The Enzyme Database

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EC 2.3.1.23     
Accepted name: 1-acylglycerophosphocholine O-acyltransferase
Reaction: acyl-CoA + 1-acyl-sn-glycero-3-phosphocholine = CoA + 1,2-diacyl-sn-glycero-3-phosphocholine
Other name(s): lysolecithin acyltransferase; 1-acyl-sn-glycero-3-phosphocholine acyltransferase; acyl coenzyme A-monoacylphosphatidylcholine acyltransferase; acyl-CoA:1-acyl-glycero-3-phosphocholine transacylase; lysophosphatide acyltransferase; lysophosphatidylcholine acyltransferase
Systematic name: acyl-CoA:1-acyl-sn-glycero-3-phosphocholine O-acyltransferase
Comments: Acts preferentially with unsaturated acyl-CoA derivatives. 1-Acyl-sn-glycero-3-phosphoinositol can also act as acceptor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9027-64-9
References:
1.  Bell, R.M. and Coleman, R.A. Enzymes of glycerolipid synthesis in eukaryotes. Annu. Rev. Biochem. 49 (1980) 459–487. [DOI] [PMID: 6250446]
2.  Hill, E.E. and Lands, W.E.M. Incorporation of long-chain and polyunsaturated acids into phosphatidate and phosphatidylcholine. Biochim. Biophys. Acta 152 (1968) 645–648. [DOI] [PMID: 5661029]
3.  Miki, Y., Hosaka, K., Yamashita, S., Handa, H. and Numa, S. Acyl-acceptor specificities of 1-acylglycerolphosphate acyltransferase and 1-acylglycerophosphorylcholine acyltransferase resolved from rat liver microsomes. Eur. J. Biochem. 81 (1977) 433–441. [DOI] [PMID: 598375]
4.  van den Bosch, H., van Golde, L.M.G., Eibl, H. and van Deenen, L.L.M. The acylation of 1-acylglycero-3-phosphorylcholines by rat-liver microsomes. Biochim. Biophys. Acta 144 (1967) 613–623. [DOI] [PMID: 6078124]
[EC 2.3.1.23 created 1972]
 
 
EC 2.3.1.230     
Accepted name: 2-heptyl-4(1H)-quinolone synthase
Reaction: octanoyl-CoA + (2-aminobenzoyl)acetate = 2-heptyl-4-quinolone + CoA + CO2 + H2O (overall reaction)
(1a) octanoyl-CoA + L-cysteinyl-[PqsC protein] = S-octanoyl-L-cysteinyl-[PqsC protein] + CoA
(1b) S-octanoyl-L-cysteinyl-[PqsC protein] + (2-aminobenzoyl)acetate = 1-(2-aminophenyl)decane-1,3-dione + CO2 + L-cysteinyl-[PqsC protein]
(1c) 1-(2-aminophenyl)decane-1,3-dione = 2-heptyl-4-quinolone + H2O
Glossary: 2-heptyl-4-quinolone = 2-heptylquinolin-4(1H)-one
Other name(s): pqsBC (gene names); malonyl-CoA:anthraniloyl-CoA C-acetyltransferase (decarboxylating)
Systematic name: octanoyl-CoA:(2-aminobenzoyl)acetate octanoyltransferase
Comments: The enzyme, characterized from the bacterium Pseudomonas aeruginosa, is a heterodimeric complex. The PqsC subunit acquires an octanoyl group from octanoyl-CoA and attaches it to an internal cysteine residue. Together with the PqsB subunit, the proteins catalyse the coupling of the octanoyl group with (2-aminobenzoyl)acetate, leading to decarboxylation and dehydration events that result in closure of the quinoline ring.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Dulcey, C.E., Dekimpe, V., Fauvelle, D.A., Milot, S., Groleau, M.C., Doucet, N., Rahme, L.G., Lepine, F. and Deziel, E. The end of an old hypothesis: the pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines derive from fatty acids, not 3-ketofatty acids. Chem. Biol. 20 (2013) 1481–1491. [DOI] [PMID: 24239007]
2.  Drees, S.L., Li, C., Prasetya, F., Saleem, M., Dreveny, I., Williams, P., Hennecke, U., Emsley, J. and Fetzner, S. PqsBC, a condensing enzyme in the biosynthesis of the Pseudomonas aeruginosa quinolone signal: crystal structure, inhibition, and reaction mechanism. J. Biol. Chem. 291 (2016) 6610–6624. [DOI] [PMID: 26811339]
[EC 2.3.1.230 created 2013, modified 2017]
 
 
EC 2.3.1.231     
Accepted name: tRNAPhe {7-[3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methoxycarbonyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe + CO2 = S-adenosyl-L-homocysteine + wybutosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37-N}-methyltransferase (carbon dioxide-adding)
Comments: The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-[2-hydroxy-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe as substrate. The enzyme also has the activity of EC 2.1.1.290, tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
2.  Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910–2925. [DOI] [PMID: 19287006]
3.  Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]
[EC 2.3.1.231 created 2013]
 
 
EC 2.3.1.232     
Accepted name: methanol O-anthraniloyltransferase
Reaction: anthraniloyl-CoA + methanol = CoA + O-methyl anthranilate
Glossary: anthraniloyl-CoA = 2-aminobenzoyl-CoA
Other name(s): AMAT; anthraniloyl-coenzyme A (CoA):methanol acyltransferase
Systematic name: anthraniloyl-CoA:methanol O-anthraniloyltransferase
Comments: The enzyme from Concord grape (Vitis labrusca) is solely responsible for the production of O-methyl anthranilate, an important aroma and flavor compound in the grape. The enzyme has a broad substrate specificity, and can use a range of alcohols with substantial activity, the best being butanol, benzyl alcohol, iso-pentanol, octanol and 2-propanol. It can use benzoyl-CoA and acetyl-CoA as acyl donors with lower efficiency. In addition to O-methyl anthranilate, the enzyme might be responsible for the production of ethyl butanoate, methyl-3-hydroxy butanoate and ethyl-3-hydroxy butanoate, which are present in large quantities in the grapes. Also catalyses EC 2.3.1.196, benzyl alcohol O-benzoyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Wang, J. and De Luca, V. The biosynthesis and regulation of biosynthesis of Concord grape fruit esters, including ’foxy’ methylanthranilate. Plant J. 44 (2005) 606–619. [DOI] [PMID: 16262710]
[EC 2.3.1.232 created 2014]
 
 
EC 2.3.1.233     
Accepted name: 1,3,6,8-tetrahydroxynaphthalene synthase
Reaction: 5 malonyl-CoA = 1,3,6,8-tetrahydroxynaphthalene + 5 CoA + 5 CO2 + H2O
For diagram of polyketides biosynthesis, click here
Other name(s): PKS1; THNS; SCO1206; RppA
Systematic name: malonyl-CoA C-acyl transferase (1,3,6,8-tetrahydroxynaphthalene forming)
Comments: Isolated from the fungus Colletotrichum lagenarium [1], and the bacteria Streptomyces coelicolor [2,3] and Streptomyces peucetius [4]. It only uses malonyl-CoA, without invovement of acetyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Fujii, I., Mori, Y., Watanabe, A., Kubo, Y., Tsuji, G. and Ebizuka, Y. Enzymatic synthesis of 1,3,6,8-tetrahydroxynaphthalene solely from malonyl coenzyme A by a fungal iterative type I polyketide synthase PKS1. Biochemistry 39 (2000) 8853–8858. [DOI] [PMID: 10913297]
2.  Izumikawa, M., Shipley, P.R., Hopke, J.N., O'Hare, T., Xiang, L., Noel, J.P. and Moore, B.S. Expression and characterization of the type III polyketide synthase 1,3,6,8-tetrahydroxynaphthalene synthase from Streptomyces coelicolor A3(2). J Ind Microbiol Biotechnol 30 (2003) 510–515. [DOI] [PMID: 12905073]
3.  Austin, M.B., Izumikawa, M., Bowman, M.E., Udwary, D.W., Ferrer, J.L., Moore, B.S. and Noel, J.P. Crystal structure of a bacterial type III polyketide synthase and enzymatic control of reactive polyketide intermediates. J. Biol. Chem. 279 (2004) 45162–45174. [DOI] [PMID: 15265863]
4.  Ghimire, G.P., Oh, T.J., Liou, K. and Sohng, J.K. Identification of a cryptic type III polyketide synthase (1,3,6,8-tetrahydroxynaphthalene synthase) from Streptomyces peucetius ATCC 27952. Mol. Cells 26 (2008) 362–367. [PMID: 18612244]
[EC 2.3.1.233 created 2014]
 
 
EC 2.3.1.234     
Accepted name: N6-L-threonylcarbamoyladenine synthase
Reaction: L-threonylcarbamoyladenylate + adenine37 in tRNA = AMP + N6-L-threonylcarbamoyladenine37 in tRNA
For diagram of N6-L-threonylcarbamoyladenosine37 modified tRNA biosynthesis, click here
Glossary: N6-L-threonylcarbamoyladenine37 = t6A37
Other name(s): t6A synthase; Kae1; ygjD (gene name); Qri7
Systematic name: L-threonylcarbamoyladenylate:adenine37 in tRNA N6-L-threonylcarbamoyltransferase
Comments: The enzyme is involved in the synthesis of N6-threonylcarbamoyladenosine37 in tRNAs, which is found in tRNAs with the anticodon NNU, i.e. tRNAIle, tRNAThr, tRNAAsn, tRNALys, tRNASer and tRNAArg [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lauhon, C.T. Mechanism of N6-threonylcarbamoyladenonsine (t6A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 51 (2012) 8950–8963. [DOI] [PMID: 23072323]
2.  Deutsch, C., El Yacoubi, B., de Crecy-Lagard, V. and Iwata-Reuyl, D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J. Biol. Chem. 287 (2012) 13666–13673. [DOI] [PMID: 22378793]
3.  Perrochia, L., Crozat, E., Hecker, A., Zhang, W., Bareille, J., Collinet, B., van Tilbeurgh, H., Forterre, P. and Basta, T. In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. Nucleic Acids Res. 41 (2013) 1953–1964. [DOI] [PMID: 23258706]
4.  Wan, L.C.K., Mao, D.Y.L., Neculai, D., Strecker, J., Chiovitti, D., Kurinov, I., Poda, G., Thevakumaran, N., Yuan, F., Szilard, R.K., Lissina, E., Nislow, C., Caudy, A.A., Durocher, D. and Sicheri, F. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res. 41 (2013) 6332–6346. [DOI] [PMID: 23620299]
[EC 2.3.1.234 created 2014 as EC 2.6.99.4, transferred 2014 to EC 2.3.1.234]
 
 
EC 2.3.1.235     
Accepted name: tetracenomycin F2 synthase
Reaction: 10 malonyl-CoA = tetracenomycin F2 + 10 CoA + 10 CO2 + 2 H2O
For diagram of polyketides biosynthesis, click here
Glossary: tetracenomycin F2 = 4-(3-acetyl-4,5,7,10-tetrahydroxyanthracen-2-yl)-3-oxobutanoic acid
Other name(s): TCM PKS
Systematic name: malonyl-CoA:acetate malonyltransferase (tetracenomycin F2 forming)
Comments: A multi-domain polyketide synthase involved in the synthesis of tetracenomycin in the bacterium Streptomyces glaucescens. It involves a ketosynthase complex (TcmKL), an acyl carrier protein (TcmM), a malonyl CoA:ACP acyltransferase (MAT), and a cyclase (TcmN). A malonyl-CoA molecule is initially bound to the acyl carrier protein and decarboxylated to form an acetyl starter unit. Additional two-carbon units are added from nine more malonyl-CoA molecules.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bao, W., Wendt-Pienkowski, E. and Hutchinson, C.R. Reconstitution of the iterative type II polyketide synthase for tetracenomycin F2 biosynthesis. Biochemistry 37 (1998) 8132–8138. [DOI] [PMID: 9609708]
[EC 2.3.1.235 created 2014]
 
 
EC 2.3.1.236     
Accepted name: 5-methylnaphthoic acid synthase
Reaction: acetyl-CoA + 5 malonyl-CoA + 3 NADPH + 3 H+ = 5-methyl-1-naphthoate + 6 CoA + 5 CO2 + 4 H2O + 3 NADP+
For diagram of polyketides biosynthesis, click here
Other name(s): AziB
Systematic name: malonyl-CoA:acetyl-CoA malonyltransferase (5-methyl-1-naphthoic acid forming)
Comments: A multi-domain polyketide synthase involved in the synthesis of azinomycin B in the bacterium Streptomyces griseofuscus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Zhao, Q., He, Q., Ding, W., Tang, M., Kang, Q., Yu, Y., Deng, W., Zhang, Q., Fang, J., Tang, G. and Liu, W. Characterization of the azinomycin B biosynthetic gene cluster revealing a different iterative type I polyketide synthase for naphthoate biosynthesis. Chem. Biol. 15 (2008) 693–705. [DOI] [PMID: 18635006]
[EC 2.3.1.236 created 2014]
 
 
EC 2.3.1.237     
Accepted name: neocarzinostatin naphthoate synthase
Reaction: acetyl-CoA + 5 malonyl-CoA + 2 NADPH + 2 H+ = 2-hydroxy-5-methyl-1-naphthoate + 6 CoA + 5 CO2 + 3 H2O + 2 NADP+
For diagram of polyketides biosynthesis, click here
Other name(s): naphthoic acid synthase; NNS; ncsB (gene name)
Systematic name: malonyl-CoA:acetyl-CoA malonyltransferase (2-hydroxy-5-methyl-1-naphthoic acid forming)
Comments: A multi-domain polyketide synthase involved in the synthesis of neocarzinostatin in the bacterium Streptomyces carzinostaticus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sthapit, B., Oh, T.J., Lamichhane, R., Liou, K., Lee, H.C., Kim, C.G. and Sohng, J.K. Neocarzinostatin naphthoate synthase: an unique iterative type I PKS from neocarzinostatin producer Streptomyces carzinostaticus. FEBS Lett. 566 (2004) 201–206. [DOI] [PMID: 15147895]
[EC 2.3.1.237 created 2014]
 
 
EC 2.3.1.238     
Accepted name: monacolin J acid methylbutanoate transferase
Reaction: monacolin J acid + (S)-2-methylbutanoyl-[2-methylbutanoate polyketide synthase] = lovastatin acid + [2-methylbutanoate polyketide synthase]
For diagram of lovastatin biosynthesis, click here
Glossary: monacolin J acid = (3R,5R)-7-[(1S,2S,6R,8S,8aR)-8-hydroxy-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate
lovastatin acid = (3R,5R)-7-[(1S,2S,6R,8S,8aR)-2,6-dimethyl-8-{[(2S)-2-methylbutanoyl]oxy}-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]-3,5-dihydroxyheptanoate
Other name(s): LovD
Systematic name: monacolin J acid:(S)-2-methylbutanoyl-[2-methylbutanoate polyketide synthase] (S)-2-methylbutanoate transferase
Comments: The enzyme catalyses the ultimate reaction in the lovastatin biosynthesis pathway of the filamentous fungus Aspergillus terreus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  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. [DOI] [PMID: 10334994]
2.  Xie, X., Watanabe, K., Wojcicki, W.A., Wang, C.C. and Tang, Y. Biosynthesis of lovastatin analogs with a broadly specific acyltransferase. Chem. Biol. 13 (2006) 1161–1169. [DOI] [PMID: 17113998]
3.  Xie, X., Meehan, M.J., Xu, W., Dorrestein, P.C. and Tang, Y. Acyltransferase mediated polyketide release from a fungal megasynthase. J. Am. Chem. Soc. 131 (2009) 8388–8389. [DOI] [PMID: 19530726]
[EC 2.3.1.238 created 2014]
 
 
EC 2.3.1.239     
Accepted name: 10-deoxymethynolide synthase
Reaction: malonyl-CoA + 5 (2S)-methylmalonyl-CoA + 5 NADPH + 5 H+ = 10-deoxymethynolide + 6 CoA + 6 CO2 + 5 NADP+ + 2 H2O
For diagram of methymycin and pikromycin biosynthesis, click here
Other name(s): pikromycin PKS
Systematic name: (2S)-methylmalonyl-CoA:malonyl-CoA malonyltransferase (10-deoxymethynolide forming)
Comments: The product, 10-deoxymethynolide, contains a 12-membered ring and is an intermediate in the biosynthesis of methymycin in the bacterium Streptomyces venezuelae. The enzyme also produces narbonolide (see EC 2.3.1.240, narbonolide synthase). The enzyme has 29 active sites arranged in four polypeptides (pikAI - pikAIV) with a loading domain, six extension modules and a terminal thioesterase domain. Each extension module contains a ketosynthase (KS), keto reductase (KR), an acyltransferase (AT) and an acyl-carrier protein (ACP). Not all active sites are used in the biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lu, H., Tsai, S.C., Khosla, C. and Cane, D.E. Expression, site-directed mutagenesis, and steady state kinetic analysis of the terminal thioesterase domain of the methymycin/picromycin polyketide synthase. Biochemistry 41 (2002) 12590–12597. [DOI] [PMID: 12379101]
2.  Kittendorf, J.D., Beck, B.J., Buchholz, T.J., Seufert, W. and Sherman, D.H. Interrogating the molecular basis for multiple macrolactone ring formation by the pikromycin polyketide synthase. Chem. Biol. 14 (2007) 944–954. [DOI] [PMID: 17719493]
3.  Yan, J., Gupta, S., Sherman, D.H. and Reynolds, K.A. Functional dissection of a multimodular polypeptide of the pikromycin polyketide synthase into monomodules by using a matched pair of heterologous docking domains. Chembiochem 10 (2009) 1537–1543. [DOI] [PMID: 19437523]
4.  Whicher, J.R., Dutta, S., Hansen, D.A., Hale, W.A., Chemler, J.A., Dosey, A.M., Narayan, A.R., Hakansson, K., Sherman, D.H., Smith, J.L. and Skiniotis, G. Structural rearrangements of a polyketide synthase module during its catalytic cycle. Nature 510 (2014) 560–564. [DOI] [PMID: 24965656]
[EC 2.3.1.239 created 2014]
 
 


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