2O
(1c) a 14α-formylsteroid + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ + O2 = a Δ14-steroid + formate + 2 oxidized ferredoxin [iron-sulfur] cluster + H2O

For diagram of reaction click here.

Other name(s): cyp51 (gene name)

Systematic name: sterol,reduced ferredoxin:oxygen oxidoreductase (14-methyl cleaving)

Comments: A cytochrome P-450 (heme-thiolate) protein found in several bacterial species. The enzyme, which is involved in sterol biosynthesis, catalyses a hydroxylation and a reduction of the 14α-methyl group, followed by a second hydroxylation, resulting in the elimination of formate and formation of a 14(15) double bond. The enzyme from Methylococcus capsulatus is fused to the ferredoxin by an alanine-rich linker. cf. EC 1.14.14.154, sterol 14α-demethylase.

References:

1. Jackson, C.J., Lamb, D.C., Marczylo, T.H., Warrilow, A.G., Manning, N.J., Lowe, D.J., Kelly, D.E. and Kelly, S.L. A novel sterol 14α-demethylase/ferredoxin fusion protein (MCCYP51FX) from Methylococcus capsulatus represents a new class of the cytochrome P450 superfamily. J. Biol. Chem 277 (2002) 46959-46965. [PMID: 12235134]

2. Rezen, T., Debeljak, N., Kordis, D. and Rozman, D. New aspects on lanosterol 14α-demethylase and cytochrome P450 evolution: lanosterol/cycloartenol diversification and lateral transfer. J. Mol. Evol. 59 (2004) 51-58. [PMID: 15383907]

3. Desmond, E. and Gribaldo, S. Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature. Genome Biol Evol 1 (2009) 364-381. [PMID: 20333205]

[EC 1.14.15.36 created 2019]

EC 1.14.15.37

Accepted name: luteothin monooxygenase

Reaction: luteothin + 2 O2 + 4 reduced ferredoxin [iron-sulfur] cluster + 4 H+ = aureothin + 3 H2O + 4 oxidized ferredoxin [iron-sulfur] cluster (overall reaction)
(1a) luteothin + O2 + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = (7R)-7-hydroxyluteothin + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster
(1b) (7R)-7-hydroxyluteothin + O2 + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = aureothin + 2 H2O + 2 oxidized ferredoxin [iron-sulfur] cluster

For diagram of reaction click here.

Glossary: luteothin = 2-[(3E,5E)-3,5-dimethyl-6-(4-nitrophenyl)hexa-3,5-dien-1-yl]-6-methoxy-3,5-dimethyl-4H-pyran-4-one
aureothin = 2-methoxy-3,5-dimethyl-6-[(2R,4Z)-4-[(2E)-2-methyl-3-(4-nitrophenyl)prop-2-en-1-ylidene]oxolan-2-yl]-4H-pyran-4-one
spectinabilin = neoaureothin = 2-methoxy-3,5-dimethyl-6-[(2R,4Z)-4-[(2E,4E,6E)-2,4,6-trimethyl-7-(4-nitrophenyl)hepta-2,4,6-trien-1-ylidene]oxolan-2-yl]-4H-pyran-4-one

Other name(s): aurH (gene name)

Systematic name: luteothin,ferredoxin:oxygen oxidoreductase (aureothin-forming)

Comments: The enzyme, characterized from the bacterium Streptomyces thioluteus, is a bifunctional cytochrome P-450 (heme-thiolate) protein that catalyses both the hydroxylation of its substrate and formation of a furan ring, the final step in the biosynthesis of the antibiotic aureothin. In the bacteria Streptomyces orinoci and Streptomyces spectabilis an orthologous enzyme catalyses a similar reaction that forms spectinabilin.

References:

1. He, J., Muller, M. and Hertweck, C. Formation of the aureothin tetrahydrofuran ring by a bifunctional cytochrome P450 monooxygenase. J. Am. Chem. Soc. 126 (2004) 16742-16743. [PMID: 15612710]

2. Traitcheva, N., Jenke-Kodama, H., He, J., Dittmann, E. and Hertweck, C. Non-colinear polyketide biosynthesis in the aureothin and neoaureothin pathways: an evolutionary perspective. Chembiochem 8 (2007) 1841-1849. [PMID: 17763486]

[EC 1.14.15.37 created 2019]

EC 1.14.99.65

Accepted name: 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] 3-hydroxylase

Reaction: 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein] + reduced acceptor + O2 = 2-(4-aminophenyl)-L-seryl-[CmlP-peptidyl-carrier-protein] + acceptor + H2O

Other name(s): cmlA (gene name)

Systematic name: 4-amino-L-phenylalanyl-[CmlP-peptidyl-carrier-protein],acceptor:oxygen 3-oxidoreductase

Comments: The enzyme, characterized from the bacterium Streptomyces venezuelae, participates in the biosynthesis of the antibiotic chloramphenicol. It carries an oxygen-bridged dinuclear iron cluster. The native electron donor remains unknown, and the enzyme was assayed in vitro using sodium dithionite. The enzyme only acts on its substrate when it is loaded onto the peptidyl-carrier domain of the CmlP non-ribosomal peptide synthase.

References:

1. Makris, T.M., Chakrabarti, M., Munck, E. and Lipscomb, J.D. A family of diiron monooxygenases catalyzing amino acid β-hydroxylation in antibiotic biosynthesis. Proc. Natl Acad. Sci. USA 107 (2010) 15391-15396. [PMID: 20713732]

[EC 1.14.99.65 created 2019]

EC 2.1.1.353

Accepted name: demethylluteothin O-methyltransferase

Reaction: S-adenosyl-L-methionine + demethylluteothin = S-adenosyl-L-homocysteine + luteothin

For diagram of reaction click here.

Glossary: luteothin = 2-[(3E,5E)-3,5-dimethyl-6-(4-nitrophenyl)hexa-3,5-dien-1-yl]-6-methoxy-3,5-dimethyl-4H-pyran-4-one
aureothin = 2-methoxy-3,5-dimethyl-6-[(2R,4Z)-4-[(2E)-2-methyl-3-(4-nitrophenyl)prop-2-en-1-ylidene]oxolan-2-yl]-4H-pyran-4-one
spectinabilin = neoaureothin = 2-methoxy-3,5-dimethyl-6-[(2R,4Z)-4-[(2E,4E,6E)-2,4,6-trimethyl-7-(4-nitrophenyl)hepta-2,4,6-trien-1-ylidene]oxolan-2-yl]-4H-pyran-4-one

Other name(s): aurI (gene name)

Systematic name: S-adenosyl-L-methionine:demethylluteothin O-methyltransferase

Comments: The enzyme, characterized from the bacterium Streptomyces thioluteus, participates in the biosynthesis of the antibiotic aureothin. An orthologous enzyme in the bacteria Streptomyces orinoci and Streptomyces spectabilis catalyses a similar reaction in the biosynthesis of spectinabilin.

References:

1. He, J., Muller, M. and Hertweck, C. Formation of the aureothin tetrahydrofuran ring by a bifunctional cytochrome P450 monooxygenase. J. Am. Chem. Soc. 126 (2004) 16742-16743. [PMID: 15612710]

2. Muller, M., He, J. and Hertweck, C. Dissection of the late steps in aureothin biosynthesis. Chembiochem 7 (2006) 37-39. [PMID: 16292785]

[EC 2.1.1.353 created 2019]

*EC 2.3.1.85

Accepted name: fatty-acid synthase system

Reaction: acetyl-CoA + n malonyl-CoA + 2n NADPH + 2n H+ = a long-chain fatty acid + (n+1) CoA + n CO2 + 2n NADP+

Glossary: a long-chain-fatty acid = a fatty acid with an aliphatic chain of 13-22 carbons.

Other name(s): FASN (gene name); fatty-acid synthase

Systematic name: acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing and thioester-hydrolysing)

Comments: The animal enzyme is a multi-functional protein catalysing the reactions of EC 2.3.1.38 [acyl-carrier-protein] S-acetyltransferase, EC 2.3.1.39 [acyl-carrier-protein] S-malonyltransferase, EC 2.3.1.41 β-ketoacyl-[acyl-carrier-protein] synthase I, EC 1.1.1.100 3-oxoacyl-[acyl-carrier-protein] reductase, EC 4.2.1.59 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, EC 1.3.1.39 enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) and EC 3.1.2.14 oleoyl-[acyl-carrier-protein] hydrolase. cf. EC 2.3.1.86, fatty-acyl-CoA synthase system.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number: 9045-77-6

References:

1. Stoops, J.K., Ross, P., Arslanian, M.J., Aune, K.C., Wakil, S.J. and Oliver, R.M. Physicochemical studies of the rat liver and adipose fatty acid synthetases. J. Biol. Chem. 254 (1979) 7418-7426. [PMID: 457689]

2. Wakil, S.J., Stoops, J.K. and Joshi, V.C. Fatty acid synthesis and its regulation. Annu. Rev. Biochem. 52 (1983) 537-579. [PMID: 6137188]

[EC 2.3.1.85 created 1984, modified 2019]

*EC 2.3.1.86

Accepted name: fatty-acyl-CoA synthase system

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

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

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

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

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number: 94219-29-1

References:

1. Schweitzer, E., Kniep, B., Castorph, H. and Holzner, U. Pantetheine-free mutants of the yeast fatty-acid-synthetase complex. Eur. J. Biochem. 39 (1973) 353-362. [PMID: 4590449]

2. Wakil, S.J., Stoops, J.K. and Joshi, V.C. Fatty acid synthesis and its regulation. Annu. Rev. Biochem. 52 (1983) 537-579. [PMID: 6137188]

3. Tehlivets, O., Scheuringer, K. and Kohlwein, S.D. Fatty acid synthesis and elongation in yeast. Biochim. Biophys. Acta 1771 (2007) 255-270. [PMID: 16950653]

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

*EC 2.3.1.161

Accepted name: lovastatin nonaketide synthase

Reaction: 9 malonyl-CoA + 11 NADPH + 10 H+ + S-adenosyl-L-methionine + holo-[lovastatin nonaketide synthase] = dihydromonacolin L-[lovastatin nonaketide synthase] + 9 CoA + 9 CO2 + 11 NADP+ + S-adenosyl-L-homocysteine + 6 H2O

For diagram of reaction click here.

Glossary: dihydromonacolin L acid = (3R,5R)-7-[(1S,2S,4aR,6R,8aS)-2,6-dimethyl-1,2,4a,5,6,7,8,8a-octahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate

Other name(s): LNKS; LovB; LovC; acyl-CoA:malonyl-CoA C-acyltransferase (decarboxylating, oxoacyl- and enoyl-reducing, thioester-hydrolysing)

Systematic name: acyl-CoA:malonyl-CoA C-acyltransferase (dihydromonacolin L acid-forming)

Comments: This fungal enzyme system comprises a multi-functional polyketide synthase (PKS) and an enoyl reductase. The PKS catalyses many of the chain building reactions of EC 2.3.1.85, fatty-acid synthase system, as well as a reductive methylation and a Diels-Alder reaction, while the reductase is responsible for three enoyl reductions that are necessary for dihydromonacolin L acid production.

Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, CAS registry number: 235426-97-8

References:

1. Ma, S.M., Li, J.W., Choi, J.W., Zhou, H., Lee, K.K., Moorthie, V.A., Xie, X., Kealey, J.T., Da Silva, N.A., Vederas, J.C. and Tang, Y. Complete reconstitution of a highly reducing iterative polyketide synthase. Science 326 (2009) 589-592. [PMID: 19900898]

2. Kennedy, J., Auclair, K., Kendrew, S.G., Park, C., Vederas, J.C. and Hutchinson, C.R. Modulation of polyketide synthase activity by accessory proteins during lovastatin biosynthesis. Science 284 (1999) 1368-1372. [PMID: 10334994]

3. Auclair, K., Sutherland, A., Kennedy, J., Witter, D.J., van der Heever, J.P., Hutchinson, C.R. and Vederas, J.C. Lovastatin nonaketide synthase catalyses an intramolecular Diels-Alder reaction of a substrate analogue. J. Am. Chem. Soc. 122 (2000) 11519-11520.

[EC 2.3.1.161 created 2002, modified 2015, modified 2016, modified 2019]

EC 2.3.1.281

Accepted name: 5-hydroxydodecatetraenal polyketide synthase

Reaction: 6 malonyl-CoA + 5 NADPH + NADH + 6 H+ = (2E,5S,6E,8E,10E)-5-hydroxydodeca-2,6,8,10-tetraenal + 6 CoA + 5 NADP+ + NAD+ + 6 CO2 + 4 H2O

For diagram of reaction click here.

Glossary: coelimycin P1 = N-[(3R)-8-[(2E)-but-2-enoyl]-6-[(2E)-5,6-dihydropyridin-2(1H)-ylidene]-2-oxo-3,4-dihydro-2H,6H-1,5-oxathiocin-3-yl]acetamide

Other name(s): cpkABC (gene names)

Systematic name: malonyl-CoA:malonyl-CoA malonyltransferase ((2E,5S,6E,8E,10E)-5-hydroxydodeca-2,6,8,10-tetraenal-forming)

Comments: This polyketide synthase enzyme, characterized from the bacterium Streptomyces coelicolor A3(2), catalyses the first reaction in the biosynthesis of coelimycin P1. The enzyme is made of three proteins which together comprise six modules that contain a total of 28 domains. An NADH-dependent terminal reductase domain at the C-terminus of the enzyme catalyses the reductive release of the product.

References:

1. Pawlik, K., Kotowska, M., Chater, K.F., Kuczek, K. and Takano, E. A cryptic type I polyketide synthase (cpk) gene cluster in Streptomyces coelicolor A3(2). Arch. Microbiol. 187 (2007) 87-99. [PMID: 17009021]

2. Awodi, U.R., Ronan, J.L., Masschelein, J., Santos, E.LC. and Challis, G.L. Thioester reduction and aldehyde transamination are universal steps in actinobacterial polyketide alkaloid biosynthesis. Chem. Sci. 8 (2017) 411-415. [PMID: 28451186]

[EC 2.3.1.281 created 2019]

EC 2.3.1.282

Accepted name: phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase

Reaction: (1) 2 a mycocerosyl-[mycocerosic acid synthase] + a phthiocerol = a dimycocerosyl phthiocerol + 2 holo-[mycocerosic acid synthase]
(2) 2 a mycocerosyl-[mycocerosic acid synthase] + a phthiodiolone = a dimycocerosyl phthiodiolone + 2 holo-[mycocerosic acid synthase]
(3) 2 a mycocerosyl-[mycocerosic acid synthase] + a phenolphthiocerol = a dimycocerosyl phenolphthiocerol + 2 holo-[mycocerosic acid synthase]

Glossary: a mycocerosate = 2,4,6-trimethyl- and 2,4,6,8-tetramethyl-2-alkanoic acids present in many pathogenic mycobacteria. The chiral centers bearing the methyl groups have an L (levorotatory) stereo configuration.
a phthiocerol = a linear carbohydrate molecule to which one methoxyl group, one methyl group, and two secondary hydroxyl groups are attached.
a phthiodiolone = an intermediate in phthiocerol biosynthesis, containing an oxo group where phthiocerols contain a methoxyl group
a phenolphthiocerol = a compound related to phthiocerol that contains a phenol group at the ω end of the molecule

Other name(s): papA5 (gene name)

Systematic name: mycocerosyl-[mycocerosic acid synthase]:phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase

Comments: The enzyme, present in certain pathogenic species of mycobacteria, catalyses the transfer of mycocerosic acids to the two hydroxyl groups at the common lipid core of phthiocerol, phthiodiolone, and phenolphthiocerol, forming dimycocerosate esters. The fatty acid precursors of mycocerosic acids are activated by EC 6.2.1.49, long-chain fatty acid adenylyltransferase FadD28, which loads them onto EC 2.3.1.111, mycocerosate synthase. That enzyme extends the precursors to form mycocerosic acids that remain attached until transferred by EC 2.3.1.282.

References:

1. Onwueme, K.C., Ferreras, J.A., Buglino, J., Lima, C.D. and Quadri, L.E. Mycobacterial polyketide-associated proteins are acyltransferases: proof of principle with Mycobacterium tuberculosis PapA5. Proc. Natl Acad. Sci. USA 101 (2004) 4608-4613. [PMID: 15070765]

2. Buglino, J., Onwueme, K.C., Ferreras, J.A., Quadri, L.E. and Lima, C.D. Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis. J. Biol. Chem 279 (2004) 30634-30642. [PMID: 15123643]

3. Chavadi, S.S., Onwueme, K.C., Edupuganti, U.R., Jerome, J., Chatterjee, D., Soll, C.E. and Quadri, L.E. The mycobacterial acyltransferase PapA5 is required for biosynthesis of cell wall-associated phenolic glycolipids. Microbiology 158 (2012) 1379-1387. [PMID: 22361940]

4. Touchette, M.H., Bommineni, G.R., Delle Bovi, R.J., Gadbery, J.E., Nicora, C.D., Shukla, A.K., Kyle, J.E., Metz, T.O., Martin, D.W., Sampson, N.S., Miller, W.T., Tonge, P.J. and Seeliger, J.C. Diacyltransferase activity and chain length specificity of Mycobacterium tuberculosis PapA5 in the synthesis of alkyl β-diol lipids. Biochemistry 54 (2015) 5457-5468. [PMID: 26271001]

[EC 2.3.1.282 created 2019]

EC 2.3.1.283

Accepted name: 2'-acyl-2-O-sulfo-trehalose (hydroxy)phthioceranyltransferase

Reaction: a (hydroxy)phthioceranyl-[(hydroxy)phthioceranic acid synthase] + 2'-palmitoyl/stearoyl-2-O-sulfo-α,α-trehalose = a 3'-(hydroxy)phthioceranyl-2'-palmitoyl/stearoyl-2-O-sulfo-α,α-trehalose + holo-[(hydroxy)phthioceranic acid synthase]

Other name(s): papA1 (gene name)

Systematic name: (hydroxy)phthioceranyl-[(hydroxy)phthioceranic acid synthase]:2'-acyl-2-O-sulfo-α,α-trehalose 3'-(hydroxy)phthioceranyltransferase

Comments: This mycobacterial enzyme catalyses the acylation of 2'-palmitoyl/stearoyl-2-O-sulfo-α,α-trehalose at the 3' position by a (hydroxy)phthioceranoyl group during the biosynthesis of mycobacterial sulfolipids.

References:

1. Bhatt, K., Gurcha, S.S., Bhatt, A., Besra, G.S. and Jacobs, W.R., Jr. Two polyketide-synthase-associated acyltransferases are required for sulfolipid biosynthesis in Mycobacterium tuberculosis. Microbiology 153 (2007) 513-520. [PMID: 17259623]

2. Kumar, P., Schelle, M.W., Jain, M., Lin, F.L., Petzold, C.J., Leavell, M.D., Leary, J.A., Cox, J.S. and Bertozzi, C.R. PapA1 and PapA2 are acyltransferases essential for the biosynthesis of the Mycobacterium tuberculosis virulence factor sulfolipid-1. Proc. Natl Acad. Sci. USA 104 (2007) 11221-11226. [PMID: 17592143]

[EC 2.3.1.283 created 2019]

EC 2.3.1.284

Accepted name: 3'-(hydroxy)phthioceranyl-2'-palmitoyl(stearoyl)-2-O-sulfo-trehalose (hydroxy)phthioceranyltransferase

Reaction: 3 3'-(hydroxy)phthioceranyl-2'-palmitoyl(stearoyl)-2-O-sulfo-α,α-trehalose = 3,6,6'-tris-(hydroxy)phthioceranyl-2-palmitoyl(stearoyl)-2'-sulfo-α-alpha-trehalose + 2 2'-palmitoyl/stearoyl-2-O-sulfo-α,α-trehalose

Glossary: 3,6,6'-tris-(hydroxy)phthioceranyl-2-palmitoyl(stearoyl)-2'-sulfo-α-alpha-trehalose = a mycobacterial sulfolipid

Other name(s): chp1 (gene name)

Systematic name: 3'-(hydroxy)phthioceranyl-2'-palmitoyl(stearoyl)-2-O-sulfo-α,α-trehalose:3'-(hydroxy)phthioceranyl-2'-palmitoyl(stearoyl)-2-O-sulfo-α,α-trehalose 6,6'-di(hydroxy)phthioceranyltransferase

Comments: The enzyme, present in mycobacteria, catalyses the ultimate step in the biosynthesis of mycobacterial sulfolipids. It catalyses two successive transfers of a (hydroxy)phthioceranyl group from two diacylated intermediates to third diacylated intermediate, generating the tetraacylated sulfolipid.

References:

1. Seeliger, J.C., Holsclaw, C.M., Schelle, M.W., Botyanszki, Z., Gilmore, S.A., Tully, S.E., Niederweis, M., Cravatt, B.F., Leary, J.A. and Bertozzi, C.R. Elucidation and chemical modulation of sulfolipid-1 biosynthesis in Mycobacterium tuberculosis. J. Biol. Chem 287 (2012) 7990-8000. [PMID: 22194604]

[EC 2.3.1.284 created 2019]

EC 2.3.1.285

Accepted name: (13S,14R)-1,13-dihydroxy-N-methylcanadine 13-O-acetyltransferase

Reaction: acetyl-CoA + (13S,14R)-1,13-dihydroxy-N-methylcanadine = (13S,14R)-13-O-acetyl-1-hydroxy-N-methylcanadine + CoA

For diagram of reaction click here.

Other name(s): AT1 (gene name)

Systematic name: acetyl-CoA:(13S,14R)-1,13-dihydroxy-N-methylcanadine O-acetyltransferase

Comments: The enzyme, characterized from the plant Papaver somniferum (opium poppy), participates in the biosynthesis of the isoquinoline alkaloid noscapine.

References:

1. Dang, T.T., Chen, X. and Facchini, P.J. Acetylation serves as a protective group in noscapine biosynthesis in opium poppy. Nat. Chem. Biol. 11 (2015) 104-106. [PMID: 25485687]

2. Li, Y., Li, S., Thodey, K., Trenchard, I., Cravens, A. and Smolke, C.D. Complete biosynthesis of noscapine and halogenated alkaloids in yeast. Proc. Natl Acad. Sci. USA 115 (2018) E3922-E3931. [PMID: 29610307]

[EC 2.3.1.285 created 2019]

EC 2.4.1.361

Accepted name: GDP-mannose:di-myo-inositol-1,3'-phosphate β-1,2-mannosyltransferase

Reaction: 2 GDP-α-D-mannose + bis(myo-inositol) 1,3'-phosphate = 2 GDP + 2-O-(β-D-mannosyl-(1→2)-β-D-mannosyl)-bis(myo-inositol) 1,3'-phosphate (overall reaction)
(1a) GDP-α-D-mannose + bis(myo-inositol) 1,3'-phosphate = GDP + 2-O-(β-D-mannosyl)-bis(myo-inositol) 1,3'-phosphate
(1b) GDP-α-D-mannose + 2-O-(β-D-mannosyl)-bis(myo-inositol) 1,3'-phosphate = GDP + 2-O-(β-D-mannosyl-(1→2)-β-D-mannosyl)-bis(myo-inositol) 1,3'-phosphate

Other name(s): MDIP synthase

Systematic name: GDP-α-D-mannose:bis(myo-inositol)-1,3'-phosphate 2-β-D-mannosyltransferase

Comments: The enzyme from the hyperthermophilic bacterium Thermotoga maritima is involved in the synthesis of the solutes 2-O-(β-D-mannosyl)-bis(myo-inositol) 1,3'-phosphate and 2-O-(β-D-mannosyl-(1→2)-β-D-mannosyl)-bis(myo-inositol) 1,3'-phosphate.

References:

1. Rodrigues, M.V., Borges, N., Almeida, C.P., Lamosa, P. and Santos, H. A unique β-1,2-mannosyltransferase of Thermotoga maritima that uses di-myo-inositol phosphate as the mannosyl acceptor. J. Bacteriol. 191 (2009) 6105-6115. [PMID: 19648237]

[EC 2.4.1.361 created 2019]

EC 2.4.1.362

Accepted name: α-(1→3) branching sucrase

Reaction: sucrose + a (1→6)-α-D-glucan = D-fructose + a (1→6)-α-D-glucan containing a (1→3)-α-D-glucose branch

Other name(s): branching sucrase A; BRS-A; brsA (gene name)

Systematic name: sucrose:(1→6)-α-D-glucan 3-α-D-[(1→3)-α-D-glucosyl]-transferase

Comments: The enzyme from Leuconostoc spp. is responsible for producing α-(1→3) branches in α-(1→6) glucans by transferring the glucose residue from fructose to a 3-hydroxyl group of a glucan.

References:

1. Vuillemin, M., Claverie, M., Brison, Y., Severac, E., Bondy, P., Morel, S., Monsan, P., Moulis, C. and Remaud-Simeon, M. Characterization of the first α-(1→3) branching sucrases of the GH70 family. J. Biol. Chem 291 (2016) 7687-7702. [PMID: 26763236]

2. Moulis, C., Andre, I. and Remaud-Simeon, M. GH13 amylosucrases and GH70 branching sucrases, atypical enzymes in their respective families. Cell. Mol. Life Sci. 73 (2016) 2661-2679. [PMID: 27141938]

[EC 2.4.1.362 created 2019]

EC 2.5.1.152

Accepted name: D-histidine 2-aminobutanoyltransferase

Reaction: S-adenosyl-L-methionine + D-histidine = N-[(3S)-3-amino-3-carboxypropyl]-D-histidine + S-methyl-5'-thioadenosine

For diagram of reaction click here.

Glossary: staphylopine = N-[(3S)-3-{[(1S)-1-carboxyethyl]amino}-3-carboxypropyl]-D-histidine

Other name(s): cntL (gene name)

Systematic name: S-adenosyl-L-methionine:D-histidine N-[(3S)-3-amino-3-carboxypropyl]-transferase

Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the metallophore staphylopine, which is involved in the acquisition of nickel, copper, and cobalt.

References:

1. Ghssein, G., Brutesco, C., Ouerdane, L., Fojcik, C., Izaute, A., Wang, S., Hajjar, C., Lobinski, R., Lemaire, D., Richaud, P., Voulhoux, R., Espaillat, A., Cava, F., Pignol, D., Borezee-Durant, E. and Arnoux, P. Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus. Science 352 (2016) 1105-1109. [PMID: 27230378]

[EC 2.5.1.152 created 2019]

EC 2.6.1.115

Accepted name: 5-hydroxydodecatetraenal 1-aminotransferase

Reaction: (2E,5S,6E,8E,10E)-1-aminododeca-2,6,8,10-tetraen-5-ol + pyruvate = (2E,5S,6E,8E,10E)-5-hydroxydodeca-2,6,8,10-tetraenal + L-alanine

For diagram of reaction click here.

Glossary: coelimycin P1 = N-[(3R)-8-[(2E)-but-2-enoyl]-2-oxo-6-[(2E)-1,2,5,6-tetrahydropyridin-2-ylidene]-2,3,4,6-tetrahydro-1,5-oxathiocin-3-yl]acetamide

Other name(s): cpkG (gene name)

Systematic name: (2E,5S,6E,8E,10E)-1-aminododeca-2,6,8,10-tetraen-5-ol:pyruvate aminotransferase

Comments: The enzyme, characterized from the bacterium Streptomyces coelicolor A3(2), participates in the biosynthesis of coelimycin P1, where it catalyses the amination of (2E,5S,6E,8E,10E)-5-hydroxydodeca-2,6,8,10-tetraenal. L-glutamate can also serve as the amino group donor with lower efficiency.

References:

1. Pawlik, K., Kotowska, M., Chater, K.F., Kuczek, K. and Takano, E. A cryptic type I polyketide synthase (cpk) gene cluster in Streptomyces coelicolor A3(2). Arch. Microbiol. 187 (2007) 87-99. [PMID: 17009021]

2. Awodi, U.R., Ronan, J.L., Masschelein, J., Santos, E.LC. and Challis, G.L. Thioester reduction and aldehyde transamination are universal steps in actinobacterial polyketide alkaloid biosynthesis. Chem. Sci. 8 (2017) 411-415. [PMID: 28451186]

[EC 2.6.1.115 created 2019]

EC 2.7.1.225

Accepted name: L-serine kinase (ATP)

Reaction: ATP + L-serine = ADP + O-phospho-L-serine

For diagram of reaction click here.

Other name(s): sbnI (gene name)

Systematic name: ATP:L-serine 3-phosphotransferase

Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of L-2,3-diaminopropanoate, which is used by that organism as a precursor for the biosynthesis of the siderophore staphyloferrin B.

References:

1. Verstraete, M.M., Perez-Borrajero, C., Brown, K.L., Heinrichs, D.E. and Murphy, M.EP. SbnI is a free serine kinase that generates O -phospho-l-serine for staphyloferrin B biosynthesis in Staphylococcus aureus. J. Biol. Chem 293 (2018) 6147-6160. [PMID: 29483190]

[EC 2.7.1.225 created 2019]

EC 2.7.1.226

Accepted name: L-serine kinase (ADP)

Reaction: ADP + L-serine = AMP + O-phospho-L-serine

Other name(s): serK (gene name)

Systematic name: ADP:L-serine 3-phosphotransferase

Comments: The enzyme, characterized in the hyperthermophilic archaeon Thermococcus kodakarensis, participates in L-cysteine biosynthesis.

References:

1. Makino, Y., Sato, T., Kawamura, H., Hachisuka, S.I., Takeno, R., Imanaka, T. and Atomi, H. An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism. Nat Commun 7 (2016) 13446. [PMID: 27857065]

2. Nagata, R., Fujihashi, M., Kawamura, H., Sato, T., Fujita, T., Atomi, H. and Miki, K. Structural study on the reaction mechanism of a free serine kinase involved in cysteine biosynthesis. ACS Chem. Biol. 12 (2017) 1514-1523. [PMID: 28358477]

[EC 2.7.1.226 created 2019]

EC 3.1.1.105

Accepted name: 3-O-acetylpapaveroxine carboxylesterase

Reaction: 3-O-acetylpapaveroxine + H2O = narcotine hemiacetal + acetate

For diagram of reaction click here.

Glossary: 3-O-acetylpapaveroxine = 6-{(S)-acetoxy[(5R)-4-methoxy-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]methyl}-2,3-dimethoxybenzaldehyde
narcotine hemiacetal = (3S)-6,7-dimethoxy-3-[(5R)-4-methoxy-6-methyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-1,3-dihydroisobenzofuran-1-ol

Other name(s): CXE1 (gene name)

Systematic name: 3-O-acetylpapaveroxine acetatehydrolase

Comments: The enzyme, characterized from the plant Papaver somniferum (opium poppy), participates in the biosynthesis of the isoquinoline alkaloid noscapine.

References:

1. Dang, T.T., Chen, X. and Facchini, P.J. Acetylation serves as a protective group in noscapine biosynthesis in opium poppy. Nat. Chem. Biol. 11 (2015) 104-106. [PMID: 25485687]

2. Park, M.R., Chen, X., Lang, D.E., Ng, K.KS. and Facchini, P.J. Heterodimeric O-methyltransferases involved in the biosynthesis of noscapine in opium poppy. Plant J. 95 (2018) 252-267. [PMID: 29723437]

[EC 3.1.1.105 created 2019]

EC 3.1.4.59

Accepted name: cyclic-di-AMP phosphodiesterase

Reaction: cyclic di-3',5'-adenylate + H2O = 5'-O-phosphonoadenylyl-(3'→5')-adenosine

For diagram of reaction click here.

Glossary: cyclic di-3',5'-adenylate = cyclic bis(3'→5')diadenylate
5'-O-phosphonoadenylyl-(3'→5')-adenosine = pApA

Other name(s): gdpP (gene name)

Systematic name: cyclic bis(3'→5')diadenylate 3'-adenylylhydrolase

Comments: The enzyme, described from Gram-positive bacteria, degrades the second messenger cyclic di-3',5'-adenylate. It is a membrane-bound protein that contains a cytoplasmic facing Per-Arnt-Sim (PAS) domain, a modified GGDEF domain, and a DHH/DHHA1 domain, which confers the phosphodiesterase activity. Activity requires Mn2+ and is inhibited by pApA.

References:

1. Rao, F., See, R.Y., Zhang, D., Toh, D.C., Ji, Q. and Liang, Z.X. YybT is a signaling protein that contains a cyclic dinucleotide phosphodiesterase domain and a GGDEF domain with ATPase activity. J. Biol. Chem 285 (2010) 473-482. [PMID: 19901023]

2. Corrigan, R.M., Abbott, J.C., Burhenne, H., Kaever, V. and Grundling, A. c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress. PLoS Pathog. 7 (2011) e1002217. [PMID: 21909268]

3. Griffiths, J.M. and O'Neill, A.J. Loss of function of the gdpP protein leads to joint β-lactam/glycopeptide tolerance in Staphylococcus aureus. Antimicrob. Agents Chemother. 56 (2012) 579-581. [PMID: 21986827]

4. Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem 291 (2016) 26970-26986. [PMID: 27834680]

[EC 3.1.4.59 created 2019]

EC 3.1.4.60

Accepted name: pApA phosphodiesterase

Reaction: 5'-O-phosphonoadenylyl-(3'→5')-adenosine + H2O = 2 AMP

For diagram of reaction click here.

Other name(s): pde2 (gene name); pApA hydrolase

Systematic name: 5'-O-phosphonoadenylyl-(3'→5')-adenosine phosphohydrolase

Comments: The enzyme, characterized from the Gram-positive bacterium Staphylococcus aureus, is a cytoplasmic protein that contains a DHH/DHHA1 domain. It can act on cyclic di-3',5'-adenylate with a much lower activity (cf. EC 3.1.4.59, cyclic-di-AMP phosphodiesterase). Activity requires Mn2+ and is inhibited by ppGpp.

References:

1. Bai, Y., Yang, J., Eisele, L.E., Underwood, A.J., Koestler, B.J., Waters, C.M., Metzger, D.W. and Bai, G. Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence. J. Bacteriol. 195 (2013) 5123-5132. [PMID: 24013631]

2. Ye, M., Zhang, J.J., Fang, X., Lawlis, G.B., Troxell, B., Zhou, Y., Gomelsky, M., Lou, Y. and Yang, X.F. DhhP, a cyclic di-AMP phosphodiesterase of Borrelia burgdorferi, is essential for cell growth and virulence. Infect. Immun. 82 (2014) 1840-1849. [PMID: 24566626]

3. Tang, Q., Luo, Y., Zheng, C., Yin, K., Ali, M.K., Li, X. and He, J. Functional analysis of a c-di-AMP-specific phosphodiesterase MsPDE from Mycobacterium smegmatis. Int J Biol Sci 11 (2015) 813-824. [PMID: 26078723]

4. Kuipers, K., Gallay, C., Martinek, V., Rohde, M., Martinkova, M., van der Beek, S.L., Jong, W.S., Venselaar, H., Zomer, A., Bootsma, H., Veening, J.W. and de Jonge, M.I. Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae. Mol. Microbiol. 101 (2016) 12-26. [PMID: 26691161]

5. Bowman, L., Zeden, M.S., Schuster, C.F., Kaever, V. and Grundling, A. New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus. J. Biol. Chem 291 (2016) 26970-26986. [PMID: 27834680]

[EC 3.1.4.60 created 2019]

*EC 3.2.1.15

Accepted name: endo-polygalacturonase

Reaction: (1,4-α-D-galacturonosyl)n+m + H2O = (1,4-α-D-galacturonosyl)n + (1,4-α-D-galacturonosyl)m

Other name(s): pectin depolymerase (ambiguous); pectinase (ambiguous); endopolygalacturonase; pectolase (ambiguous); pectin hydrolase (ambiguous); pectin polygalacturonase (ambiguous); polygalacturonase (ambiguous); poly-α-1,4-galacturonide glycanohydrolase (ambiguous); endogalacturonase; endo-D-galacturonase; poly(1,4-α-D-galacturonide) glycanohydrolase (ambiguous)

Systematic name: (1→4)-α-D-galacturonan glycanohydrolase (endo-cleaving)

Comments: The enzyme catalyses the random hydrolysis of (1→4)-α-D-galactosiduronic linkages in pectate and other galacturonans. Different forms of the enzyme have different tolerances to methyl esterification of the substrate.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, PDB, CAS registry number: 9032-75-1

References:

1. Lineweaver, H. and Jansen, E.F. Pectic enzymes. Adv. Enzymol. Relat. Subj. Biochem. 11 (1951) 267-295.

2. McCready, R.M. and Seegmiller, C.G. Action of pectic enzymes on oligogalacturonic acids and some of their derivatives. Arch. Biochem. Biophys. 50 (1954) 440-450. [PMID: 13159344]

3. Phaff, H.J. and Demain, A.L. The unienzymatic nature of yeast polygalacturonase. J. Biol. Chem. 218 (1956) 875-884. [PMID: 13295238]

4. Deuel, H. and Stutz, E. Pectic substances and pectic enzymes. Adv. Enzymol. Relat. Areas Mol. Biol. 20 (1958) 341-382. [PMID: 13605988]

5. Mill, P.J. and Tuttobello, R. The pectic enzymes of Aspergillus niger. 2. Endopolygalacturonase. Biochem. J. 79 (1961) 57-64. [PMID: 13770689]

[EC 3.2.1.15 created 1961, modified 2019]

*EC 3.2.1.67

Accepted name: galacturonan 1,4-α-galacturonidase

Reaction: [(1→4)-α-D-galacturonide]n + H2O = [(1→4)-α-D-galacturonide]n-1 + D-galacturonate

Other name(s): exo-polygalacturonase; poly(galacturonate) hydrolase (ambiguous); exo-D-galacturonase; exo-D-galacturonanase; exopoly-D-galacturonase; poly(1,4-α-D-galacturonide) galacturonohydrolase (ambiguous); pgaA (gene name); pgaB (gene name); pgaC (gene name); pgaD (gene name); pgaE (gene name); pgaI (gene name); pgaII (gene name); poly[(1→4)-α-D-galacturonide] galacturonohydrolase; galacturan 1,4-α-galacturonidase (incorrect)

Systematic name: poly[(1→4)-α-D-galacturonide] non-reducing-end galacturonohydrolase

Comments: The enzyme hydrolyses the first glycosidic bond from the non-reducing end of the substrate. It is specific for saturated oligomers of D-homogalacturonan, and is unable to degrade unsaturated substrates or methyl-esterified substrates.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 9045-35-6

References:

1. Hasegawa, H. and Nagel, C.W. Isolation of an oligogalacturonate hydrolase from a Bacillus species. Arch. Biochem. Biophys. 124 (1968) 513-520. [PMID: 5661621]

2. Kluskens, L.D., van Alebeek, G.J., Walther, J., Voragen, A.G., de Vos, W.M. and van der Oost, J. Characterization and mode of action of an exopolygalacturonase from the hyperthermophilic bacterium Thermotoga maritima. FEBS J. 272 (2005) 5464-5473. [PMID: 16262687]

3. Martens-Uzunova, E.S., Zandleven, J.S., Benen, J.A., Awad, H., Kools, H.J., Beldman, G., Voragen, A.G., Van den Berg, J.A. and Schaap, P.J. A new group of exo-acting family 28 glycoside hydrolases of Aspergillus niger that are involved in pectin degradation. Biochem. J. 400 (2006) 43-52. [PMID: 16822232]

4. Pijning, T., van Pouderoyen, G., Kluskens, L., van der Oost, J. and Dijkstra, B.W. The crystal structure of a hyperthermoactive exopolygalacturonase from Thermotoga maritima reveals a unique tetramer. FEBS Lett. 583 (2009) 3665-3670. [PMID: 19854184]

[EC 3.2.1.67 created 1972, modified 2019]

*EC 3.2.1.82

Accepted name: exo-poly-α-digalacturonosidase

Reaction: [(1→4)-α-D-galacturonosyl]n + H2O = α-D-galacturonosyl-(1→4)-D-galacturonate + [(1→4)-α-D-galacturonosyl]n-2

Other name(s): pehX (gene name); poly(1,4-α-D-galactosiduronate) digalacturonohydrolase; exopolygalacturonosidase (misleading); poly[(1→4)-α-D-galactosiduronate] digalacturonohydrolase; exo-poly-α-galacturonosidase

Systematic name: poly[(1→4)-α-D-galactosiduronate] non-reducing-end-digalacturonohydrolase

Comments: The enzyme, characterized from bacteria, hydrolyses the second α-1,4-glycosidic bond from the non-reducing end of polygalacturonate, releasing digalacturonate.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 37288-58-7

References:

1. Hasegawa, H. and Nagel, C.W. Isolation of an oligogalacturonate hydrolase from a Bacillus species. Arch. Biochem. Biophys. 124 (1968) 513-520. [PMID: 5661621]

2. Hatanaka, C. and Ozawa, J. Enzymic degradation of pectic acid. XIII. New exopolygalacturonase producing digalacturonic acid from pectic acid. J. Agric. Chem. Soc. Jpn.. 43 (1968) 764-772.

3. Hatanaka, C. and Ozawa, J. Ber. des O'Hara Inst. 15 (1971) 47.

4. He, S.Y. and Collmer, A. Molecular cloning, nucleotide sequence, and marker exchange mutagenesis of the exo-poly-α-D-galacturonosidase-encoding pehX gene of Erwinia chrysanthemi EC16. J. Bacteriol. 172 (1990) 4988-4995. [PMID: 2168372]

[EC 3.2.1.82 created 1972, modified 2019]

*EC 3.4.19.13

Accepted name: glutathione γ-glutamate hydrolase

Reaction: (1) glutathione + H2O = L-cysteinylglycine + L-glutamate
(2) a glutathione-S-conjugate + H2O = an (L-cysteinylglycine)-S-conjugate + L-glutamate

Other name(s): glutathionase; γ-glutamyltranspeptidase (ambiguous); glutathione hydrolase; GGT (gene name); ECM38 (gene name)

Comments: This is a bifunctional protein that also has the activity of EC 2.3.2.2, γ-glutamyltransferase. The enzyme binds its substrate by forming an initial γ-glutamyl-enzyme intermediate, releasing the L-cysteinylglycine part of the molecule. The enzyme then reacts with either a water molecule or a different acceptor substrate (usually an L-amino acid or a dipeptide) to form L-glutamate or a product containing a new γ-glutamyl isopeptide bond, respectively. The enzyme acts on glutathione, glutathione-S-conjugates, and, at a lower level, on other substrates with an N-terminal L-γ-glutamyl residue. It plays a crucial part in the glutathione-mediated xenobiotic detoxification pathway. The enzyme consists of two chains that are created by the proteolytic cleavage of a single precursor polypeptide.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:

References:

1. Hanigan, M.H. and Ricketts, W.A. Extracellular glutathione is a source of cysteine for cells that express γ-glutamyl transpeptidase. Biochemistry 32 (1993) 6302-6306. [PMID: 8099811]

2. 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. [PMID: 9139674]

3. Suzuki, H. and Kumagai, H. Autocatalytic processing of γ-glutamyltranspeptidase. J. Biol. Chem. 277 (2002) 43536-43543. [PMID: 12207027]

4. Okada, T., Suzuki, H., Wada, K., Kumagai, H. and Fukuyama, K. Crystal structures of γ-glutamyltranspeptidase from Escherichia coli, a key enzyme in glutathione metabolism, and its reaction intermediate. Proc. Natl. Acad. Sci. USA 103 (2006) 6471-6476. [PMID: 16618936]

5. Boanca, G., Sand, A., Okada, T., Suzuki, H., Kumagai, H., Fukuyama, K. and Barycki, J.J. Autoprocessing of Helicobacter pylori γ-glutamyltranspeptidase leads to the formation of a threonine-threonine catalytic dyad. J. Biol. Chem. 282 (2007) 534-541. [PMID: 17107958]

6. Okada, T., Suzuki, H., Wada, K., Kumagai, H. and Fukuyama, K. Crystal structure of the γ-glutamyltranspeptidase precursor protein from Escherichia coli. Structural changes upon autocatalytic processing and implications for the maturation mechanism. J. Biol. Chem. 282 (2007) 2433-2439. [PMID: 17135273]

7. Grzam, A., Martin, M.N., Hell, R. and Meyer, A.J. γ-Glutamyl transpeptidase GGT4 initiates vacuolar degradation of glutathione S-conjugates in Arabidopsis. FEBS Lett. 581 (2007) 3131-3138. [PMID: 17561001]

8. 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. [PMID: 21447318]

9. Keillor, J.W., Castonguay, R. and Lherbet, C. Gamma-glutamyl transpeptidase substrate specificity and catalytic mechanism. Methods Enzymol. 401 (2005) 449-467. [PMID: 16399402]

[EC 3.4.19.13 created 2011, modified 2019]

*EC 3.5.1.84

Accepted name: biuret amidohydrolase

Reaction: biuret + H2O = urea-1-carboxylate + NH3

For diagram of reaction click here.

Glossary: biuret = imidodicarbonic diamide
allophanate = urea-1-carboxylate

Other name(s): biuH (gene name)

Systematic name: biuret amidohydrolase

Comments: The enzyme, characterized from the bacterium Rhizobium leguminosarum bv. viciae 3841, participates in the degradation of cyanuric acid, an intermediate in the degradation of s-triazide herbicides such as atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine]. The substrate, biuret, forms by the spontaneous decarboxylation of 1-carboxybiuret in the absence of EC 3.5.1.131, 1-carboxybiuret hydrolase.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, UM-BBD, CAS registry number: 95567-88-7

References:

1. Cameron, S.M., Durchschein, K., Richman, J.E., Sadowsky, M.J. and Wackett, L.P. A new family of biuret hydrolases involved in s-triazine ring metabolism. ACS Catal. 2011 (2011) 1075-1082. [PMID: 21897878]

2. Esquirol, L., Peat, T.S., Wilding, M., Lucent, D., French, N.G., Hartley, C.J., Newman, J. and Scott, C. Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminosarum bv. viciae 3841. PLoS One 13 (2018) e0192736. [PMID: 29425231]

3. Esquirol, L., Peat, T.S., Wilding, M., Liu, J.W., French, N.G., Hartley, C.J., Onagi, H., Nebl, T., Easton, C.J., Newman, J. and Scott, C. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. J. Biol. Chem 293 (2018) 7880-7891. [PMID: 29523689]

[EC 3.5.1.84 created 2000, modified 2008, modified 2019]

EC 3.5.1.130

Accepted name: [lysine-biosynthesis-protein LysW]-lysine/ornithine hydrolase

Reaction: (1) [lysine-biosynthesis-protein LysW]-C-terminal-γ-(L-ornithyl)-L-glutamate + H2O = [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-ornithine
(2) [lysine-biosynthesis-protein LysW]-C-terminal-γ-(L-lysyl)-L-glutamate + H2O = [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-lysine

Other name(s): lysK (gene name)

Systematic name: [lysine-biosynthesis-protein LysW]-C-terminal-γ-(L-ornithyl/L-lysyl)-L-glutamate amidohydrolase

Comments: The enzyme participates in L-arginine and L-lysine biosynthetic pathways in certain species of archaea and bacteria. In some organisms the enzyme also catalyses the activity of EC 3.5.1.132, [amino group carrier protein]-ornithine hydrolase.

References:

1. 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. [PMID: 19620981]

[EC 3.5.1.130 created 2019]

EC 3.5.1.131

Accepted name: 1-carboxybiuret hydrolase

Reaction: 1-carboxybiuret + H2O = urea-1,3-dicarboxylate + NH3

For diagram of reaction click here.

Glossary: carboxybiuret = carbamoylcarbamoylcarbamic acid

Other name(s): atzEG (gene names)

Systematic name: 1-carboxybiuret amidohydrolase

Comments: The enzyme, characterized from the bacterium Pseudomonas sp. ADP, participates in the degradation of cyanuric acid, an intermediate in the degradation of s-triazine herbicides such as atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine]. The enzyme is a heterotetramer composed of a catalytic subunit (AtzE) and an accessory subunit (AtzG) that stabilizes the complex.

References:

1. Esquirol, L., Peat, T.S., Wilding, M., Liu, J.W., French, N.G., Hartley, C.J., Onagi, H., Nebl, T., Easton, C.J., Newman, J. and Scott, C. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. J. Biol. Chem 293 (2018) 7880-7891. [PMID: 29523689]

[EC 3.5.1.131 created 2019]

EC 3.5.1.132

Accepted name: [amino group carrier protein]-ornithine hydrolase

Reaction: [amino group carrier protein]-C-terminal-γ-(L-ornithyl)-L-glutamate + H2O = [amino group carrier protein]-C-terminal-L-glutamate + L-ornithine

Other name(s): lysK (gene name)

Systematic name: [amino group carrier protein]-C-terminal-γ-L-ornithyl-L-glutamate amidohydrolase

Comments: The enzyme participates in an L-arginine biosynthetic pathways in certain species of archaea and bacteria. In all cases known so far the enzyme also catalyses the activity of EC 3.5.1.130, [amino group carrier protein]-lysine hydrolase.

References:

1. 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. [PMID: 23434852]

2. Yoshida, A., Tomita, T., Atomi, H., Kuzuyama, T. and Nishiyama, M. Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system. J. Biol. Chem. 291 (2016) 21630-21643. [PMID: 27566549]

[EC 3.5.1.132 created 2019]

*EC 3.5.2.15

Accepted name: cyanuric acid amidohydrolase

Reaction: cyanuric acid + H2O = 1-carboxybiuret

For diagram of reaction click here.

Glossary: cyanuric acid = 1,3,5-triazine-2,4,6(1H,3H,5H)-trione = 2,4,6-trihydroxy-s-triazine
1-carboxybiuret = N-[(carbamoylamino)carbonyl]carbamate

Other name(s): atzD (gene name); trzD (gene name)

Systematic name: cyanuric acid amidohydrolase

Comments: The enzyme catalyses the ring cleavage of cyanuric acid, an intermediate in the degradation of s-triazide herbicides such as atrazine [2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine]. The enzyme is highly specific for cyanuric acid. The product was initially thought to be bioret, but was later shown to be 1-carboxybioret.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, UM-BBD, CAS registry number: 132965-78-7

References:

1. Eaton, R.W. and Karns, J.S. Cloning and comparison of the DNA encoding ammelide aminohydrolase and cyanuric acid amidohydrolase from three s-triazine-degrading bacterial strains. J. Bacteriol. 173 (1991) 1363-1366. [PMID: 1991731]

2. Eaton, R.W. and Karns, J.S. Cloning and analysis of s-triazine catabolic genes from Pseudomonas sp. strain NRRLB-12227. J. Bacteriol. 173 (1991) 1215-1222. [PMID: 1846859]

3. Karns, J.S. Gene sequence and properties of an s-triazine ring-cleavage enzyme from Pseudomonas sp. strain NRRLB-12227. Appl. Environ. Microbiol. 65 (1999) 3512-3517. [PMID: 10427042]

4. Fruchey, I., Shapir, N., Sadowsky, M.J. and Wackett, L.P. On the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of AtzD from Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 69 (2003) 3653-3657. [PMID: 12788776]

5. Esquirol, L., Peat, T.S., Wilding, M., Liu, J.W., French, N.G., Hartley, C.J., Onagi, H., Nebl, T., Easton, C.J., Newman, J. and Scott, C. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme. J. Biol. Chem 293 (2018) 7880-7891. [PMID: 29523689]

[EC 3.5.2.15 created 2000, modified 2008, modified 2019]

[EC 4.1.1.70 Transferred entry: glutaconyl-CoA decarboxylase. Now EC 7.2.4.5, glutaconyl-CoA decarboxylase (EC 4.1.1.70 created 1986, modified 2003, deleted 2018)]

EC 4.1.1.115

Accepted name: indoleacetate decarboxylase

Reaction: (1H-indol-3-yl)acetate = skatole + CO2

For diagram of reaction click here.

Glossary: (1H-indol-3-yl)acetate = indoleacetate
skatole = 3-methyl-1H-indole

Other name(s): IAD

Systematic name: (1H-indol-3-yl)acetate carboxy-lyase (skatole-forming)

Comments: This glycyl radical enzyme has been isolate from a number of bacterial species. Skatole contributes to the characteristic smell of animal faeces.

References:

1. Liu, D., Wei, Y., Liu, X., Zhou, Y., Jiang, L., Yin, J., Wang, F., Hu, Y., Nanjaraj Urs, A.N., Liu, Y., Ang, E.L., Zhao, S., Zhao, H. and Zhang, Y. Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nat. Commun. 9 (2018) 4224. [PMID: 30310076]

[EC 4.1.1.115 created 2019]

EC 4.1.1.116

Accepted name: D-ornithine/D-lysine decarboxylase

Reaction: (1) D-ornithine = putrescine + CO2
(2) D-lysine = cadaverine + CO2

For diagram of reaction click here.

Glossary: cadaverine = pentane-1,5-diamine
putrescine = butane-1,4-diamine

Other name(s): dokD (gene name); DOKDC

Systematic name: D-ornithine/D-lysine carboxy-lyase

Comments: The enzyme, characterized from the bacterium Salmonella typhimurium LT2, is specific for D-ornithine and D-lysine. Requires pyridoxal 5'-phosphate.

References:

1. Phillips, R.S., Poteh, P., Miller, K.A. and Hoover, T.R. STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella enterica serovar typhimurium. Arch. Biochem. Biophys. 634 (2017) 83-87. [PMID: 29024617]

[EC 4.1.1.116 created 2019]

EC 4.1.1.117

Accepted name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate decarboxylase

Reaction: 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate = 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate + CO2

Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate

Other name(s): sbnH (gene name)

Systematic name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate carboxy-lyase (2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate-forming)

Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the siderophore staphyloferrin B.

References:

1. Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594-608. [PMID: 19775248]

[EC 4.1.1.117 created 2019]

*EC 4.2.1.139

Accepted name: pterocarpan synthase

Reaction: a (4R)-4,2'-dihydroxyisoflavan = a pterocarpan + H2O

For diagram of reaction click here

Glossary: an isoflavan = an isoflavonoid with a 3,4-dihydro-3-aryl-2H-1-benzopyran skeleton.
(-)-medicarpin = (6aR,11aR)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
(+)-medicarpin = (6aS,11aS)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
(-)-maackiain = (6aR,12aR)-6a,12a-dihydro-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-3-ol
(+)-maackiain = (6aS,12aS)-6a,12a-dihydro-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-3-ol
(+)-pterocarpan = (6aR,11aR)-6a,11a-dihydro-6H-[1]benzofuran[3,2-c][1]benzopyran

Other name(s): medicarpin synthase; medicarpan synthase; 7,2'-dihydroxy-4'-methoxyisoflavanol dehydratase; 2',7-dihydroxy-4'-methoxyisoflavanol dehydratase; DMI dehydratase; DMID; 2'-hydroxyisoflavanol 4,2'-dehydratase; PTS (gene name); 4'-methoxyisoflavan-2',4,7-triol hydro-lyase [(-)-medicarpin-forming]

Systematic name: (4R)-4,2'-dihydroxyisoflavan hydro-lyase (pterocarpan-forming)

Comments: The enzyme catalyses the formation of the additional ring in pterocarpan, the basic structure of phytoalexins produced by leguminous plants, including (-)-medicarpin, (+)-medicarpin, (-)-maackiain and (+)-maackiain. The enzyme requires that the hydroxyl group at C-4 of the substrate is in the (4R) configuration. The configuration of the hydrogen atom at C-3 determines whether the pterocarpan is the (+)- or (-)-enantiomer. The enzyme contains amino acid motifs characteristic of dirigent proteins.

Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, CAS registry number:

References:

1. Guo, L., Dixon, R.A. and Paiva, N.L. The ‘pterocarpan synthase’ of alfalfa: association and co-induction of vestitone reductase and 7,2'-dihydroxy-4'-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett. 356 (1994) 221-225. [PMID: 7805842]

2. Guo, L., Dixon, R.A. and Paiva, N.L. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2'-dihydroxy-4'-methoxyisoflavanol dehydratase. J. Biol. Chem. 269 (1994) 22372-22378. [PMID: 8071365]

3. Uchida, K., Akashi, T. and Aoki, T. The missing link in leguminous pterocarpan biosynthesis is a dirigent domain-containing protein with isoflavanol dehydratase activity. Plant Cell Physiol 58 (2017) 398-408. [PMID: 28394400]

[EC 4.2.1.139 created 2013, modified 2019]

EC 4.2.99.24

Accepted name: thebaine synthase

Reaction: salutaridinol 7-O-acetate = thebaine + acetate

For diagram of reaction click here

Other name(s): THS

Systematic name: salutaridinol 7-O-acetate acetate-lyase (thebaine forming)

Comments: Isolated from the plant Papaver somniferum (opium poppy). The reaction occurs spontaneously when the pH is between 8-9, but the enzyme is required at the physiological pH, which is close to 7.

References:

1. Chen, X., Hagel, J.M., Chang, L., Tucker, J.E., Shiigi, S.A., Yelpaala, Y., Chen, H.Y., Estrada, R., Colbeck, J., Enquist-Newman, M., Ibanez, A.B., Cottarel, G., Vidanes, G.M. and Facchini, P.J. A pathogenesis-related 10 protein catalyzes the final step in thebaine biosynthesis. Nat. Chem. Biol. 14 (2018) 738-743. [PMID: 29807982]

[EC 4.2.99.24 created 2019]

EC 5.1.1.24

Accepted name: histidine racemase

Reaction: L-histidine = D-histidine

For diagram of reaction click here.

Glossary: staphylopine = (2S)-4-{[(1R)-1-carboxy-2-(1H-imidazol-4-yl)ethyl]amino}-2-[(1-carboxyethyl)amino]butanoate

Other name(s): cntK (gene name)

Systematic name: histidine racemase

Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the metallophore staphylopine, which is involved in the acquisition of nickel, copper, and cobalt.

References:

1. Ghssein, G., Brutesco, C., Ouerdane, L., Fojcik, C., Izaute, A., Wang, S., Hajjar, C., Lobinski, R., Lemaire, D., Richaud, P., Voulhoux, R., Espaillat, A., Cava, F., Pignol, D., Borezee-Durant, E. and Arnoux, P. Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus. Science 352 (2016) 1105-1109. [PMID: 27230378]

[EC 5.1.1.24 created 2019]

EC 5.1.3.43

Accepted name: sulfoquinovose mutarotase

Reaction: 6-sulfo-α-D-quinovose = 6-sulfo-β-D-quinovose

Systematic name: 6-sulfo-D-quinovose 1-epimerase

Comments: The enzyme is found in bacteria that possess sulfoglycolytic pathways. The enzyme can also act on other aldohexoses such as D-galactose, D-glucose, D-glucose-6-phosphate, and D-glucuronate, but with lower efficiency. Does not act on D-mannose.

References:

1. Abayakoon, P., Lingford, J.P., Jin, Y., Bengt, C., Davies, G.J., Yao, S., Goddard-Borger, E.D. and Williams, S.J. Discovery and characterization of a sulfoquinovose mutarotase using kinetic analysis at equilibrium by exchange spectroscopy. Biochem. J. 475 (2018) 1371-1383. [PMID: 29535276]

[EC 5.1.3.43 created 2019]

*EC 6.2.1.40

Accepted name: 4-hydroxybutyrate—CoA ligase (AMP-forming)

Reaction: ATP + 4-hydroxybutanoate + CoA = AMP + diphosphate + 4-hydroxybutanoyl-CoA

For diagram of reaction click here

Other name(s): 4-hydroxybutyrate-CoA synthetase (ambiguous); 4-hydroxybutyrate:CoA ligase (ambiguous); hbs (gene name); 4-hydroxybutyrate—CoA ligase

Systematic name: 4-hydroxybutanoate:CoA ligase (AMP-forming)

Comments: Isolated from the archaeon Metallosphaera sedula. Involved in the 3-hydroxypropanoate/4-hydroxybutanoate cycle. cf. EC 6.2.1.56, 4-hydroxybutyrate—CoA ligase (ADP-forming).

Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, CAS registry number:

References:

1. Ramos-Vera, W.H., Weiss, M., Strittmatter, E., Kockelkorn, D. and Fuchs, G. Identification of missing genes and enzymes for autotrophic carbon fixation in crenarchaeota. J. Bacteriol. 193 (2011) 1201-1211. [PMID: 21169482]

2. Hawkins, A.S., Han, Y., Bennett, R.K., Adams, M.W. and Kelly, R.M. Role of 4-hydroxybutyrate-CoA synthetase in the CO2 fixation cycle in thermoacidophilic archaea. J. Biol. Chem. 288 (2013) 4012-4022. [PMID: 23258541]

[EC 6.2.1.40 created 2014, modified 2019]

EC 6.2.1.56

Accepted name: 4-hydroxybutyrate—CoA ligase (ADP-forming)

Reaction: ATP + 4-hydroxybutanoate + CoA = ADP + phosphate + 4-hydroxybutanoyl-CoA

For diagram of reaction click here

Other name(s): Nmar_0206 (locus name)

Systematic name: 4-hydroxybutanoate:CoA ligase (ADP-forming)

Comments: The enzyme, characterized from the marine ammonia-oxidizing archaeon Nitrosopumilus maritimus, participates in a variant of the 3-hydroxypropanoate/4-hydroxybutanate CO2 fixation cycle. cf. EC 6.2.1.40, 4-hydroxybutyrate—CoA ligase (AMP-forming).

References:

1. Konneke, M., Schubert, D.M., Brown, P.C., Hugler, M., Standfest, S., Schwander, T., Schada von Borzyskowski, L., Erb, T.J., Stahl, D.A. and Berg, I.A. Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation. Proc. Natl Acad. Sci. USA 111 (2014) 8239-8244. [PMID: 24843170]

[EC 6.2.1.56 created 2019]

*EC 6.3.2.39

Accepted name: aerobactin synthase

Reaction: ATP + N2-citryl-N6-acetyl-N6-hydroxy-L-lysine + N6-acetyl-N6-hydroxy-L-lysine = AMP + diphosphate + aerobactin

For diagram of reaction click here

Other name(s): iucC (gene name)

Systematic name: N2-citryl-N6-acetyl-N6-hydroxy-L-lysine:N6-acetyl-N6-hydroxy-L-lysine ligase (AMP-forming)

Comments: Requires Mg2+. The enzyme is involved in the biosynthesis of aerobactin, a dihydroxamate siderophore. It belongs to a class of siderophore synthases known as type C nonribosomal peptide synthase-independent synthases (NIS). Type C enzymes are responsible for the formation of amide or ester bonds between a variety of substrates and a prochiral carboxyl group of a citrate molecule that is already linked to a different moiety at its other prochiral carboxyl group. The enzyme is believed to form an adenylate intermediate prior to ligation.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:

References:

1. Gibson, F. and Magrath, D.I. The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-I. Biochim. Biophys. Acta 192 (1969) 175-184. [PMID: 4313071]

2. Maurer, P.J. and Miller, M. Microbial iron chelators: total synthesis of aerobactin and its constituent amino acid, N6-acetyl-N6-hydroxylysine. J. Am. Chem. Soc. 104 (1982) 3096-3101.

3. Appanna, D.L., Grundy, B.J., Szczepan, E.W. and Viswanatha, T. Aerobactin synthesis in a cell-free system of Aerobacter aerogenes 62-1. Biochim. Biophys. Acta 801 (1984) 437-443.

4. de Lorenzo, V., Bindereif, A., Paw, B.H. and Neilands, J.B. Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12. J. Bacteriol. 165 (1986) 570-578. [PMID: 2935523]

5. de Lorenzo, V. and Neilands, J.B. Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 in Escherichia coli. J. Bacteriol. 167 (1986) 350-355. [PMID: 3087960]

6. Challis, G.L. A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. ChemBioChem 6 (2005) 601-611. [PMID: 15719346]

7. Oves-Costales, D., Kadi, N. and Challis, G.L. The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis. Chem. Commun. (Camb.) (2009) 6530-6541. [PMID: 19865642]

[EC 6.3.2.39 created 2012, modified 2019]

EC 6.3.2.54

Accepted name: L-2,3-diaminopropanoate—citrate ligase

Reaction: ATP + L-2,3-diaminopropanoate + citrate = AMP + diphosphate + 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate

Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate

Other name(s): sbnE (gene name); 2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate synthtase

Systematic name: L-2,3-diaminopropanoate:citrate ligase (2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate-forming)

Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B. It belongs to a class of siderophore synthases known as type A nonribosomal peptide synthase-independent synthases (NIS). Type A NIS enzymes are responsible for the formation of amide or ester bonds between polyamines or amino alcohols and a prochiral carboxyl group of citrate. The enzyme forms a citrate adenylate intermediate prior to ligation.

References:

1. Dale, S.E., Doherty-Kirby, A., Lajoie, G. and Heinrichs, D.E. Role of siderophore biosynthesis in virulence of Staphylococcus aureus: identification and characterization of genes involved in production of a siderophore. Infect. Immun. 72 (2004) 29-37. [PMID: 14688077]

2. Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594-608. [PMID: 19775248]

[EC 6.3.2.54 created 2019]

EC 6.3.2.55

Accepted name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate synthase

Reaction: ATP + 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate + L-2,3-diaminopropanoate = AMP + diphosphate + 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate

For diagram of reaction click here

Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate

Other name(s): sbnF (gene name)

Systematic name: 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate:L-2,3-diaminopropanoate ligase {2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate-forming}

Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, is involved in the biosynthesis of the siderophore staphyloferrin B. It belongs to a class of siderophore synthases known as type C nonribosomal peptide synthase-independent synthases (NIS). Type C NIS enzymes recognize esterified or amidated derivatives of carboxylic acids. The enzyme likely forms a 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate adenylate intermediate prior to ligation.

References:

1. Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594-608. [PMID: 19775248]

[EC 6.3.2.55 created 2019]

EC 6.3.2.56

Accepted name: staphyloferrin B synthase

Reaction: ATP + 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate + 2-oxoglutarate = AMP + diphosphate + staphyloferrin B

For diagram of reaction click here

Glossary: staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate

Other name(s): sbnC (gene name)

Systematic name: 2-[(L-alanin-3-ylcarbamoyl)methyl]-3-(2-aminoethylcarbamoyl)-2-hydroxypropanoate:2-oxoglutarate ligase (staphyloferrin B-forming)

Comments: Requires Mg2+. The enzyme, characterized from the bacterium Staphylococcus aureus, catalyses the last step in the biosynthesis of the siderophore staphyloferrin B. It belongs to a class of siderophore synthases known as type B nonribosomal peptide synthase-independent synthases (NIS). Type B NIS enzymes recognize the δ-acid group of 2-oxoglutarate. The enzyme forms a 2-oxoglutarate adenylate intermediate prior to ligation.

References:

1. Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594-608. [PMID: 19775248]

[EC 6.3.2.56 created 2019]

*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, ExplorEnz, KEGG, MetaCyc, 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. [PMID: 9789001]

2. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [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. [PMID: 11880622]

[EC 6.3.5.6 created 2002, modified 2012, modified 2019]

*EC 6.3.5.7

Accepted name: glutaminyl-tRNA synthase (glutamine-hydrolysing)

Reaction: ATP + L-glutamyl-tRNAGln + L-glutamine = ADP + phosphate + L-glutaminyl-tRNAGln + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + L-glutamyl-tRNAGln = ADP + 5-phosphooxy-L-glutamyl-tRNAGln
(1c) 5-phosphooxy-L-glutamyl-tRNAGln + NH3 = L-glutaminyl-tRNAGln + phosphate

Other name(s): Glu-AdT; Glu-tRNAGln amidotransferase; glutamyl-tRNAGln amidotransferase; Glu-tRNAGln:L-glutamine amido-ligase (ADP-forming); GatCAB; GatFAB; GatDE

Systematic name: L-glutamyl-tRNAGln:L-glutamine amido-ligase (ADP-forming)

Comments: In systems lacking discernible glutamine—tRNA ligase (EC 6.1.1.18), glutaminyl-tRNAGln is formed by a two-enzyme system. In the first step, a nondiscriminating ligase (EC 6.1.1.24, glutamate—tRNAGln ligase) mischarges tRNAGln with glutamate, forming glutamyl-tRNAGln. The glutamyl-tRNAGln is not used in protein synthesis until the present enzyme converts it into glutaminyl-tRNAGln (glutamyl-tRNAGlu 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. Some bacterial GatCAB complexes also has the activity of EC 6.3.5.6 (asparaginyl-tRNA synthase [glutamine-hydrolysing]).

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number: 52232-48-1

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. [PMID: 9789001]

2. Ibba, M. and Söll, D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69 (2000) 617-650. [PMID: 10966471]

3. Raczniak, G., Becker, H.D., Min, B. and Soll, D. A single amidotransferase forms asparaginyl-tRNA and glutaminyl-tRNA in Chlamydia trachomatis. J. Biol. Chem 276 (2001) 45862-45867. [PMID: 11585842]

4. Horiuchi, K.Y., Harpel, M.R., Shen, L., Luo, Y., Rogers, K.C. and Copeland, R.A. Mechanistic studies of reaction coupling in Glu-tRNAGln amidotransferase. Biochemistry 40 (2001) 6450-6457. [PMID: 11371208]

5. Feng, L., Sheppard, K., Tumbula-Hansen, D. and Soll, D. Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase. J. Biol. Chem 280 (2005) 8150-8155. [PMID: 15611111]

6. Nakamura, A., Yao, M., Chimnaronk, S., Sakai, N. and Tanaka, I. Ammonia channel couples glutaminase with transamidase reactions in GatCAB. Science 312 (2006) 1954-1958. [PMID: 16809541]

7. Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Kwon, S.T., Soll, D. and Smith, J.L. Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme. J. Mol. Biol. 391 (2009) 703-716. [PMID: 19520089]

8. Araiso, Y., Huot, J.L., Sekiguchi, T., Frechin, M., Fischer, F., Enkler, L., Senger, B., Ishitani, R., Becker, H.D. and Nureki, O. Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases. Nucleic Acids Res. 42 (2014) 6052-6063. [PMID: 24692665]

[EC 6.3.5.7 created 2002, modified 2019]

EC 6.3.5.13

Accepted name: lipid II isoglutaminyl synthase (glutamine-hydrolysing)

Reaction: ATP + β-D-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)-diphospho-ditrans,octacis-undecaprenol + L-glutamine + H2O = ADP + phosphate + β-D-GlcNAc-(1→4)-MurNAc-L-Ala-D-isoglutaminyl-L-Lys-D-Ala-D-Ala-diphospho-ditrans,octacis-undecaprenol + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) ATP + β-D-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)-diphospho-ditrans,octacis-undecaprenol = ADP + β-D-GlcNAc-(1→4)-MurNAc-L-Ala-γ-D-O-P-Glu-L-Lys-D-Ala-D-Ala-diphospho-ditrans,octacis-undecaprenol
(1c) β-D-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-O-P-Glu-L-Lys-D-Ala-D-Ala)-diphospho-ditrans,octacis-undecaprenol + NH3 = β-D-GlcNAc-(1→4)-MurNAc-L-Ala-D-isoglutaminyl-L-Lys-D-Ala-D-Ala-diphospho-ditrans,octacis-undecaprenol + phosphate

Glossary: lipid II = undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl peptide; the peptide element refers to L-alanyl-D-γ-glutamyl-L-lysyl/meso-2,6-diaminopimelyl-D-alanyl-D-alanine or a modified version thereof = undecaprenyldiphospho-4-O-(N-acetyl-β-D-glucosaminyl)-3-O-peptidyl-α-N-acetylmuramate; the peptide element refers to L-alanyl-D-γ-glutamyl-L-lysyl/meso-2,6-diaminopimelyl-D-alanyl-D-alanine or a modified version thereof

Other name(s): MurT/GatD; MurT/GatD complex

Systematic name: β-D-GlcNAc-(1→4)-Mur2Ac(oyl-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala)-diphospho-ditrans,octacis-undecaprenol:L-glutamine amidoligase (ADP-forming)

Comments: The enzyme complex, found in Gram-positive bacteria, consists of two subunits. A glutaminase subunit (cf. EC 3.5.1.2, glutaminase) produces an ammonia molecule that is channeled to a ligase subunit, which adds it to the activated D-glutamate residue of lipid II, converting it to an isoglutamine residue.

References:

1. Munch, D., Roemer, T., Lee, S.H., Engeser, M., Sahl, H.G. and Schneider, T. Identification and in vitro analysis of the GatD/MurT enzyme-complex catalyzing lipid II amidation in Staphylococcus aureus. PLoS Pathog. 8 (2012) e1002509. [PMID: 22291598]

2. Noldeke, E.R., Muckenfuss, L.M., Niemann, V., Muller, A., Stork, E., Zocher, G., Schneider, T. and Stehle, T. Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus. Sci Rep 8 (2018) 12953. [PMID: 30154570]

3. Morlot, C., Straume, D., Peters, K., Hegnar, O.A., Simon, N., Villard, A.M., Contreras-Martel, C., Leisico, F., Breukink, E., Gravier-Pelletier, C., Le Corre, L., Vollmer, W., Pietrancosta, N., Havarstein, L.S. and Zapun, A. Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae. Nat Commun 9 (2018) 3180. [PMID: 30093673]

[EC 6.3.5.13 created 2019]

EC 7.2.4.5

Accepted name: glutaconyl-CoA decarboxylase

Reaction: (2E)-4-carboxybut-2-enoyl-CoA + Na+[side 1] = (2E)-but-2-enoyl-CoA + CO2 + Na+[side 2]

Glossary: (E)-glutaconyl-CoA = (2E)-4-carboxybut-2-enoyl-CoA

Other name(s): glutaconyl coenzyme A decarboxylase; pent-2-enoyl-CoA carboxy-lyase; 4-carboxybut-2-enoyl-CoA carboxy-lyase

Systematic name: (2E)-4-carboxybut-2-enoyl-CoA carboxy-lyase [(2E)-but-2-enoyl-CoA-forming]

Comments: The enzyme from the bacterium Acidaminococcus fermentans is a biotinyl-protein, requires Na+, and acts as a sodium pump. Prior to the Na+-dependent decarboxylation, the carboxylate is transferred to biotin in a Na+-independent manner. The conserved lysine, to which biotin forms an amide bond, is located 34 amino acids before the C-terminus, flanked on both sides by two methionine residues, which are conserved in every biotin-dependent enzyme.

References:

1. Buckel, W.S. and Semmler, R. Purification, characterisation and reconstitution of glutaconyl-CoA decarboxylase, a biotin-dependent sodium pump from anaerobic bacteria. Eur. J. Biochem. 136 (1983) 427-434. [PMID: 6628393]

2. Buckel, W. Sodium ion-translocating decarboxylases. Biochim. Biophys. Acta 1505 (2001) 15-27. [PMID: 11248185]

[EC 7.2.4.5 created 1986 as EC 4.1.1.70, modified 2003, transferred 2019 to EC 7.2.4.5]


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