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, 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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.419 nepetalactol dehydrogenase (1 November 2019)
EC 1.1.5.13 (S)-2-hydroxyglutarate dehydrogenase (1 November 2019)
*EC 2.1.1.308 cytidylyl-2-hydroxyethylphosphonate methyltransferase (1 November 2019)
EC 2.1.4.3 L-arginine:L-lysine amidinotransferase (1 November 2019)
*EC 2.3.1.26 sterol O-acyltransferase (1 November 2019)
*EC 2.3.1.252 mycolipanoate synthase (1 November 2019)
EC 2.3.1.292 (phenol)carboxyphthiodiolenone synthase (1 November 2019)
EC 2.3.1.293 meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I (1 November 2019)
EC 2.3.1.294 meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase II (1 November 2019)
EC 2.3.1.295 mycoketide-CoA synthase (1 November 2019)
EC 2.3.1.296 ω-hydroxyceramide transacylase (1 November 2019)
EC 2.3.1.297 very-long-chain ceramide synthase (1 November 2019)
EC 2.3.1.298 ultra-long-chain ceramide synthase (1 November 2019)
EC 2.3.1.299 sphingoid base N-stearoyltransferase (1 November 2019)
EC 2.6.1.116 6-aminohexanoate aminotransferase (1 November 2019)
EC 2.6.1.117 L-glutamine—4-(methylsulfanyl)-2-oxobutanoate aminotransferase (1 November 2019)
EC 2.7.1.227 inositol phosphorylceramide synthase (1 November 2019)
EC 2.7.1.228 mannosyl-inositol-phosphoceramide inositolphosphotransferase (1 November 2019)
EC 2.7.1.229 deoxyribokinase (1 November 2019)
EC 2.8.1.16 L-aspartate semialdehyde sulfurtransferase (1 November 2019)
*EC 2.8.3.17 3-(aryl)acryloyl-CoA:(R)-3-(aryl)lactate CoA-transferase (1 November 2019)
*EC 3.1.1.96 D-aminoacyl-tRNA deacylase (1 November 2019)
EC 3.1.1.110 xylono-1,5-lactonase (1 November 2019)
EC 3.1.1.111 phosphatidylserine sn-1 acylhydrolase (1 November 2019)
EC 3.1.1.112 isoamyl acetate esterase (1 November 2019)
EC 3.1.1.113 ethyl acetate hydrolase (1 November 2019)
EC 3.1.1.114 methyl acetate hydrolase (1 November 2019)
EC 3.1.27.10 transferred now EC 4.6.1.23 (1 November 2019)
*EC 3.2.1.113 mannosyl-oligosaccharide 1,2-α-mannosidase (1 November 2019)
EC 3.2.1.210 endoplasmic reticulum Man8GlcNAc2 1,2-α-mannosidase (1 November 2019)
EC 3.4.13.23 cysteinylglycine-S-conjugate dipeptidase (1 November 2019)
*EC 3.5.1.60 N-(long-chain-acyl)ethanolamine deacylase (1 November 2019)
EC 3.5.1.134 (indol-3-yl)acetyl-L-aspartate hydrolase (1 November 2019)
EC 3.6.3.3 transferred now EC 7.2.2.21 (1 November 2019)
EC 4.1.1.118 isophthalyl-CoA decarboxylase (1 November 2019)
EC 4.2.1.175 (R)-3-(aryl)lactoyl-CoA dehydratase (1 November 2019)
EC 4.2.3.205 sodorifen synthase (1 November 2019)
EC 4.6.1.23 ribotoxin (1 November 2019)
EC 5.4.99.67 4-amino-4-deoxychorismate mutase (1 November 2019)
EC 5.6.1.10 (R)-2-hydroxyacyl-CoA dehydratase activating ATPase (1 November 2019)
EC 6.2.1.58 isophthalate—CoA ligase (1 November 2019)
EC 6.2.1.59 long-chain fatty acid adenylase/transferase FadD26 (1 November 2019)
EC 6.2.1.60 marinolic acid—CoA ligase (1 November 2019)
EC 7.2.2.21 Cd2+-exporting ATPase (1 November 2019)
*EC 7.4.2.5 bacterial ABC-type protein transporter (1 November 2019)

EC 1.1.1.419

Accepted name: nepetalactol dehydrogenase

Reaction: (1) (+)-cis,cis-nepetalactol + NAD+ = (+)-cis,cis-nepetalactone + NADH + H+
(2) (+)-cis,trans-nepetalactol + NAD+ = (+)-cis,trans-nepetalactone + NADH + H+

Glossary: (+)-cis,cis-nepetalactol = (4aR,7S,7aS)-4,7-dimethyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-1-ol
(+)-cis,trans-nepetalactol = (+)-iridodial lactol = (4aS,7S,7aR)-4,7-dimethyl-1,4a,5,6,7,7a-hexahydrocyclopenta[c]pyran-1-ol

Other name(s): NEPS1 (gene name)

Systematic name: nepetalactol:NAD+ 1-oxidoreductase

Comments: The enzyme, characterized from the plant Nepeta mussinii, binds an NAD+ cofactor. It also catalyses the activity of EC 5.5.1.34, (+)-cis,trans-nepetalactol synthase.

References:

1. Lichman, B.R., Kamileen, M.O., Titchiner, G.R., Saalbach, G., Stevenson, C.EM., Lawson, D.M. and O'Connor, S.E. Uncoupled activation and cyclization in catmint reductive terpenoid biosynthesis. Nat. Chem. Biol. 15 (2019) 71-79. [PMID: 30531909]

2. Lichman, B.R., O'Connor, S.E. and Kries, H. Biocatalytic strategies towards [4+2] cycloadditions. Chemistry 25 (2019) 6864-6877. [PMID: 30664302]

[EC 1.1.1.419 created 2019]

EC 1.1.5.13

Accepted name: (S)-2-hydroxyglutarate dehydrogenase

Reaction: (S)-2-hydroxyglutarate + a quinone = 2-oxoglutarate + a quinol

Other name(s): L-2-hydroxyglutarate dehydrogenase; lhgO (gene name); ygaF (gene name)

Systematic name: (S)-2-hydroxyglutarate:quinone oxidoreductase

Comments: The enzyme, characterized from the bacterium Escherichia coli, contains an FAD cofactor that is not covalently attached. It is bound to the cytoplasmic membrane and is coupled to the membrane quinone pool.

References:

1. Kalliri, E., Mulrooney, S.B. and Hausinger, R.P. Identification of Escherichia coli YgaF as an L-2-hydroxyglutarate oxidase. J. Bacteriol. 190 (2008) 3793-3798. [PMID: 18390652]

2. Knorr, S., Sinn, M., Galetskiy, D., Williams, R.M., Wang, C., Muller, N., Mayans, O., Schleheck, D. and Hartig, J.S. Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate. Nat. Commun. 9 (2018) 5071. [PMID: 30498244]

[EC 1.1.5.13 created 2019]

*EC 2.1.1.308

Accepted name: cytidylyl-2-hydroxyethylphosphonate methyltransferase

Reaction: 2 S-adenosyl-L-methionine + cytidine 5'-{[hydroxy(2-hydroxyethyl)phosphonoyl]phosphate} + reduced acceptor = S-adenosyl-L-homocysteine + 5'-deoxyadenosine + L-methionine + cytidine 5'-{[hydroxy(2-hydroxypropyl)phosphonoyl]phosphate} + oxidized acceptor

For diagram of reaction, click here

Other name(s): Fom3; S-adenosyl-L-methionine:methylcob(III)alamin:2-hydroxyethylphosphonate methyltransferase (incorrect); 2-hydroxyethylphosphonate methyltransferase (incorrect)

Systematic name: S-adenosyl-L-methionine:cytidine 5'-{[hydroxy(2-hydroxyethyl)phosphonoyl]phosphate} C-methyltransferase

Comments: Requires cobalamin. The enzyme, isolated from the bacterium Streptomyces wedmorensis, is involved in fosfomycin biosynthesis. It is a radical S-adenosyl-L-methionine (SAM) enzyme that contains a [4Fe-4S] center and a methylcob(III)alamin cofactor. The enzyme uses two molecues of SAM for the reaction. One molecule forms a 5'-deoxyadenosyl radical, while the other is used to methylate the cobalamin cofactor. The 5'-deoxyadenosyl radical abstracts a hydrogen from the C2 position of cytidine 5'-{[(2-hydroxyethyl)phosphonoyl]phosphate} forming a free radical that reacts with the methyl group on methylcob(III)alamin at the opposite side from SAM and the [4Fe-4S]cluster to produce a racemic mix of methylated products and cob(II)alamin. Both the [4Fe-4S]cluster and the cob(II)alamin need to be reduced by an unknown factor(s) before the enzyme could catalyse another cycle.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Woodyer, R.D., Li, G., Zhao, H. and van der Donk, W.A. New insight into the mechanism of methyl transfer during the biosynthesis of fosfomycin. Chem. Commun. (Camb.) (2007) 359-361. [PMID: 17220970]

2. Allen, K.D. and Wang, S.C. Initial characterization of Fom3 from Streptomyces wedmorensis: The methyltransferase in fosfomycin biosynthesis. Arch. Biochem. Biophys. 543 (2014) 67-73. [PMID: 24370735]

3. Sato, S., Kudo, F., Kim, S.Y., Kuzuyama, T. and Eguchi, T. Methylcobalamin-dependent radical SAM C-methyltransferase Fom3 recognizes cytidylyl-2-hydroxyethylphosphonate and catalyzes the nonstereoselective C-methylation in fosfomycin biosynthesis. Biochemistry 56 (2017) 3519-3522. [PMID: 28678474]

4. Blaszczyk, A.J. and Booker, S.J. A (re)discovery of the Fom3 substrate. Biochemistry 57 (2018) 891-892. [PMID: 29345912]

[EC 2.1.1.308 created 2014, modified 2019]

EC 2.1.4.3

Accepted name: L-arginine:L-lysine amidinotransferase

Reaction: L-arginine + L-lysine = L-ornithine + L-homoarginine

Glossary: phaseolotoxin = N5-[amino(sulfoamino)phosphoryl]-L-ornithyl-L-alanyl-L-arginine

Other name(s): amtA (gene name)

Systematic name: L-arginine:L-lysine amidinotransferase

Comments: The enzyme, characterized from the bacterium Pseudomonas savastanoi pv. phaseolicola, is involved in the biosynthesis of the toxin phaseolotoxin, a modified tripeptide that causes the 'halo blight' disease of beans.

References:

1. Hernandez-Guzman, G. and Alvarez-Morales, A. Isolation and characterization of the gene coding for the amidinotransferase involved in the biosynthesis of phaseolotoxin in Pseudomonas syringae pv. phaseolicola. Mol. Plant Microbe Interact. 14 (2001) 545-554. [PMID: 11310742]

2. Li, M., Chen, L., Deng, Z. and Zhao, C. Characterization of AmtA, an amidinotransferase involved in the biosynthesis of phaseolotoxins. FEBS Open Bio 6 (2016) 603-609. [PMID: 27419063]

[EC 2.1.4.3 created 2019]

*EC 2.3.1.26

Accepted name: sterol O-acyltransferase

Reaction: a long-chain acyl-CoA + a sterol = CoA + a long-chain 3-hydroxysterol ester

Other name(s): cholesterol acyltransferase; sterol-ester synthase; acyl coenzyme A-cholesterol-O-acyltransferase; acyl-CoA:cholesterol acyltransferase; ACAT; acylcoenzyme A:cholesterol O-acyltransferase; cholesterol ester synthase; cholesterol ester synthetase; cholesteryl ester synthetase; SOAT1 (gene name); SOAT2 (gene name); ARE1 (gene name); ARE2 (gene name); acyl-CoA:cholesterol O-acyltransferase

Systematic name: long-chain acyl-CoA:sterol O-acyltransferase

Comments: The enzyme catalyses the formation of sterol esters from a sterol and long-chain fatty acyl-coenzyme A. The enzyme from yeast, but not from mammals, prefers monounsaturated acyl-CoA. In mammals the enzyme acts mainly on cholesterol and forms cholesterol esters that are stored in cytosolic droplets, which may serve to protect cells from the toxicity of free cholesterol. In macrophages, the accumulation of cytosolic droplets of cholesterol esters results in the formation of `foam cells', a hallmark of early atherosclerotic lesions. In hepatocytes and enterocytes, cholesterol esters can be incorporated into apolipoprotein B-containing lipoproteins for secretion from the cell.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9027-63-8

References:

1. Spector, A.A., Mathur, S.N. and Kaduce, T.L. Role of acylcoenzyme A: cholesterol O-acyltransferase in cholesterol metabolism. Prog. Lipid Res. 18 (1979) 31-53. [PMID: 42927]

2. Taketani, S., Nishino, T. and Katsuki, H. Characterization of sterol-ester synthetase in Saccharomyces cerevisiae. Biochim. Biophys. Acta 575 (1979) 148-155. [PMID: 389289]

3. Lee, O., Chang, C.C., Lee, W. and Chang, T.Y. Immunodepletion experiments suggest that acyl-coenzyme A:cholesterol acyltransferase-1 (ACAT-1) protein plays a major catalytic role in adult human liver, adrenal gland, macrophages, and kidney, but not in intestines. J. Lipid Res. 39 (1998) 1722-1727. [PMID: 9717734]

4. Yang, H., Cromley, D., Wang, H., Billheimer, J.T. and Sturley, S.L. Functional expression of a cDNA to human acyl-coenzyme A:cholesterol acyltransferase in yeast. Species-dependent substrate specificity and inhibitor sensitivity. J. Biol. Chem 272 (1997) 3980-3985. [PMID: 9020103]

5. Chang, C.C., Lee, C.Y., Chang, E.T., Cruz, J.C., Levesque, M.C. and Chang, T.Y. Recombinant acyl-CoA:cholesterol acyltransferase-1 (ACAT-1) purified to essential homogeneity utilizes cholesterol in mixed micelles or in vesicles in a highly cooperative manner. J. Biol. Chem 273 (1998) 35132-35141. [PMID: 9857049]

6. Das, A., Davis, M.A. and Rudel, L.L. Identification of putative active site residues of ACAT enzymes. J. Lipid Res. 49 (2008) 1770-1781. [PMID: 18480028]

[EC 2.3.1.26 created 1972, modified 2019]

*EC 2.3.1.252

Accepted name: mycolipanoate synthase

Reaction: a long-chain acyl-CoA + 3 (S)-methylmalonyl-CoA + 6 NADPH + 6 H+ + holo-[mycolipanoate synthase] = mycolipanoyl-[mycolipanoate synthase] + 4 CoA + 3 CO2 + 6 NADP+ + 3 H2O

Glossary: mycolipanoic acid = (2S,4S,6S)-2,4,6-trimethyl-very-long-chain fatty acid

Other name(s): msl3 (gene name); Pks3/4; mycolipanoic acid synthase; long-chain acyl-CoA:methylmalonyl-CoA C-acyltransferase (mycolipanoate-forming)

Systematic name: long-chain acyl-CoA:(S)-methylmalonyl-CoA C-acyltransferase (mycolipanoate-forming)

Comments: This mycobacterial enzyme accepts long-chain fatty acyl groups from their CoA esters and extends them by incorporation of three methylmalonyl (but not malonyl) residues, forming trimethyl-branched fatty-acids such as (2S,4S,6S)-2,4,6-trimethyltetracosanoate (C27-mycolipanoate). Since the enzyme lacks a thioesterase domain, the product remains bound to the enzyme and requires additional enzyme(s) for removal.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Sirakova, T.D., Thirumala, A.K., Dubey, V.S., Sprecher, H. and Kolattukudy, P.E. The Mycobacterium tuberculosis pks2 gene encodes the synthase for the hepta- and octamethyl-branched fatty acids required for sulfolipid synthesis. J. Biol. Chem 276 (2001) 16833-16839. [PMID: 11278910]

2. Dubey, V.S., Sirakova, T.D. and Kolattukudy, P.E. Disruption of msl3 abolishes the synthesis of mycolipanoic and mycolipenic acids required for polyacyltrehalose synthesis in Mycobacterium tuberculosis H37Rv and causes cell aggregation. Mol. Microbiol. 45 (2002) 1451-1459. [PMID: 12207710]

[EC 2.3.1.252 created 2016, modified 2019]

EC 2.3.1.292

Accepted name: (phenol)carboxyphthiodiolenone synthase

Reaction: (1) 3 malonyl-CoA + 2 (S)-methylmalonyl-CoA + icosanoyl-[(phenol)carboxyphthiodiolenone synthase] + 5 NADPH = C32-carboxyphthiodiolenone-[(phenol)carboxyphthiodiolenone synthase] + 5 CoA + 5 NADP+ + 5 CO2 + 2 H2O
(2) 3 malonyl-CoA + 2 (S)-methylmalonyl-CoA + docosanoyl-[(phenol)carboxyphthiodiolenone synthase] + 5 NADPH = C34-carboxyphthiodiolenone-[(phenol)carboxyphthiodiolenone synthase] + 5 CoA + 5 NADP+ + 5 CO2 + 2 H2O
(3) 3 malonyl-CoA + 2 (S)-methylmalonyl-CoA + 19-(4-hydroxyphenyl)-nonadecanoyl-[(phenol)carboxyphthiodiolenone synthase] + 5 NADPH = C37-(phenol)carboxyphthiodiolenone-[(phenol)carboxyphthiodiolenone synthase] + 5 CoA + 5 NADP+ + 5 CO2 + 2 H2O
(4) 3 malonyl-CoA + 2 (S)-methylmalonyl-CoA + 17-(4-hydroxyphenyl)heptadecanoyl-[(phenol)carboxyphthiodiolenone synthase] + 5 NADPH = C35-(phenol)carboxyphthiodiolenone-[(phenol)carboxyphthiodiolenone synthase] + 5 CoA + 5 NADP+ + 5 CO2 + 2 H2O

Glossary: C32-carboxyphthiodiolenone = (4E,9R,11R)-9,11-dihydroxy-2,4-dimethyl-3-oxotriacont-4-enoate
C34-carboxyphthiodiolenone = (4E,9R,11R)-9,11-dihydroxy-2,4-dimethyl-3-oxodotriacont-4-enoate
C35-phenolcarboxyphthiodiolenone = (4E)-9,11-dihydroxy-27-(4-hydroxyphenyl)-2,4-dimethyl-3-oxoheptacos-4-enoate
C37-phenolcarboxyphthiodiolenone = (4E,9R,11R)-9,11-dihydroxy-29-(4-hydroxyphenyl)-2,4-dimethyl-3-oxononacos-4-enoate
phthiocerols = linear carbohydrates containing one methoxyl group, one methyl group, and two secondary hydroxyl groups that serve as a backbone for certain lipids and glycolipids found in many species of Mycobacteriaceae

Other name(s): ppsABCDE (gene names)

Systematic name: (methyl)malonyl-CoA:long-chain acyl-[(phenol)carboxyphthiodiolenone synthase] (methyl)malonyltransferase {carboxyphthiodiolenone-[(phenol)carboxyphthiodiolenone synthase]-forming}

Comments: The enzyme, which is a complex of five polyketide synthase proteins, is involved in the synthesis of the lipid core common to phthiocerols and phenolphthiocerols. The first protein, PpsA, can accept either a C18 or C20 long-chain fatty acyl, or a (4-hydroxyphenyl)-C17 or C19 fatty acyl. The substrates must first be adenylated by EC 6.2.1.59, long-chain fatty acid adenylase/transferase FadD26, which also loads them onto PpsA. PpsA then extends them using a malonyl-CoA extender unit. The PpsB protein adds the next malonyl-CoA extender unit. The absence of a dehydratase and an enoyl reductase domains in the PpsA and PpsB modules results in the formation of the diol portion of the phthiocerol moiety. PpsC adds a third malonyl unit (releasing a water molecule due to its dehydratase domain), PpsD adds an (R)-methylmalonyl unit, releasing a water molecule, and PpsE adds a second (R)-methylmalonyl unit, without releasing a water molecule. The incorporation of the methylmalonyl units results in formation of two branched methyl groups in the elongated product. The enzyme does not contain a thioesterase domain [2], and release of the products requires the tesA-encoded type II thioesterase [1].

References:

1. Rao, A. and Ranganathan, A. Interaction studies on proteins encoded by the phthiocerol dimycocerosate locus of Mycobacterium tuberculosis. Mol. Genet. Genomics 272 (2004) 571-579. [PMID: 15668773]

2. Trivedi, O.A., Arora, P., Vats, A., Ansari, M.Z., Tickoo, R., Sridharan, V., Mohanty, D. and Gokhale, R.S. Dissecting the mechanism and assembly of a complex virulence mycobacterial lipid. Mol. Cell 17 (2005) 631-643. [PMID: 15749014]

[EC 2.3.1.292 created 2019]

EC 2.3.1.293

Accepted name: meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase I

Reaction: an ultra-long-chain mono-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain mono-unsaturated 3-oxo-fatty acyl-[acp] + CO2 + an [acyl-carrier protein]

Other name(s): kasA (gene name); β-ketoacyl-acyl carrier protein synthase KasA

Systematic name: ultra-long-chain mono-unsaturated fattyl acyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)

Comments: The enzyme is part of the fatty acid synthase (FAS) II system of mycobacteria, which extends modified products of the FAS I system, eventually forming meromycolic acids that are incorporated into mycolic acids. Meromycolic acids consist of a long chain, typically 50-60 carbons, which is functionalized by different groups.Two 3-oxoacyl-(acyl carrier protein) synthases function within the FAS II system, encoded by the kasA and kasB genes. The two enzymes share some sequence identity but function independently on separate sets of substrates. KasA differs from KasB (EC 2.3.1.294), by preferring shorter (C-22 to C-36) and more saturated (only one double bond) substrates.

References:

1. Schaeffer, M.L., Agnihotri, G., Volker, C., Kallender, H., Brennan, P.J. and Lonsdale, J.T. Purification and biochemical characterization of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthases KasA and KasB. J. Biol. Chem 276 (2001) 47029-47037. [PMID: 11600501]

2. Bhatt, A., Kremer, L., Dai, A.Z., Sacchettini, J.C. and Jacobs, W.R., Jr. Conditional depletion of KasA, a key enzyme of mycolic acid biosynthesis, leads to mycobacterial cell lysis. J. Bacteriol. 187 (2005) 7596-7606. [PMID: 16267284]

3. Luckner, S.R., Machutta, C.A., Tonge, P.J. and Kisker, C. Crystal structures of Mycobacterium tuberculosis KasA show mode of action within cell wall biosynthesis and its inhibition by thiolactomycin. Structure 17 (2009) 1004-1013. [PMID: 19604480]

[EC 2.3.1.293 created 2019]

EC 2.3.1.294

Accepted name: meromycolic acid 3-oxoacyl-(acyl carrier protein) synthase II

Reaction: an ultra-long-chain di-unsaturated acyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = an ultra-long-chain di-unsaturated 3-oxo-fatty acyl-[acp] + CO2 + an [acyl-carrier protein]

Other name(s): kasB (gene name); β-ketoacyl-acyl carrier protein synthase KasB

Systematic name: ultra-long-chain di-unsaturated fattyl acyl-[acyl-carrier protein]:malonyl-[acyl-carrier protein] C-acyltransferase (decarboxylating)

Comments: The enzyme is part of the fatty acid synthase (FAS) II system of mycobacteria, which extends modified products of the FAS I system, eventually forming meromycolic acids that are incorporated into mycolic acids. Meromycolic acids consist of a long chain, typically 50-60 carbons, which is functionalized by different groups.Two 3-oxoacyl-(acyl carrier protein) synthases function within the FAS II system, encoded by the kasA and kasB genes. The two enzymes share some sequence identity but function independently on separate sets of substrates. KasB differs from KasA (EC 2.3.1.293), by preferring longer substrates (closer to the upper limit), which also contain two double bonds.

References:

1. Schaeffer, M.L., Agnihotri, G., Volker, C., Kallender, H., Brennan, P.J. and Lonsdale, J.T. Purification and biochemical characterization of the Mycobacterium tuberculosis β-ketoacyl-acyl carrier protein synthases KasA and KasB. J. Biol. Chem 276 (2001) 47029-47037. [PMID: 11600501]

2. Gao, L.Y., Laval, F., Lawson, E.H., Groger, R.K., Woodruff, A., Morisaki, J.H., Cox, J.S., Daffe, M. and Brown, E.J. Requirement for kasB in Mycobacterium mycolic acid biosynthesis, cell wall impermeability and intracellular survival: implications for therapy. Mol. Microbiol. 49 (2003) 1547-1563. [PMID: 12950920]

3. Molle, V., Brown, A.K., Besra, G.S., Cozzone, A.J. and Kremer, L. The condensing activities of the Mycobacterium tuberculosis type II fatty acid synthase are differentially regulated by phosphorylation. J. Biol. Chem 281 (2006) 30094-30103. [PMID: 16873379]

4. Bhatt, A., Fujiwara, N., Bhatt, K., Gurcha, S.S., Kremer, L., Chen, B., Chan, J., Porcelli, S.A., Kobayashi, K., Besra, G.S. and Jacobs, W.R., Jr. Deletion of kasB in Mycobacterium tuberculosis causes loss of acid-fastness and subclinical latent tuberculosis in immunocompetent mice. Proc. Natl Acad. Sci. USA 104 (2007) 5157-5162. [PMID: 17360388]

5. Yamada, H., Bhatt, A., Danev, R., Fujiwara, N., Maeda, S., Mitarai, S., Chikamatsu, K., Aono, A., Nitta, K., Jacobs, W.R., Jr. and Nagayama, K. Non-acid-fastness in Mycobacterium tuberculosis Δ kasB mutant correlates with the cell envelope electron density. Tuberculosis (Edinb) 92 (2012) 351-357. [PMID: 22516756]

6. Vilcheze, C., Molle, V., Carrere-Kremer, S., Leiba, J., Mourey, L., Shenai, S., Baronian, G., Tufariello, J., Hartman, T., Veyron-Churlet, R., Trivelli, X., Tiwari, S., Weinrick, B., Alland, D., Guerardel, Y., Jacobs, W.R., Jr. and Kremer, L. Phosphorylation of KasB regulates virulence and acid-fastness in Mycobacterium tuberculosis. PLoS Pathog. 10 (2014) e1004115. [PMID: 24809459]

[EC 2.3.1.294 created 2019]

EC 2.3.1.295

Accepted name: mycoketide-CoA synthase

Reaction: a medium-chain acyl-CoA + 5 malonyl-CoA + 5 (S)-methylmalonyl-CoA + 22 NADPH + 22 H+ = a mycoketide-CoA + 10 CO2 + 10 CoA + 22 NADP+ + 11 H2O

Glossary: a mycoketide-CoA = a 4,8,12,16,20-pentamethyl-(long-chain fatty acyl)-CoA

Other name(s): pks12 (gene name)

Systematic name: malonyl-CoA/(S)-methylmalonyl-CoA:heptanoyl-CoA malonyltransferase (mycoketide-CoA-forming)

Comments: The enzyme, found in mycobacteria, is involved in the synthesis of β-D-mannosyl phosphomycoketides. It is a very large polyketide synthase that contains two complete sets of FAS-like fatty acid synthase modules. It binds an acyl-CoA with 5-9 carbons as a starter unit, and extends it by five rounds of alternative additions of malonyl-CoA and methylmalonyl-CoA extender units. Depending on the starter unit, the enzyme forms mycoketide-CoAs of different lengths.

References:

1. Matsunaga, I., Bhatt, A., Young, D.C., Cheng, T.Y., Eyles, S.J., Besra, G.S., Briken, V., Porcelli, S.A., Costello, C.E., Jacobs, W.R., Jr. and Moody, D.B. Mycobacterium tuberculosis pks12 produces a novel polyketide presented by CD1c to T cells. J. Exp. Med. 200 (2004) 1559-1569. [PMID: 15611286]

[EC 2.3.1.295 created 2019]

EC 2.3.1.296

Accepted name: ω-hydroxyceramide transacylase

Reaction: a linoleate-containing triacyl-sn-glycerol + an ultra-long-chain ω-hydroxyceramide = a diacyl-sn-glycerol + a linoleate-esterified acylceramide

Glossary: an ultra-long-chain fatty acid = ULCFA = a fatty acid with aliphatic chain of 28 or more carbons
an ultra-long-chain ω-hydroxyceramide = a ceramide that contains an ultra-long-chain ω-hydroxyfatty acid moiety (C28-C36)
acylceramide = ω-O-acylceramide = a ceramide that contains an ultra-long-chain ω-hydroxyfatty acid moiety (C28-C36) that is further extended by ω-esterification with linoleic acid.

Other name(s): PNPLA1 (gene name)

Systematic name: triacyl-sn-glycerol:ultra-long-chain ω-hydroxyceramide ω-O-linoleoyltransferase

Comments: The enzyme participates in the production of acylceramides in the stratum corneum, the outermost layer of the epidermis. Acylceramides are crucial components of the skin permeability barrier.

References:

1. Ohno, Y., Kamiyama, N., Nakamichi, S. and Kihara, A. PNPLA1 is a transacylase essential for the generation of the skin barrier lipid ω-O-acylceramide. Nat. Commun. 8 (2017) 14610. [PMID: 28248318]

[EC 2.3.1.296 created 2019]

EC 2.3.1.297

Accepted name: very-long-chain ceramide synthase

Reaction: a very-long-chain fatty acyl-CoA + a sphingoid base = a very-long-chain ceramide + CoA

Glossary: a sphingoid base = an amino alcohol, composed predominantly of 18 carbon atoms, characterized by the presence of a hydroxyl group at C-1 (and often also at C-3), and an amine group at C-2.

Other name(s): sphingoid base N-very-long-chain fatty acyl-coA transferase; mammalian ceramide synthase 2; CERS3 (gene name); LASS3 (gene name); LAG1 (gene name); LAC1 (gene name); LOH1 (gene name); LOH3 (gene name)

Systematic name: very-long-chain fatty acyl-coA:sphingoid base N-acyltransferase

Comments: This entry describes ceramide synthase enzymes that are specific for very-long-chain fatty acyl-CoA substrates. The two isoforms from yeast and the plant LOH1 and LOH3 isoforms transfer 24:0 and 26:0 acyl chains preferentially and use phytosphingosine as the preferred sphingoid base. The mammalian CERS2 isoform is specific for acyl donors of 20-26 carbons, which can be saturated or unsaturated. The mammalian CERS3 isoform catalyses this activity, but has a broader substrate range and also catalyses the activity of EC 2.3.1.298, ultra-long-chain ceramide synthase. Both mammalian enzymes can use multiple sphingoid bases, including sphinganine, sphingosine, and phytosphingosine.

References:

1. Guillas, I., Kirchman, P.A., Chuard, R., Pfefferli, M., Jiang, J.C., Jazwinski, S.M. and Conzelmann, A. C26-CoA-dependent ceramide synthesis of Saccharomyces cerevisiae is operated by Lag1p and Lac1p. EMBO J. 20 (2001) 2655-2665. [PMID: 11387200]

2. Pan, H., Qin, W.X., Huo, K.K., Wan, D.F., Yu, Y., Xu, Z.G., Hu, Q.D., Gu, K.T., Zhou, X.M., Jiang, H.Q., Zhang, P.P., Huang, Y., Li, Y.Y. and Gu, J.R. Cloning, mapping, and characterization of a human homologue of the yeast longevity assurance gene LAG1. Genomics 77 (2001) 58-64. [PMID: 11543633]

3. Schorling, S., Vallee, B., Barz, W.P., Riezman, H. and Oesterhelt, D. Lag1p and Lac1p are essential for the Acyl-CoA-dependent ceramide synthase reaction in Saccharomyces cerevisae. Mol. Biol. Cell 12 (2001) 3417-3427. [PMID: 11694577]

4. Mizutani, Y., Kihara, A. and Igarashi, Y. Mammalian Lass6 and its related family members regulate synthesis of specific ceramides. Biochem. J. 390 (2005) 263-271. [PMID: 15823095]

5. Laviad, E.L., Albee, L., Pankova-Kholmyansky, I., Epstein, S., Park, H., Merrill, A.H., Jr. and Futerman, A.H. Characterization of ceramide synthase 2: tissue distribution, substrate specificity, and inhibition by sphingosine 1-phosphate. J. Biol. Chem 283 (2008) 5677-5684. [PMID: 18165233]

6. Imgrund, S., Hartmann, D., Farwanah, H., Eckhardt, M., Sandhoff, R., Degen, J., Gieselmann, V., Sandhoff, K. and Willecke, K. Adult ceramide synthase 2 (CERS2)-deficient mice exhibit myelin sheath defects, cerebellar degeneration, and hepatocarcinomas. J. Biol. Chem 284 (2009) 33549-33560. [PMID: 19801672]

[EC 2.3.1.297 created 2019]

EC 2.3.1.298

Accepted name: ultra-long-chain ceramide synthase

Reaction: an ultra-long-chain fatty acyl-CoA + a sphingoid base = an ultra-long-chain ceramide + CoA

Glossary: a sphingoid base = an amino alcohol, composed predominantly of 18 carbon atoms, characterized by the presence of a hydroxyl group at C-1 (and often also at C-3), and an amine group at C-2.
an ultra-long-chain fatty acyl-CoA = an acyl-CoA with a chain length of 28 or longer.

Other name(s): mammalian ceramide synthase 3; sphingoid base N-ultra-long-chain fatty acyl-coA transferase; CERS3 (gene name)

Systematic name: ultra-long-chain fatty acyl-coA:sphingoid base N-acyltransferase

Comments: Mammals have six ceramide synthases that exhibit relatively strict specificity regarding the chain-length of their acyl-CoA substrates. Ceramide synthase 3 (CERS3) is the only enzyme that is active with ultra-long-chain acyl-CoA donors (C28 or longer). It is active in the epidermis, where its products are incorporated into acylceramides. CERS3 also accepts (2R)-2-hydroxy fatty acids and ω-hydroxy fatty acids, and can accept very-long-chain acyl-CoA substrates (see EC 2.3.1.297, very-long-chain ceramide synthase). It can use multiple sphingoid bases including sphinganine, sphingosine, phytosphingosine, and (6R)-6-hydroxysphingosine.

References:

1. Mizutani, Y., Kihara, A. and Igarashi, Y. LASS3 (longevity assurance homologue 3) is a mainly testis-specific (dihydro)ceramide synthase with relatively broad substrate specificity. Biochem. J. 398 (2006) 531-538. [PMID: 16753040]

2. Mizutani, Y., Kihara, A., Chiba, H., Tojo, H. and Igarashi, Y. 2-Hydroxy-ceramide synthesis by ceramide synthase family: enzymatic basis for the preference of FA chain length. J. Lipid Res. 49 (2008) 2356-2364. [PMID: 18541923]

3. Jennemann, R., Rabionet, M., Gorgas, K., Epstein, S., Dalpke, A., Rothermel, U., Bayerle, A., van der Hoeven, F., Imgrund, S., Kirsch, J., Nickel, W., Willecke, K., Riezman, H., Grone, H.J. and Sandhoff, R. Loss of ceramide synthase 3 causes lethal skin barrier disruption. Hum. Mol. Genet. 21 (2012) 586-608. [PMID: 22038835]

4. Mizutani, Y., Sun, H., Ohno, Y., Sassa, T., Wakashima, T., Obara, M., Yuyama, K., Kihara, A. and Igarashi, Y. Cooperative synthesis of ultra long-chain fatty acid and ceramide during keratinocyte differentiation. PLoS One 8 (2013) e67317. [PMID: 23826266]

[EC 2.3.1.298 created 2019]

EC 2.3.1.299

Accepted name: sphingoid base N-stearoyltransferase

Reaction: stearoyl-CoA + a sphingoid base = an N-(stearoyl)-sphingoid base + CoA

Glossary: a sphingoid base = an amino alcohol, composed predominantly of 18 carbon atoms, characterized by the presence of a hydroxyl group at C-1 (and often also at C-3), and an amine group at C-2.

Other name(s): mammalian ceramide synthase 1; LASS1 (gene name); UOG1 (gene name); CERS1 (gene name)

Systematic name: stearoyl-CoA:sphingoid base N-stearoyltransferase

Comments: Mammals have six ceramide synthases that exhibit relatively strict specificity regarding the chain-length of their acyl-CoA substrates. Ceramide synthase 1 (CERS1) is structurally and functionally distinctive from all other CERS enzymes, and is specific for stearoyl-CoA as the acyl donor. It can use multiple sphingoid bases including sphinganine, sphingosine, and phytosphingosine.

References:

1. Venkataraman, K., Riebeling, C., Bodennec, J., Riezman, H., Allegood, J.C., Sullards, M.C., Merrill, A.H., Jr. and Futerman, A.H. Upstream of growth and differentiation factor 1 (uog1), a mammalian homolog of the yeast longevity assurance gene 1 (LAG1), regulates N-stearoyl-sphinganine (C18-(dihydro)ceramide) synthesis in a fumonisin B1-independent manner in mammalian cells. J. Biol. Chem 277 (2002) 35642-35649. [PMID: 12105227]

2. Kim, H.J., Qiao, Q., Toop, H.D., Morris, J.C. and Don, A.S. A fluorescent assay for ceramide synthase activity. J. Lipid Res. 53 (2012) 1701-1707. [PMID: 22661289]

3. Wang, Z., Wen, L., Zhu, F., Wang, Y., Xie, Q., Chen, Z. and Li, Y. Overexpression of ceramide synthase 1 increases C18-ceramide and leads to lethal autophagy in human glioma. Oncotarget 8 (2017) 104022-104036. [PMID: 29262618]

4. Turpin-Nolan, S.M., Hammerschmidt, P., Chen, W., Jais, A., Timper, K., Awazawa, M., Brodesser, S. and Bruning, J.C. CerS1-derived C18:0 ceramide in skeletal muscle promotes obesity-induced insulin resistance. Cell Rep. 26 (2019) 1-10.e7. [PMID: 30605666]

[EC 2.3.1.299 created 2019]

EC 2.6.1.116

Accepted name: 6-aminohexanoate aminotransferase

Reaction: 6-aminohexanoate + 2-oxoglutarate = 6-oxohexanoate + L-glutamate

Other name(s): nylD (gene name)

Systematic name: 6-aminohexanoate:2-oxogutarate aminotransferase

Comments: The enzyme, characterized from the bacterium Arthrobacter sp. KI72, participates in the degradation of nylon-6. Glyoxylate can serve as an alternative amino group acceptor with similar efficiency.

References:

1. Takehara, I., Fujii, T., Tanimoto, Y., Kato, D.I., Takeo, M. and Negoro, S. Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate. Appl. Microbiol. Biotechnol. 102 (2018) 801-814. [PMID: 29188330]

[EC 2.6.1.116 created 2019]

EC 2.6.1.117

Accepted name: L-glutamine—4-(methylsulfanyl)-2-oxobutanoate aminotransferase

Reaction: L-glutamine + 4-(methylsulfanyl)-2-oxobutanoate = 2-oxoglutaramate + L-methionine

Other name(s): mtnE (gene name); Solyc11g013170.1 (locus name)

Systematic name: L-glutamine:4-(methylsulfanyl)-2-oxobutanoate aminotransferase

Comments: A pyridoxal-phosphate protein. The enzyme, found in both prokaryotes and eukaryotes, catalyses the last reaction in a methionine salvage pathway. In mammals this activity is catalysed by the multifunctional glutamine transaminase K (cf. EC 2.6.1.64, glutamine–phenylpyruvate transaminase).

References:

1. Berger, B.J., English, S., Chan, G. and Knodel, M.H. Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis. J. Bacteriol. 185 (2003) 2418-2431. [PMID: 12670965]

2. Ellens, K.W., Richardson, L.G., Frelin, O., Collins, J., Ribeiro, C.L., Hsieh, Y.F., Mullen, R.T. and Hanson, A.D. Evidence that glutamine transaminase and ω-amidase potentially act in tandem to close the methionine salvage cycle in bacteria and plants. Phytochemistry 113 (2015) 160-169. [PMID: 24837359]

[EC 2.6.1.117 created 2019]

EC 2.7.1.227

Accepted name: inositol phosphorylceramide synthase

Reaction: 1-phosphatidyl-1D-myo-inositol + a very-long-chain (2'R)-2'-hydroxy-phytocermide = 1,2-diacyl-sn-glycerol + a very-long-chain inositol phospho-(2'R)-2'-hydroxyphytoceramide

Glossary: a very-long-chain inositol phospho-(2'R)-2'-hydroxyphytoceramide = a very-long-chain inositol phospho-α-hydroxyphytoceramide = IPC

Other name(s): AUR1 (gene name); KEI1 (gene name)

Systematic name: 1-phosphatidyl-1D-myo-inositol:(2'R)-2'-hydroxy-phytocermide phosphoinositoltransferase

Comments: The enzyme, characterized from yeast, attaches a phosphoinositol headgroup to α-hydroxyphytoceramides, generating a very-long-chain inositol phospho-α hydroxyphytoceramide (IPC), the simplest of the three complex sphingolipids produced by yeast.

References:

1. Nagiec, M.M., Nagiec, E.E., Baltisberger, J.A., Wells, G.B., Lester, R.L. and Dickson, R.C. Sphingolipid synthesis as a target for antifungal drugs. Complementation of the inositol phosphorylceramide synthase defect in a mutant strain of Saccharomyces cerevisiae by the AUR1 gene. J. Biol. Chem 272 (1997) 9809-9817. [PMID: 9092515]

2. Levine, T.P., Wiggins, C.A. and Munro, S. Inositol phosphorylceramide synthase is located in the Golgi apparatus of Saccharomyces cerevisiae. Mol. Biol. Cell 11 (2000) 2267-2281. [PMID: 10888667]

3. Sato, K., Noda, Y. and Yoda, K. Kei1: a novel subunit of inositolphosphorylceramide synthase, essential for its enzyme activity and Golgi localization. Mol. Biol. Cell 20 (2009) 4444-4457. [PMID: 19726565]

[EC 2.7.1.227 created 2019]

EC 2.7.1.228

Accepted name: mannosyl-inositol-phosphoceramide inositolphosphotransferase

Reaction: 1-phosphatidyl-1D-myo-inositol + a very-long-chain mannosylinositol phospho-(2'R)-2'-hydroxyphytoceramide = 1,2-diacyl-sn-glycerol + a very-long-chain mannosyl-diphosphoinositol-(2'R)-2'-hydroxyphytoceramide

Glossary: a very-long-chain mannosyl-diphosphoinositol-(2'R)-2'-hydroxyphytoceramide = a very-long-chain mannosyl-diphosphoinositol-α-hydroxyphytoceramide = MIP2C

Other name(s): IPT1 (gene name)

Systematic name: 1-phosphatidyl-1D-myo-inositol:mannosylinositol phospho-(2'R)-2'-hydroxyphytoceramide phosphoinositoltransferase

Comments: This enzyme catalyses the ultimate reaction in the yeast sphingolipid biosynthesis pathway. It transfers a second phosphoinositol group to mannosyl-inositol-phospho-α-hydroxyphytoceramide (MIPC), forming the final and most abundant yeast sphingolipid, mannosyl-diphosphoinositol-ceramide (MIP2C).

References:

1. Dickson, R.C., Nagiec, E.E., Wells, G.B., Nagiec, M.M. and Lester, R.L. Synthesis of mannose-(inositol-P)2-ceramide, the major sphingolipid in Saccharomyces cerevisiae, requires the IPT1 (YDR072c) gene. J. Biol. Chem 272 (1997) 29620-29625. [PMID: 9368028]

[EC 2.7.1.228 created 2019]

EC 2.7.1.229

Accepted name: deoxyribokinase

Reaction: ATP + 2-deoxy-D-ribose = ADP + 2-deoxy-D-ribose 5-phosphate

Other name(s): deoK (gene name)

Systematic name: ATP:2-deoxy-D-ribose 5-phosphotransferase

Comments: The enzyme, characterized from bacteria, is much more active with 2-deoxy-D-ribose than with D-ribose. cf. EC 2.7.1.15, ribokinase.

References:

1. Domagk, G.F. and Horecker, B.L. Pentose fermentation by Lactobacillus plantarum. V. Fermentation of 2-deoxy-D-ribose. J. Biol. Chem 233 (1958) 283-286. [PMID: 13563487]

2. Ginsburg, A. A deoxyribokinase from Lactobacillus plantarum. J. Biol. Chem. 234 (1959) 481-487. [PMID: 13641245]

3. Hoffee, P.A. 2-deoxyribose gene-enzyme complex in Salmonella typhimurium. I. Isolation and enzymatic characterization of 2-deoxyribose-negative mutants. J. Bacteriol. 95 (1968) 449-457. [PMID: 4867740]

4. Tourneux, L., Bucurenci, N., Saveanu, C., Kaminski, P.A., Bouzon, M., Pistotnik, E., Namane, A., Marliere, P., Barzu, O., Li De La Sierra, I., Neuhard, J. and Gilles, A.M. Genetic and biochemical characterization of Salmonella enterica serovar Typhi deoxyribokinase. J. Bacteriol. 182 (2000) 869-873. [PMID: 10648508]

[EC 2.7.1.229 created 2019]

EC 2.8.1.16

Accepted name: L-aspartate semialdehyde sulfurtransferase

Reaction: hydrogen sulfide + L-aspartate 4-semialdehyde + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = L-homocysteine + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster

Other name(s): MA1821 (locus name); MJ0100 (locus name)

Systematic name: hydrogen sulfide:L-aspartate-4-semialdehyde sulfurtransferase

Comments: The enzyme, characterized from the archaeon Methanosarcina acetivorans, participates in an L-methionine biosysnthetic pathway found in most of the methanogenic archaea.

References:

1. Rauch, B.J., Gustafson, A. and Perona, J.J. Novel proteins for homocysteine biosynthesis in anaerobic microorganisms. Mol. Microbiol. 94 (2014) 1330-1342. [PMID: 25315403]

2. Allen, K.D., Miller, D.V., Rauch, B.J., Perona, J.J. and White, R.H. Homocysteine is biosynthesized from aspartate semialdehyde and hydrogen sulfide in methanogenic archaea. Biochemistry 54 (2015) 3129-3132. [PMID: 25938369]

[EC 2.8.1.16 created 2019]

*EC 2.8.3.17

Accepted name: 3-(aryl)acryloyl-CoA:(R)-3-(aryl)lactate CoA-transferase

Reaction: (1) (E)-cinnamoyl-CoA + (R)-(phenyl)lactate = (E)-cinnamate + (R)-(phenyl)lactoyl-CoA
(2) (E)-4-coumaroyl-CoA + (R)-3-(4-hydroxyphenyl)lactate = 4-coumarate + (R)-3-(4-hydroxyphenyl)lactoyl-CoA
(3) 3-(indol-3-yl)acryloyl-CoA + (R)-3-(indol-3-yl)lactate = 3-(indol-3-yl)acrylate + (R)-3-(indol-3-yl)lactoyl-CoA

Other name(s): FldA; cinnamoyl-CoA:phenyllactate CoA-transferase

Systematic name: 3-(aryl)acryloyl-CoA:(R)-3-(aryl)lactate CoA-transferase

Comments: The enzyme, found in some amino acid-fermenting anaerobic bacteria, participates in the fermentation pathways of L-phenylalanine, L-tyrosine, and L-tryptophan. It forms a complex with EC 4.2.1.175, (R)-3-(aryl)lactoyl-CoA dehydratase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 289682-21-9

References:

1. Dickert, S., Pierik, A.J., Linder, D. and Buckel, W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. Eur. J. Biochem. 267 (2000) 3874-3884. [PMID: 10849007]

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

[EC 2.8.3.17 created 2003, modified 2019]

*EC 3.1.1.96

Accepted name: D-aminoacyl-tRNA deacylase

Reaction: (1) a D-aminoacyl-tRNA + H2O = a D-amino acid + tRNA
(2) glycyl-tRNAAla + H2O = glycine + tRNAAla

Other name(s): Dtd2; D-Tyr-tRNA(Tyr) deacylase; D-Tyr-tRNATyr deacylase; D-tyrosyl-tRNATyr aminoacylhydrolase; dtdA (gene name)

Systematic name: D-aminoacyl-tRNA aminoacylhydrolase

Comments: The enzyme, found in all domains of life, can cleave mischarged glycyl-tRNAAla [5]. The enzyme from Escherichia coli can cleave D-tyrosyl-tRNATyr, D-aspartyl-tRNAAsp and D-tryptophanyl-tRNATrp [1]. Whereas the enzyme from the archaeon Pyrococcus abyssi is a zinc protein, the enzyme from Escherichia coli does not carry any zinc [2].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Soutourina, J., Plateau, P. and Blanquet, S. Metabolism of D-aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae cells. J. Biol. Chem. 275 (2000) 32535-32542. [PMID: 10918062]

2. Ferri-Fioni, M.L., Schmitt, E., Soutourina, J., Plateau, P., Mechulam, Y. and Blanquet, S. Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases. J. Biol. Chem. 276 (2001) 47285-47290. [PMID: 11568181]

3. Ferri-Fioni, M.L., Fromant, M., Bouin, A.P., Aubard, C., Lazennec, C., Plateau, P. and Blanquet, S. Identification in archaea of a novel D-Tyr-tRNATyr deacylase. J. Biol. Chem. 281 (2006) 27575-27585. [PMID: 16844682]

4. Wydau, S., Ferri-Fioni, M.L., Blanquet, S. and Plateau, P. GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase. Nucleic Acids Res. 35 (2007) 930-938. [PMID: 17251192]

5. Pawar, K.I., Suma, K., Seenivasan, A., Kuncha, S.K., Routh, S.B., Kruparani, S.P. and Sankaranarayanan, R. Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS. Elife 6 (2017) . [PMID: 28362257]

[EC 3.1.1.96 created 2014, modified 2019]

EC 3.1.1.110

Accepted name: xylono-1,5-lactonase

Reaction: D-xylono-1,5-lactone + H2O = D-xylonate

Other name(s): xylC (gene name); D-xylono-1,5-lactone lactonase

Systematic name: D-xylono-1,5-lactone lactonohydrolase

Comments: The enzyme, found in bacteria, participates in the degradation of D-xylose. cf. EC 3.1.1.68, xylono-1,4-lactonase.

References:

1. Toivari, M., Nygard, Y., Kumpula, E.P., Vehkomaki, M.L., Bencina, M., Valkonen, M., Maaheimo, H., Andberg, M., Koivula, A., Ruohonen, L., Penttila, M. and Wiebe, M.G. Metabolic engineering of Saccharomyces cerevisiae for bioconversion of D-xylose to D-xylonate. Metab. Eng. 14 (2012) 427-436. [PMID: 22709678]

2. Nygard, Y., Maaheimo, H., Mojzita, D., Toivari, M., Wiebe, M., Resnekov, O., Gustavo Pesce, C., Ruohonen, L. and Penttila, M. Single cell and in vivo analyses elucidate the effect of xylC lactonase during production of D-xylonate in Saccharomyces cerevisiae. Metab. Eng. 25 (2014) 238-247. [PMID: 25073011]

[EC 3.1.1.110 created 2019]

EC 3.1.1.111

Accepted name: phosphatidylserine sn-1 acylhydrolase

Reaction: (1) a phosphatidylserine + H2O = a 2-acyl-1-lyso-phosphatidylserine + a fatty acid
(2) a 1-acyl-2-lyso-phosphatidylserine + H2O = glycerophosphoserine + a fatty acid

Glossary: phosphatidylserine = 3-sn-phosphatidyl-L-serine = 1,2-diacyl-sn-glycero-3-phospho-L-serine
glycerophosphoserine = sn-glycero-3-phospho-L-serine

Other name(s): phosphatidylserine-specific phospholipase A1; PS-PLA1; PLA1A (gene name)

Systematic name: 3-sn-phosphatidyl-L-serine sn-1 acylhydrolase

Comments: The enzyme, which has described from mammals, is specific for phosphatidylserine and 2-lysophosphatidylserine, and does not act on phosphatidylcholine, phosphatidylethanolamine, phosphatidic acid or phosphatidylinositol.

References:

1. Sato, T., Aoki, J., Nagai, Y., Dohmae, N., Takio, K., Doi, T., Arai, H. and Inoue, K. Serine phospholipid-specific phospholipase A that is secreted from activated platelets. A new member of the lipase family. J. Biol. Chem 272 (1997) 2192-2198. [PMID: 8999922]

2. Nagai, Y., Aoki, J., Sato, T., Amano, K., Matsuda, Y., Arai, H. and Inoue, K. An alternative splicing form of phosphatidylserine-specific phospholipase A1 that exhibits lysophosphatidylserine-specific lysophospholipase activity in humans. J. Biol. Chem 274 (1999) 11053-11059. [PMID: 10196188]

3. Hosono, H., Aoki, J., Nagai, Y., Bandoh, K., Ishida, M., Taguchi, R., Arai, H. and Inoue, K. Phosphatidylserine-specific phospholipase A1 stimulates histamine release from rat peritoneal mast cells through production of 2-acyl-1-lysophosphatidylserine. J. Biol. Chem 276 (2001) 29664-29670. [PMID: 11395520]

4. Aoki, J., Nagai, Y., Hosono, H., Inoue, K. and Arai, H. Structure and function of phosphatidylserine-specific phospholipase A1. Biochim. Biophys. Acta 1582 (2002) 26-32. [PMID: 12069807]

[EC 3.1.1.111 created 2019]

EC 3.1.1.112

Accepted name: isoamyl acetate esterase

Reaction: 3-methylbutyl acetate + H2O = 3-methylbutanol + acetate

Other name(s): IAH1 (gene name)

Systematic name: 3-methylbutyl acetate acetohydrolase

Comments: The enzyme, characterized from the yeast Saccharomyces cerevisiae, hydrolyses acetate esters. It acts preferentially on 3-methylbutyl acetate, a major determinant of sake flavor.

References:

1. Fukuda, K., Kiyokawa, Y., Yanagiuchi, T., Wakai, Y., Kitamoto, K., Inoue, Y. and Kimura, A. Purification and characterization of isoamyl acetate-hydrolyzing esterase encoded by the IAH1 gene of Saccharomyces cerevisiae from a recombinant Escherichia coli. Appl. Microbiol. Biotechnol. 53 (2000) 596-600. [PMID: 10855721]

[EC 3.1.1.112 created 2019]

EC 3.1.1.113

Accepted name: ethyl acetate hydrolase

Reaction: ethyl acetate + H2O = acetate + ethanol

Other name(s): mekB (gene name); estZ (gene name)

Systematic name: ethyl acetate acetohydrolase

Comments: The enzyme, characterized from Pseudomonas strains, is involved in degradation of short chain alkyl methyl ketones.

References:

1. Hasona, A., York, S.W., Yomano, L.P., Ingram, L.O. and Shanmugam, K.T. Decreasing the level of ethyl acetate in ethanolic fermentation broths of Escherichia coli KO11 by expression of Pseudomonas putida estZ esterase. Appl. Environ. Microbiol. 68 (2002) 2651-2659. [PMID: 12039716]

2. Onaca, C., Kieninger, M., Engesser, K.H. and Altenbuchner, J. Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J. Bacteriol. 189 (2007) 3759-3767. [PMID: 17351032]

[EC 3.1.1.113 created 2019]

EC 3.1.1.114

Accepted name: methyl acetate hydrolase

Reaction: methyl acetate + H2O = acetate + methanol

Other name(s): acmB (gene name)

Systematic name: methyl acetate acetohydrolase

Comments: The enzyme, characterized from the bacterium Gordonia sp. TY-5, participates in a propane utilization pathway.

References:

1. Kotani, T., Yurimoto, H., Kato, N. and Sakai, Y. Novel acetone metabolism in a propane-utilizing bacterium, Gordonia sp. strain TY-5. J. Bacteriol. 189 (2007) 886-893. [PMID: 17071761]

[EC 3.1.1.114 created 2019]

[EC 3.1.27.10 Transferred entry: rRNA endonuclease. Now EC 4.6.1.23, ribotoxin, since the primary reaction is that of a lyase. (EC 3.1.27.10 created 1992, deleted 2019)]

*EC 3.2.1.113

Accepted name: mannosyl-oligosaccharide 1,2-α-mannosidase

Reaction: (1) Man9GlcNAc2-[protein] + 4 H2O = Man5GlcNAc2-[protein] + 4 β-D-mannopyranose (overall reaction)
(1a) Man9GlcNAc2-[protein] + H2O = Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,2) + β-D-mannopyranose
(1b) Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,2) + H2O = Man7GlcNAc2-[protein] (isomer 7A1,2,3B2) + β-D-mannopyranose
(1c) Man7GlcNAc2-[protein] (isomer 7A1,2,3B2) + H2O = Man6GlcNAc2-[protein] (isomer 6A1,2B2) + β-D-mannopyranose
(1d) Man6GlcNAc2-[protein] (isomer 6A1,2B2) + H2O = Man5GlcNAc2-[protein] + β-D-mannopyranose
(2) Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) + 3 H2O = Man5GlcNAc2-[protein] + 3 β-D-mannopyranose
(2a) Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) + H2O = Man7GlcNAc2-[protein] (isomer 7A1,2,3B1) + β-D-mannopyranose
(2b) Man7GlcNAc2-[protein] (isomer 7A1,2,3B1) + H2O = Man6GlcNAc2-[protein] (isomer 6A1,2,3) + β-D-mannopyranose
(2c) Man6GlcNAc2-[protein] (isomer 6A1,2,3) + H2O = Man5GlcNAc2-[protein] + β-D-mannopyranose

Glossary: Man9GlcNAc2-[protein] = [α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-{α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)}-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc]-N-Asn-[protein]
Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) = [α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-{α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)}-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc]-N-Asn-[protein]
Man5GlcNAc2-[protein] = [α-D-Man-(1→3)-{α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)}-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc]-N-Asn-[protein]

Other name(s): mannosidase 1A; mannosidase 1B; 1,2-α-mannosidase; exo-α-1,2-mannanase; mannose-9 processing α-mannosidase; glycoprotein processing mannosidase I; mannosidase I; Man9-mannosidase; ManI; 1,2-α-mannosyl-oligosaccharide α-D-mannohydrolase; MAN1A1 (gene name); MAN1A2 (gene name); MAN1C1 (gene name); 2-α-mannosyl-oligosaccharide α-D-mannohydrolase

Systematic name: Man9GlcNAc2-[protein] α-2-mannohydrolase (configuration-inverting)

Comments: This family of mammalian enzymes, located in the Golgi system, participates in the maturation process of N-glycans that leads to formation of hybrid and complex structures. The enzymes catalyse the hydrolysis of the four (1→2)-linked α-D-mannose residues from the Man9GlcNAc2 oligosaccharide attached to target proteins as described in reaction (1). Alternatively, the enzymes act on the Man8GlcNAc2 isomer formed by EC 3.2.1.209, endoplasmic reticulum Man9GlcNAc2 1,2-α-mannosidase, as described in reaction (2). The enzymes are type II membrane proteins, require Ca2+, and use an inverting mechanism. While all three human enzymes can catalyse the reactions listed here, some of the enzymes can additionally catalyse hydrolysis in an alternative order, generating additional isomeric intermediates, although the final product is the same. The names of the isomers listed here are based on a nomenclature system proposed by Prien et al. [7].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9068-25-1

References:

1. Tabas, I. and Kornfeld, S. Purification and characterization of a rat liver Golgi α-mannosidase capable of processing asparagine-linked oligosaccharides. J. Biol. Chem. 254 (1979) 11655-11663. [PMID: 500665]

2. Tulsiani, D.R.P., Hubbard, S.C., Robbins, P.W. and Touster, O. α-D-Mannosidases of rat liver Golgi membranes. Mannosidase II is the GlcNAcMAN5-cleaving enzyme in glycoprotein biosynthesis and mannosidases IA and IB are the enzymes converting Man9 precursors to Man5 intermediates. J. Biol. Chem. 257 (1982) 3660-3668. [PMID: 7061502]

3. Bieberich, E. and Bause, E. Man9-mannosidase from human kidney is expressed in COS cells as a Golgi-resident type II transmembrane N-glycoprotein. Eur. J. Biochem. 233 (1995) 644-649. [PMID: 7588811]

4. Tremblay, L.O., Campbell Dyke, N. and Herscovics, A. Molecular cloning, chromosomal mapping and tissue-specific expression of a novel human α1,2-mannosidase gene involved in N-glycan maturation. Glycobiology 8 (1998) 585-595. [PMID: 9592125]

5. Lal, A., Pang, P., Kalelkar, S., Romero, P.A., Herscovics, A. and Moremen, K.W. Substrate specificities of recombinant murine Golgi α1,2-mannosidases IA and IB and comparison with endoplasmic reticulum and Golgi processing α1,2-mannosidases. Glycobiology 8 (1998) 981-995. [PMID: 9719679]

6. Tremblay, L.O. and Herscovics, A. Characterization of a cDNA encoding a novel human Golgi α 1, 2-mannosidase (IC) involved in N-glycan biosynthesis. J. Biol. Chem. 275 (2000) 31655-31660. [PMID: 10915796]

7. Prien, J.M., Ashline, D.J., Lapadula, A.J., Zhang, H. and Reinhold, V.N. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap MS. J. Am. Soc. Mass Spectrom. 20 (2009) 539-556. [PMID: 19181540]

[EC 3.2.1.113 created 1986, modified 2019]

EC 3.2.1.210

Accepted name: endoplasmic reticulum Man8GlcNAc2 1,2-α-mannosidase

Reaction: Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) + H2O = Man7GlcNAc2-[protein] (isomer 7A1,2,3B3) + -D-mannopyranose

Glossary: Man8GlcNAc2-[protein] (isomer 8A1,2,3B1,3) = {α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc}-N-Asn-[protein]
Man7GlcNAc2-[protein] (isomer 7A1,2,3B3) = {α-D-Man-(1→2)-α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→2)-α-D-Man-(1→3)-[α-D-Man-(1→6)]-α-D-Man-(1→6)]-β-D-Man-(1→4)-β-D-GlcNAc-(1→4)-α-D-GlcNAc}-N-Asn-[protein]

Other name(s): MNL1 (gene name)

Systematic name: Man8GlcNAc2-[protein] 2-α-mannohydrolase (configuration-inverting)

Comments: In yeast this activity is catalysed by a dedicated enzyme that processes unfolded protein-bound Man8GlcNAc2 N-glycans within the endoplasmic reticulum to Man7GlcNAc2. The exposed α-1,6-linked mannose residue in the product enables the recognition by the YOS9 lectin, targeting the proteins for degradation. In mammalian cells this activity is part of the regular processing of N-glycosylated proteins, and is not associated with protein degradation. It is carried out by EC 3.2.1.113, Golgi mannosyl-oligosaccharide 1,2-α-mannosidase. The names of the isomers listed here are based on a nomenclature system proposed by Prien et al [5].

References:

1. Nakatsukasa, K., Nishikawa, S., Hosokawa, N., Nagata, K. and Endo, T. Mnl1p, an α -mannosidase-like protein in yeast Saccharomyces cerevisiae, is required for endoplasmic reticulum-associated degradation of glycoproteins. J. Biol. Chem. 276 (2001) 8635-8638. [PMID: 11254655]

2. Jakob, C.A., Bodmer, D., Spirig, U., Battig, P., Marcil, A., Dignard, D., Bergeron, J.J., Thomas, D.Y. and Aebi, M. Htm1p, a mannosidase-like protein, is involved in glycoprotein degradation in yeast. EMBO Rep. 2 (2001) 423-430. [PMID: 11375935]

3. Quan, E.M., Kamiya, Y., Kamiya, D., Denic, V., Weibezahn, J., Kato, K. and Weissman, J.S. Defining the glycan destruction signal for endoplasmic reticulum-associated degradation. Mol. Cell 32 (2008) 870-877. [PMID: 19111666]

4. Clerc, S., Hirsch, C., Oggier, D.M., Deprez, P., Jakob, C., Sommer, T. and Aebi, M. Htm1 protein generates the N-glycan signal for glycoprotein degradation in the endoplasmic reticulum. J. Cell Biol. 184 (2009) 159-172. [PMID: 19124653]

5. Prien, J.M., Ashline, D.J., Lapadula, A.J., Zhang, H. and Reinhold, V.N. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap MS. J. Am. Soc. Mass Spectrom. 20 (2009) 539-556. [PMID: 19181540]

6. Chantret, I., Kodali, V.P., Lahmouich, C., Harvey, D.J. and Moore, S.E. Endoplasmic reticulum-associated degradation (ERAD) and free oligosaccharide generation in Saccharomyces cerevisiae. J. Biol. Chem. 286 (2011) 41786-41800. [PMID: 21979948]

[EC 3.2.1.210 created 2019]

EC 3.4.13.23

Accepted name: cysteinylglycine-S-conjugate dipeptidase

Reaction: an [L-cysteinylglycine]-S-conjugate + H2O = an L-cysteine-S-conjugate + glycine

Other name(s): tpdA (gene name); LAP3 (gene name)

Systematic name: cysteinylglycine-S-conjugate dipeptide hydrolase

Comments: The enzyme participates in a widespread glutathione-mediated detoxification pathway. In animals the activity is usually catalysed by enzymes that have numerous additional activities, such as EC 3.4.11.1 , leucyl aminopeptidase, EC 3.4.11.2, membrane alanyl aminopeptidase, and EC 3.4.13.19, membrane dipeptidase. However, in the bacterium Corynebacterium sp. Ax20, which degrades axillary secretions, the enzyme appears to be specific for this task.

References:

1. SEMENZA G Chromatographic purification of cysteinyl-glycinase. Biochim. Biophys. Acta 24 (1957) 401-413. [PMID: 13436444]

2. Rankin, B.B., McIntyre, T.M. and Curthoys, N.P. Brush border membrane hydrolysis of S-benzyl-cysteine-p-nitroanilide, and activity of aminopeptidase M. Biochem. Biophys. Res. Commun. 96 (1980) 991-996. [PMID: 6108111]

3. Hirota, T., Nishikawa, Y., Takahagi, H., Igarashi, T. and Kitagawa, H. Simultaneous purification and properties of dehydropeptidase-I and aminopeptidase-M from rat kidney. Res Commun Chem Pathol Pharmacol 49 (1985) 435-445. [PMID: 2865778]

4. Josch, C., Klotz, L.O. and Sies, H. Identification of cytosolic leucyl aminopeptidase (EC 3.4.11.1) as the major cysteinylglycine-hydrolysing activity in rat liver. Biol. Chem. 384 (2003) 213-218. [PMID: 12675513]

5. Emter, R. and Natsch, A. The sequential action of a dipeptidase and a β-lyase is required for the release of the human body odorant 3-methyl-3-sulfanylhexan-1-ol from a secreted Cys-Gly-(S) conjugate by Corynebacteria. J. Biol. Chem 283 (2008) 20645-20652. [PMID: 18515361]

[EC 3.4.13.23 created 2019]

*EC 3.5.1.60

Accepted name: N-(long-chain-acyl)ethanolamine deacylase

Reaction: N-(long-chain-acyl)ethanolamine + H2O = a long-chain carboxylate + ethanolamine

Other name(s): NAAA (gene name); N-acylethanolamine amidohydrolase; acylethanolamine amidase

Systematic name: N-(long-chain-acyl)ethanolamine amidohydrolase

Comments: This lysosomal enzyme acts best on palmitoyl ethanolamide, with lower activity on other N-(long-chain-acyl)ethanolamines. It is only active at acidic pH. Unlike EC 3.5.1.99, fatty acid amide hydrolase, it does not act on primary amides such as oleamide, and has only a marginal activity with anandamide. The enzyme is translated as an inactive proenzyme, followed by autocatalytic cleavage into two subunits that reassociate to form an active heterodimeric complex.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 99283-61-1

References:

1. Ueda, N., Yamanaka, K. and Yamamoto, S. Purification and characterization of an acid amidase selective for N-palmitoylethanolamine, a putative endogenous anti-inflammatory substance. J. Biol. Chem 276 (2001) 35552-35557. [PMID: 11463796]

2. Ueda, N., Yamanaka, K., Terasawa, Y. and Yamamoto, S. An acid amidase hydrolyzing anandamide as an endogenous ligand for cannabinoid receptors. FEBS Lett. 454 (1999) 267-270. [PMID: 10431820]

3. West, J.M., Zvonok, N., Whitten, K.M., Wood, J.T. and Makriyannis, A. Mass spectrometric characterization of human N-acylethanolamine-hydrolyzing acid amidase. J Proteome Res 11 (2012) 972-981. [PMID: 22040171]

4. Zhao, L.Y., Tsuboi, K., Okamoto, Y., Nagahata, S. and Ueda, N. Proteolytic activation and glycosylation of N-acylethanolamine-hydrolyzing acid amidase, a lysosomal enzyme involved in the endocannabinoid metabolism. Biochim. Biophys. Acta 1771 (2007) 1397-1405. [PMID: 17980170]

[EC 3.5.1.60 created 1989, modified 2019]

EC 3.5.1.134

Accepted name: (indol-3-yl)acetyl-L-aspartate hydrolase

Reaction: (indol-3-yl)acetyl-L-aspartate + H2O = (indol-3-yl)acetate + L-aspartate

Other name(s): indole-3-acetyl-L-aspartate hydrolase; iaaspH (gene name)

Systematic name: (indol-3-yl)acetyl-L-aspartate amidohydrolase

Comments: The enzyme, isolated from the bacterium Pantoea agglomerans, is specific for its substrate and does not act efficiently on other indole-3-acetate conjugates.

References:

1. Chou, J.C., Kuleck, G.A., Cohen, J.D. and Mulbry, W.W. Partial purification and characterization of an inducible indole-3-acetyl-L-aspartic acid hydrolase from enterobacter agglomerans. Plant Physiol. 112 (1996) 1281-1287. [PMID: 12226446]

2. Chou, J.C., Mulbry, W.W. and Cohen, J.D. The gene for indole-3-acetyl-L-aspartic acid hydrolase from Enterobacter agglomerans: molecular cloning, nucleotide sequence, and expression in Escherichia coli. Mol. Gen. Genet. 259 (1998) 172-178. [PMID: 9747708]

[EC 3.5.1.134 created 2019]

[EC 3.6.3.3 Transferred entry: Cd2+-exporting ATPase. Now EC 7.2.2.21, Cd2+-exporting ATPase (EC 3.6.3.3 created 2000, deleted 2019)]

EC 4.1.1.118

Accepted name: isophthalyl-CoA decarboxylase

Reaction: isophthalyl-CoA = benzoyl-CoA + CO2

Other name(s): IPCD

Systematic name: isophthalyl-CoA carboxy-lyase

Comments: The enzyme, characterized from the bacterium Syntrophorhabdus aromaticivorans, participates in an anaerobic isophthalate degradation pathway. The enzyme requires a prenylated flavin mononucleotide cofactor.

References:

1. Junghare, M., Spiteller, D. and Schink, B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME J. 13 (2019) 1252-1268. [PMID: 30647456]

[EC 4.1.1.118 created 2019]

EC 4.2.1.175

Accepted name: (R)-3-(aryl)lactoyl-CoA dehydratase

Reaction: (1) (R)-3-(phenyl)lactoyl-CoA = (E)-cinnamoyl-CoA + H2O
(2) (R)-3-(4-hydroxyphenyl)lactoyl-CoA = (E)-4-coumaroyl-CoA + H2O
(3) (R)-3-(indol-3-yl)lactoyl-CoA = 3-(indol-3-yl)acryloyl-CoA + H2O

Other name(s): fldBC (gene names); (R)-phenyllactoyl-CoA dehydratase; aryllactyl-CoA dehydratase

Systematic name: (R)-3-(aryl)lactoyl-CoA hydro-lyase

Comments: The enzyme, found in some amino acid-fermenting anaerobic bacteria, participates in the fermentation pathways of L-phenylalanine, L-tyrosine, and L-tryptophan. It is a heterodimeric protein consisting of the FldB and FldC polypeptides, both of which contain an [4Fe-4S]cluster, and forms a complex with EC 2.8.3.17, 3-(aryl)acryloyl-CoA:(R)-3-(aryl)lactate CoA-transferase (FldA). In order to catalyse the reaction, the enzyme requires one high-energy electron that transiently reduces the electrophilic thiol ester carbonyl of the substrate to a nucleophilic ketyl radical anion, facilitating the elimination of the hydroxyl group. This electron, which is provided by by EC 5.6.1.10, (R)-2-hydroxyacyl-CoA dehydratase activating ATPase, needs to be supplied only once, before the first reaction takes place, as it is regenerated at the end of each reaction cycle. The enzyme acts on (R)-3-(aryl)lactoyl-CoAs produced by FldA, and regenerates the CoA donors used by that enzyme.

References:

1. Dickert, S., Pierik, A.J., Linder, D. and Buckel, W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. Eur. J. Biochem. 267 (2000) 3874-3884. [PMID: 10849007]

2. Dickert, S., Pierik, A.J. and Buckel, W. Molecular characterization of phenyllactate dehydratase and its initiator from Clostridium sporogenes. Mol. Microbiol. 44 (2002) 49-60. [PMID: 11967068]

3. Kim, J., Hetzel, M., Boiangiu, C.D. and Buckel, W. Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28 (2004) 455-468. [PMID: 15374661]

4. Kim, J., Darley, D.J., Buckel, W. and Pierik, A.J. An allylic ketyl radical intermediate in clostridial amino-acid fermentation. Nature 452 (2008) 239-242. [PMID: 18337824]

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

[EC 4.2.1.175 created 2019]

EC 4.2.3.205

Accepted name: sodorifen synthase

Reaction: pre-sodorifen diphosphate = sodorifen + diphosphate

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

Other name(s): sodD (gene name)

Systematic name: pre-sodorifen diphosphate-lyase [sodorifen-forming]

Comments: The enzyme has been characterized from the bacterium Serratia plymuthica.

References:

1. Domik, D., Magnus, N. and Piechulla, B. Analysis of a new cluster of genes involved in the synthesis of the unique volatile organic compound sodorifen of Serratia plymuthica 4Rx13. FEMS Microbiol. Lett. 363(14) (2016) fnw139. [PMID: 27231241]

2. Schmidt, R., Jager, V., Zuhlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., Ijcken, W.V., Sleutels, F., Boer, W., Riedel, K. and Garbeva, P. Fungal volatile compounds induce production of the secondary metabolite sodorifen in Serratia plymuthica PRI-2C. Sci Rep 7 (2017) 862. [PMID: 28408760]

3. von Reuss, S., Domik, D., Lemfack, M.C., Magnus, N., Kai, M., Weise, T. and Piechulla, B. Sodorifen biosynthesis in the rhizobacterium Serratia plymuthica involves methylation and cyclization of MEP-derived farnesyl pyrophosphate by a SAM-dependent C-methyltransferase. J. Am. Chem. Soc. 140 (2018) 11855-11862. [PMID: 30133268]

[EC 4.2.3.205 created 2019]

EC 4.6.1.23

Accepted name: ribotoxin

Reaction: a 28S rRNA containing guanosine-adenosine pair + H2O = an [RNA fragment]-3'-adenosine-3'-phosphate + a 5'-a hydroxy-guanosine-3'-[RNA fragment] (overall reaction)
(1a) a 28S rRNA containing guanosine-adenosine pair = an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + a 5'-hydroxy-guanosine-3'-[RNA fragment]
(1b) an [RNA fragment]-3'-adenosine-2',3'-cyclophosphate + H2O = an [RNA fragment]-3'-adenosine-3'-phosphate

Other name(s): α-sarcin; rRNA endonuclease (ambiguous)

Systematic name: [28S-rRNA]-guanosine-adenosine 5'-hydroxy-guanosine-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'-adenosine-2',3'-cyclophosphate-forming and hydrolysing)

Comments: Ribotoxins are rRNA endonucleases that catalyse the cleavage of the phosphodiester bond between guanosine and adenosine residues at one specific position in 28S rRNA. The enzyme secreted by Aspergillus giganteus specifically cleaves rat 28S rRNA between G4325 and A4326 and displays cytotoxic activity toward animal cells. It can also act on bacterial rRNAs. The enzyme catalyses a two-stage endonucleolytic cleavage. The first reaction produces 5'-hydroxy-phosphooligonucletides and 3'-phosphooligonucleotides ending with 2',3'-cyclic phosphodiester, which are released from the enzyme. The enzyme then hydrolyses these cyclic compounds in a second reaction that takes place only when all the susceptible 3',5'-phosphodiester bonds have been cyclised. The second reaction is a reversal of the first reaction using the hydroxyl group of water instead of the 5'-hydroxyl group of ribose. The overall process is that of a phosphorus-oxygen lyase followed by hydrolysis to form the 3'-nucleotides.

References:

1. Chan, Y.L., Endo, Y. and Wool, I.G. The sequence of the nucleotides at the α-sarcin cleavage site in rat 28 S ribosomal ribonucleic acid. J. Biol. Chem 258 (1983) 12768-12770. [PMID: 6355092]

2. Lacadena, J., Martinez del Pozo, A., Lacadena, V., Martinez-Ruiz, A., Mancheno, J.M., Onaderra, M. and Gavilanes, J.G. The cytotoxin α-sarcin behaves as a cyclizing ribonuclease. FEBS Lett. 424 (1998) 46-48. [PMID: 9580156]

3. Citores, L., Iglesias, R., Ragucci, S., Di Maro, A. and Ferreras, J.M. Antifungal activity of α-sarcin against Penicillium digitatum: proposal of a new role for fungal ribotoxins. ACS Chem. Biol. 13 (2018) 1978-1982. [PMID: 29952541]

[EC 4.6.1.23 created 1992 as EC 3.1.27.10, transferred 2019 to EC 4.6.1.23]

EC 5.4.99.67

Accepted name: 4-amino-4-deoxychorismate mutase

Reaction: 4-amino-4-deoxychorismate = 4-amino-4-deoxyprephenate

Other name(s): cmlD (gene name); papB (gene name)

Systematic name: 4-amino-4-deoxychorismate pyruvatemutase

Comments: The enzyme, characterized from the bacteria Streptomyces venezuelae and Streptomyces pristinaespiralis, participates in the biosynthesis of the antibiotics chloramphenicol and pristinamycin IA, respectively. cf. EC 5.4.99.5, chorismate mutase.

References:

1. Blanc, V., Gil, P., Bamas-Jacques, N., Lorenzon, S., Zagorec, M., Schleuniger, J., Bisch, D., Blanche, F., Debussche, L., Crouzet, J. and Thibaut, D. Identification and analysis of genes from Streptomyces pristinaespiralis encoding enzymes involved in the biosynthesis of the 4-dimethylamino-L-phenylalanine precursor of pristinamycin I. Mol. Microbiol. 23 (1997) 191-202. [PMID: 9044253]

2. He, J., Magarvey, N., Piraee, M. and Vining, L.C. The gene cluster for chloramphenicol biosynthesis in Streptomyces venezuelae ISP5230 includes novel shikimate pathway homologues and a monomodular non-ribosomal peptide synthetase gene. Microbiology 147 (2001) 2817-2829. [PMID: 11577160]

[EC 5.4.99.67 created 2019]

EC 5.6.1.10

Accepted name: (R)-2-hydroxyacyl-CoA dehydratase activating ATPase

Reaction: 2 ATP + a reduced flavodoxin + an inactive (R)-2-hydroxyacyl-CoA dehydratase + 2 H2O = 2 ADP + 2 phosphate + a flavodoxin semiquinone + an active (R)-2-hydroxyacyl-CoA dehydratase

Other name(s): archerase; (R)-2-hydroxyacyl-CoA dehydratase activator; (R)-2-hydroxyacyl-CoA dehydratase activase; fldI (gene name); hgdC (gene name); hadI (gene name); lcdC (gene name)

Systematic name: reduced flavodoxin:(R)-2-hydroxyacyl-CoA dehydratase electron transferase (ATP-hydrolyzing)

Comments: Members of the (R)-2-hydroxyacyl-CoA dehydratase family (including EC 4.2.1.54, lactoyl-CoA dehydratase, EC 4.2.1.157, (R)-2-hydroxyisocaproyl-CoA dehydratase, EC 4.2.1.167, (R)-2-hydroxyglutaryl-CoA dehydratase and EC 4.2.1.175, (R)-3-(aryl)lactoyl-CoA dehydratase) are two-component systems composed of an activator component and a dehydratase component. The activator is an extremely oxygen-sensitive homodimer with one [4Fe-4S]cluster bound at the dimer interface. Before it can catalyse the dehydration reaction, the dehydratase requires one high-energy electron that is used to transiently reduce the electrophilic thiol ester carbonyl to a nucleophilic ketyl radical anion, facilitating the elimination of the hydroxyl group. The activator, which has been named archerase because its open position resembles an archer shooting arrows, binds two ADP molecules. Upon the reduction of its [4Fe-4S]cluster by a single electron, delivered by a dedicated flavodoxin or a clostridial ferredoxin, the two ADP molecules exchange for two ATP molecules, resulting in a large conformational change. The change allows the activator to bind to the dehydratase component and transfer the electron to it, activating it. During this event the two ATP molecules are hydrolysed and the activator returns to its resting state. Since the electron is regenerated at the end of each reaction cycle of the dehydratase, the activation is required only once, before the first reaction takes place.

References:

1. Bendrat, K., Müller, U., Klees, A.G. and Buckel, W. Identification of the gene encoding the activator of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans by gene expression in Escherichia coli. FEBS Lett. 329 (1993) 329-331. [PMID: 8365476]

2. Müller, U. and Buckel, W. Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur. J. Biochem. 230 (1995) 698-704. [PMID: 7607244]

3. Locher, K.P., Hans, M., Yeh, A.P., Schmid, B., Buckel, W. and Rees, D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307 (2001) 297-308. [PMID: 11243821]

4. Dickert, S., Pierik, A.J. and Buckel, W. Molecular characterization of phenyllactate dehydratase and its initiator from Clostridium sporogenes. Mol. Microbiol. 44 (2002) 49-60. [PMID: 11967068]

5. Thamer, W., Cirpus, I., Hans, M., Pierik, A.J., Selmer, T., Bill, E., Linder, D. and Buckel, W. A two [4Fe-4S]-cluster-containing ferredoxin as an alternative electron donor for 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Arch. Microbiol. 179 (2003) 197-204. [PMID: 12610725]

6. Kim, J., Hetzel, M., Boiangiu, C.D. and Buckel, W. Dehydration of (R)-2-Hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28 (2004) 455-468. [PMID: 15374661]

7. Kim, J., Darley, D. and Buckel, W. 2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile. FEBS J. 272 (2005) 550-561. [PMID: 15654892]

8. Kim, J., Darley, D.J., Buckel, W. and Pierik, A.J. An allylic ketyl radical intermediate in clostridial amino-acid fermentation. Nature 452 (2008) 239-242. [PMID: 18337824]

9. Knauer, S.H., Buckel, W. and Dobbek, H. On the ATP-dependent activation of the radical enzyme (R)-2-hydroxyisocaproyl-CoA dehydratase. Biochemistry 51 (2012) 6609-6622. [PMID: 22827463]

[EC 5.6.1.10 created 2019]

EC 6.2.1.58

Accepted name: isophthalate—CoA ligase

Reaction: ATP + isophthalate + CoA = AMP + diphosphate + isophthalyl-CoA

Other name(s): IPCL

Systematic name: isophthalate:CoA ligase (AMP-forming)

Comments: The enzyme, characterized from the bacterium Syntrophorhabdus aromaticivorans, catalyses the first step in an anaerobic isophthalate degradation pathway.

References:

1. Junghare, M., Spiteller, D. and Schink, B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME J. 13 (2019) 1252-1268. [PMID: 30647456]

[EC 6.2.1.58 created 2019]

EC 6.2.1.59<

Accepted name: long-chain fatty acid adenylase/transferase FadD26

Reaction: ATP + a long-chain fatty acid + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + diphosphate + a long-chain acyl-[(phenol)carboxyphthiodiolenone synthase] (overall reaction)
(1a) ATP + a long-chain fatty acid = diphosphate + a long-chain fatty-acyl adenylate ester
(1b) a long-chain fatty-acyl adenylate ester + holo-[(phenol)carboxyphthiodiolenone synthase] = AMP + a long-chain acyl-[(phenol)carboxyphthiodiolenone synthase]

Glossary: phthiocerols = linear carbohydrates containing one methoxyl group, one methyl group, and two secondary hydroxyl groups that serve as a backbone for certain lipids and glycolipids found in many species of Mycobacteriaceae
arachidate = icosanoate
behenate = docosanoate
lignocerate= tetracosanoate

Other name(s): FadD26

Systematic name: long-chain fatty acid:holo-[(phenol)carboxyphthiodiolenone synthase] ligase (AMP-forming)

Comments: The enzyme, present in pathogenic species of mycobacteria, participates in the pathway for biosynthesis of phthiocerols. It catalyses the adenylation of the long-chain fatty acids arachidate (C20) or behenate (C22) [1] and potentially the very-long-chain fatty acid lignocerate (C24) [2]. The activated fatty acids are then loaded to EC 2.3.1.292, (phenol)carboxyphthiodiolenone synthase.

References:

1. Azad, A.K., Sirakova, T.D., Fernandes, N.D. and Kolattukudy, P.E. Gene knockout reveals a novel gene cluster for the synthesis of a class of cell wall lipids unique to pathogenic mycobacteria. J. Biol. Chem 272 (1997) 16741-16745. [PMID: 9201977]

2. Simeone, R., Leger, M., Constant, P., Malaga, W., Marrakchi, H., Daffe, M., Guilhot, C. and Chalut, C. Delineation of the roles of FadD22, FadD26 and FadD29 in the biosynthesis of phthiocerol dimycocerosates and related compounds in Mycobacterium tuberculosis. FEBS J. 277 (2010) 2715-2725. [PMID: 20553505]

3. Vergnolle, O., Chavadi, S.S., Edupuganti, U.R., Mohandas, P., Chan, C., Zeng, J., Kopylov, M., Angelo, N.G., Warren, J.D., Soll, C.E. and Quadri, L.E. Biosynthesis of cell envelope-associated phenolic glycolipids in Mycobacterium marinum. J. Bacteriol. 197 (2015) 1040-1050. [PMID: 25561717]

[EC 6.2.1.59 created 2019]

EC 6.2.1.60

Accepted name: marinolic acid—CoA ligase

Reaction: (1) ATP + a marinolic acid + CoA = AMP + diphosphate + a marinoloyl-CoA
(2) ATP + a pseudomonic acid + CoA = AMP + diphosphate + a pseuodomonoyl-CoA

Glossary: thiomarinols = natural products that combine monic acid and the compact holothin core of the dithiolopyrrolones.

Other name(s): tmlU (gene name)

Systematic name: marinolic acid:CoA ligase (AMP-forming)

Comments: The enzyme, characterized from the bacterium Pseudoalteromonas sp. SANK 73390, catalyses the CoA acylation of pseudomonic and marinolic acids, as part of the biosynthesis of thiomarinols and related compounds.

References:

1. Dunn, Z.D., Wever, W.J., Economou, N.J., Bowers, A.A. and Li, B. Enzymatic basis of "hybridity" in thiomarinol biosynthesis. Angew. Chem. Int. Ed. Engl. 54 (2015) 5137-5141. [PMID: 25726835]

[EC 6.2.1.60 created 2019]

EC 7.2.2.21

Accepted name: Cd2+-exporting ATPase

Reaction: ATP + H2O + Cd2+[side 1] = ADP + phosphate + Cd2+[side 2]

Other name(s): cadmium-translocating P-type ATPase; cadmium-exporting ATPase

Systematic name: ATP phosphohydrolase (Cd2+-exporting)

Comments: A P-type ATPase that undergoes covalent phosphorylation during the transport cycle. This enzyme occurs in protozoa, fungi and plants.

References:

1. Silver, S. and Ji, G. Newer systems for bacterial resistance to toxic heavy metals. Environ. Health Perspect. 102, Suppl. 3 (1994) 107-113. [PMID: 7843081]

2. Tsai, K.J. and Linet, A.L. Formation of a phosphorylated enzyme intermediate by the cadA Cd2+-ATPase. Arch. Biochem. Biophys. 305 (1993) 267-270. [PMID: 8373163]

[EC 7.2.2.21 created 2000 as EC 3.6.3.3, transferred 2019 to EC 7.2.2.21]

*EC 7.4.2.5

Accepted name: bacterial ABC-type protein transporter

Reaction: ATP + H2O + protein[side 1] = ADP + phosphate + protein[side 2]

Other name(s): PrtDEF (gene names); hasDEF (gene names); peptide-transporting ATPase (ambiguous)

Systematic name: ATP phosphohydrolase (ABC-type, peptide-exporting)

Comments: An ATP-binding cassette (ABC) type transporter, characterized by the presence of two similar ATP-binding domains/proteins and two integral membrane domains/proteins. This entry stands for a family of bacterial enzymes that are dedicated to the secretion of one or several closely related proteins belonging to the toxin, protease and lipase families. Examples from Gram-negative bacteria include α-hemolysin, cyclolysin, colicin V and siderophores, while examples from Gram-positive bacteria include bacteriocin, subtilin, competence factor and pediocin.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc

References:

1. Letoffe, S., Delepelaire, P. and Wandersman, C. Protease secretion by Erwinia chrysanthemi: the specific secretion functions are analogous to those of Escherichia coli α-haemolysin. EMBO J. 9 (1990) 1375-1382. [PMID: 2184029]

2. Klein, C. and Entian, K.D. Genes involved in self-protection against the lantibiotic subtilin produced by Bacillus subtilis ATCC 6633. Appl. Environ. Microbiol. 60 (1994) 2793-2801. [PMID: 8085823]

3. Binet, R., Létoffé, S., Ghigo, J.M., Delepaire, P. and Wanderman, C. Protein secretion by Gram-negative bacterial ABC exporters - a review. Gene 192 (1997) 7-11. [PMID: 9224868]

[EC 7.4.2.5 created 2000 as EC 3.6.3.43, transferred 2018 to EC 7.4.2.5, modified 2019]


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