The Enzyme Database

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EC 1.3.99.41     Relevance: 100%
Accepted name: 3-(methylsulfanyl)propanoyl-CoA 2-dehydrogenase
Reaction: 3-(methylsulfanyl)propanoyl-CoA + acceptor = 3-(methylsulfanyl)acryloyl-CoA + reduced acceptor
Other name(s): dmdC (gene name)
Systematic name: 3-(methylsulfanyl)propanoyl-CoA:acceptor 2-oxidoreductase
Comments: The enzyme, found in marine bacteria, participates in a 3-(methylsulfanyl)propanoate degradation pathway. Based on similar enzymes, the in vivo electron acceptor is likely electron-transfer flavoprotein (ETF).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Reisch, C.R., Stoudemayer, M.J., Varaljay, V.A., Amster, I.J., Moran, M.A. and Whitman, W.B. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473 (2011) 208–211. [DOI] [PMID: 21562561]
2.  Bullock, H.A., Luo, H. and Whitman, W.B. Evolution of dimethylsulfoniopropionate metabolism in marine phytoplankton and bacteria. Front. Microbiol. 8:637 (2017). [DOI] [PMID: 28469605]
3.  Shao, X., Cao, H.Y., Zhao, F., Peng, M., Wang, P., Li, C.Y., Shi, W.L., Wei, T.D., Yuan, Z., Zhang, X.H., Chen, X.L., Todd, J.D. and Zhang, Y.Z. Mechanistic insight into 3-methylmercaptopropionate metabolism and kinetical regulation of demethylation pathway in marine dimethylsulfoniopropionate-catabolizing bacteria. Mol. Microbiol. 111 (2019) 1057–1073. [DOI] [PMID: 30677184]
[EC 1.3.99.41 created 2022]
 
 
EC 4.2.1.155     Relevance: 98.5%
Accepted name: (methylthio)acryloyl-CoA hydratase
Reaction: 3-(methylsulfanyl)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2 (overall reaction)
(1a) 3-(methylsulfanyl)acryloyl-CoA + H2O = 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA
(1b) 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H2O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO2
Glossary: 3-(methylsulfanyl)acryloyl-CoA = 3-(methylsulfanyl)prop-2-enoyl-CoA
Other name(s): DmdD
Systematic name: 3-(methylsulfanyl)prop-2-enoyl-CoA hydro-lyase (acetaldehyde-forming)
Comments: The enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. Isolated from the bacterium Ruegeria pomeroyi.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Tan, D., Crabb, W.M., Whitman, W.B. and Tong, L. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS One 8:e63870 (2013). [DOI] [PMID: 23704947]
[EC 4.2.1.155 created 2015]
 
 
EC 1.1.1.269     Relevance: 98.1%
Accepted name: 2-(S)-hydroxypropyl-CoM dehydrogenase
Reaction: (2S)-2-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
For diagram of epoxide carboxylation, click here
Glossary: coenzyme M (CoM) = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
Other name(s): 2-(2-(S)-hydroxypropylthio)ethanesulfonate dehydrogenase; 2-[2-(S)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase
Systematic name: 2-{[(2S)-2-hydroxypropyl]sulfanyl}ethanesulfonate:NAD+ oxidoreductase
Comments: The enzyme is highly specific for (2S)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.268, 2-(R)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (R)-enantiomer. This enzyme forms component IV of a four-component enzyme system EC 4.4.1.23 (2-hydroxypropyl-CoM lyase; component I), EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV].html">click here that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 369364-40-9
References:
1.  Allen, J.R., Clark, D.D., Krum, J.G. and Ensign, S.A. A role for coenzyme M (2-mercaptoethanesulfonic acid) in a bacterial pathway of aliphatic epoxide carboxylation. Proc. Natl. Acad. Sci. USA 96 (1999) 8432–8437. [DOI] [PMID: 10411892]
[EC 1.1.1.269 created 2001]
 
 
EC 1.14.99.69     Relevance: 96.5%
Accepted name: tRNA 2-(methylsulfanyl)-N6-isopentenyladenosine37 hydroxylase
Reaction: 2-(methylsulfanyl)-N6-prenyladenosine37 in tRNA + reduced acceptor + O2 = N6-[(2E)-4-hydroxy-3-methylbut-2-en-1-yl]-2-(methylsulfanyl)adenosine37 in tRNA + acceptor + H2O
Glossary: 2-(methylsulfanyl)-N6-prenyladenosine = N6-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenosine
Other name(s): miaE (gene name); tRNA 2-methylthio-N6-isopentenyl adenosine(37) hydroxylase; tRNA 2-(methylsulfanyl)-N6-dimethylallyladenosine37 hydroxylase
Systematic name: tRNA 2-(methylsulfanyl)-N6-prenyladenosine37,donor:oxygen 4-oxidoreductase (trans-hydroxylating)
Comments: The enzyme, found only within a small subset of facultative anaerobic bacteria, belongs to the nonheme diiron family. The enzyme from Salmonella typhimurium was shown to catalyse a stereoselective (E)-hydroxylation at the terminal C4-position of the prenyl group.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Persson, B.C. and Bjork, G.R. Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants. J. Bacteriol. 175 (1993) 7776–7785. [DOI] [PMID: 8253666]
2.  Persson, B.C., Olafsson, O., Lundgren, H.K., Hederstedt, L. and Bjork, G.R. The ms2io6A37 modification of tRNA in Salmonella typhimurium regulates growth on citric acid cycle intermediates. J. Bacteriol. 180 (1998) 3144–3151. [DOI] [PMID: 9620964]
3.  Corder, A.L., Subedi, B.P., Zhang, S., Dark, A.M., Foss, F.W., Jr. and Pierce, B.S. Peroxide-shunt substrate-specificity for the Salmonella typhimurium O2-dependent tRNA modifying monooxygenase (MiaE). Biochemistry 52 (2013) 6182–6196. [DOI] [PMID: 23906247]
[EC 1.14.99.69 created 2020]
 
 
EC 3.1.3.77     Relevance: 93.7%
Accepted name: acireductone synthase
Reaction: 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate (overall reaction)
(1a) 5-(methylsulfanyl)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate (probably spontaneous)
(1b) 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate
For diagram of methionine salvage, click here
Glossary: acireductone = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Other name(s): E1; E-1 enolase-phosphatase; 5-(methylthio)-2,3-dioxopentyl-phosphate phosphohydrolase (isomerizing)
Systematic name: 5-(methylsulfanyl)-2,3-dioxopentyl-phosphate phosphohydrolase (isomerizing)
Comments: This bifunctional enzyme first enolizes the substrate to form the intermediate 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate, which is then dephosphorylated to form the acireductone 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one [2]. The acireductone represents a branch point in the methione-salvage pathway as it is used in the formation of formate, CO and 3-(methylsulfanyl)propanoate by EC 1.13.11.53 [acireductone dioxygenase (Ni2+-requiring)] and of formate and 4-(methylsulfanyl)-2-oxobutanoate either by a spontaneous reaction under aerobic conditions or by EC 1.13.11.54 {acireductone dioxygenase [iron(II)-requiring]} [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Myers, R.W., Wray, J.W., Fish, S. and Abeles, R.H. Purification and characterization of an enzyme involved in oxidative carbon-carbon bond cleavage reactions in the methionine salvage pathway of Klebsiella pneumoniae. J. Biol. Chem. 268 (1993) 24785–24791. [PMID: 8227039]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [DOI] [PMID: 7852397]
3.  Wang, H., Pang, H., Bartlam, M. and Rao, Z. Crystal structure of human E1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase activity. J. Mol. Biol. 348 (2005) 917–926. [DOI] [PMID: 15843022]
[EC 3.1.3.77 created 2006]
 
 
EC 1.14.13.237     Relevance: 83.5%
Accepted name: aliphatic glucosinolate S-oxygenase
Reaction: an ω-(methylsulfanyl)alkyl-glucosinolate + NADPH + H+ + O2 = an ω-(methylsulfinyl)alkyl-glucosinolate + NADP+ + H2O
Glossary: ω-(methylsulfanyl)alkyl-glucosinolate = an ω-(methylsulfanyl)-N-sulfo-alkylhydroximate S-glucoside
Other name(s): ω-(methylthio)alkylglucosinolate S-oxygenase; GS-OX1 (gene name); ω-(methylthio)alkyl-glucosinolate,NADPH:oxygen S-oxidoreductase
Systematic name: ω-(methylsulfanyl)alkyl-glucosinolate,NADPH:oxygen S-oxidoreductase
Comments: The enzyme is a member of the flavin-dependent monooxygenase (FMO) family (cf. EC 1.14.13.8). The plant Arabidopsis thaliana contains five isoforms. GS-OX1 through GS-OX4 are able to catalyse the S-oxygenation independent of chain length, while GS-OX5 is specific for 8-(methylsulfanyl)octyl glucosinolate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hansen, B.G., Kliebenstein, D.J. and Halkier, B.A. Identification of a flavin-monooxygenase as the S-oxygenating enzyme in aliphatic glucosinolate biosynthesis in Arabidopsis. Plant J. 50 (2007) 902–910. [DOI] [PMID: 17461789]
2.  Li, J., Hansen, B.G., Ober, J.A., Kliebenstein, D.J. and Halkier, B.A. Subclade of flavin-monooxygenases involved in aliphatic glucosinolate biosynthesis. Plant Physiol. 148 (2008) 1721–1733. [DOI] [PMID: 18799661]
[EC 1.14.13.237 created 2017]
 
 
EC 1.14.14.43     Relevance: 82.7%
Accepted name: (methylsulfanyl)alkanaldoxime N-monooxygenase
Reaction: an (E)-ω-(methylsulfanyl)alkanal oxime + [reduced NADPH—hemoprotein reductase] + glutathione + O2 = an S-[(1E)-1-(hydroxyimino)-ω-(methylsulfanyl)alkyl]-L-glutathione + [oxidized NADPH—hemoprotein reductase] + 2 H2O (overall reaction)
(1a) an (E)-ω-(methylsulfanyl)alkanal oxime + [reduced NADPH—hemoprotein reductase] + O2 = a 1-(methylsulfanyl)-4-aci-nitroalkane + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) a 1-(methylsulfanyl)-4-aci-nitroalkane + glutathione = an S-[(1E)-1-(hydroxyimino)-ω-(methylsulfanyl)alkyl]-L-glutathione + H2O
Glossary: a 1-(methylsulfanyl)-4-aci-nitroalkane = a hydroxyoxo-λ5-azanylidene-ω-(methylsulfanyl)alkane
Other name(s): CYP83A1 (gene name); (methylthio)alkanaldoxime N-monooxygenase; (E)-ω-(methylthio)alkananaldoxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Systematic name: (E)-ω-(methylsulfanyl)alkananal oxime,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (N-hydroxylating)
Comments: This cytochrome P-450 (heme thiolate) enzyme is involved in the biosynthesis of glucosinolates in plants. The enzyme catalyses an N-hydroxylation of the E isomer of ω-(methylsulfanyl)alkanal oximes, forming an aci-nitro intermediate that reacts non-enzymically with glutathione to produce an N-alkyl-thiohydroximate adduct, the committed precursor of glucosinolates. In the absence of a thiol compound, the enzyme is suicidal, probably due to interaction of the reactive aci-nitro intermediate with active site residues.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Bak, S., Tax, F.E., Feldmann, K.A., Galbraith, D.W. and Feyereisen, R. CYP83B1, a cytochrome P450 at the metabolic branch point in auxin and indole glucosinolate biosynthesis in Arabidopsis. Plant Cell 13 (2001) 101–111. [PMID: 11158532]
2.  Naur, P., Petersen, B.L., Mikkelsen, M.D., Bak, S., Rasmussen, H., Olsen, C.E. and Halkier, B.A. CYP83A1 and CYP83B1, two nonredundant cytochrome P450 enzymes metabolizing oximes in the biosynthesis of glucosinolates in Arabidopsis. Plant Physiol. 133 (2003) 63–72. [DOI] [PMID: 12970475]
3.  Clausen, M., Kannangara, R.M., Olsen, C.E., Blomstedt, C.K., Gleadow, R.M., Jørgensen, K., Bak, S., Motawie, M.S. and Møller, B.L. The bifurcation of the cyanogenic glucoside and glucosinolate biosynthetic pathways. Plant J. 84 (2015) 558–573. [DOI] [PMID: 26361733]
[EC 1.14.14.43 created 2017]
 
 
EC 3.1.3.87     Relevance: 79.1%
Accepted name: 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase
Reaction: 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-en-1-yl phosphate + H2O = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + phosphate
Other name(s): HK-MTPenyl-1-P phosphatase; MtnX; YkrX; 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate phosphohydrolase; 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate phosphohydrolase
Systematic name: 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-en-1-yl phosphate phosphohydrolase
Comments: The enzyme participates in the methionine salvage pathway in Bacillus subtilis [2]. In some species a single bifunctional enzyme, EC 3.1.3.77, acireductone synthase, catalyses both this reaction and EC 5.3.2.5, 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Myers, R.W., Wray, J.W., Fish, S. and Abeles, R.H. Purification and characterization of an enzyme involved in oxidative carbon-carbon bond cleavage reactions in the methionine salvage pathway of Klebsiella pneumoniae. J. Biol. Chem. 268 (1993) 24785–24791. [PMID: 8227039]
2.  Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N. and Yokota, A. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 302 (2003) 286–290. [DOI] [PMID: 14551435]
[EC 3.1.3.87 created 2012]
 
 
EC 4.2.1.170     Relevance: 79.1%
Accepted name: 2-(ω-methylthio)alkylmalate dehydratase
Reaction: (1) a 2-[(ω-methylsulfanyl)alkyl]malate = a 2-[(ω-methylsulfanyl)alkyl]maleate + H2O
(2) a 3-[(ω-methylsulfanyl)alkyl]malate = a 2-[(ω-methylsulfanyl)alkyl]maleate + H2O
For diagram of L-Homomethionine biosynthesis, click here
Other name(s): IPMI (gene name); 2-[(ω-methylthio)alkyl]malate hydro-lyase (2-[(ω-methylthio)alkyl]maleate-forming)
Systematic name: 2-[(ω-methylsulfanyl)alkyl]malate hydro-lyase (2-[(ω-methylsulfanyl)alkyl]maleate-forming)
Comments: The enzyme, characterized from the plant Arabidopsis thaliana, is involved in the L-methionine side-chain elongation pathway, forming substrates for the biosynthesis of aliphatic glucosinolates. By catalysing a dehydration of a 2-[(ω-methylsulfanyl)alkyl]maleate, followed by a hydration at a different position, the enzyme achieves the isomerization of its substrates. The enzyme is a heterodimer comprising a large and a small subunits. The large subunit can also bind to an alternative small subunit, forming EC 4.2.1.33, 3-isopropylmalate dehydratase, which participates in L-leucine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Knill, T., Reichelt, M., Paetz, C., Gershenzon, J. and Binder, S. Arabidopsis thaliana encodes a bacterial-type heterodimeric isopropylmalate isomerase involved in both Leu biosynthesis and the Met chain elongation pathway of glucosinolate formation. Plant Mol. Biol. 71 (2009) 227–239. [DOI] [PMID: 19597944]
[EC 4.2.1.170 created 2016]
 
 
EC 1.1.1.268     Relevance: 78.5%
Accepted name: 2-(R)-hydroxypropyl-CoM dehydrogenase
Reaction: 2-(R)-hydroxypropyl-CoM + NAD+ = 2-oxopropyl-CoM + NADH + H+
For diagram of epoxide carboxylation, click here
Glossary: coenzyme M (CoM) = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
Other name(s): 2-(2-(R)-hydroxypropylthio)ethanesulfonate dehydrogenase; 2-[2-(R)-hydroxypropylthio]ethanesulfonate:NAD+ oxidoreductase
Systematic name: 2-{[(2R)-2-hydroxypropyl]sulfanyl}ethane-1-sulfonate:NAD+ oxidoreductase
Comments: The enzyme is highly specific for (R)-2-hydroxyalkyl thioethers of CoM, in contrast to EC 1.1.1.269, 2-(S)-hydroxypropyl-CoM dehydrogenase, which is highly specific for the (S)-enantiomer. This enzyme forms component III of a four-component enzyme system (comprising EC 4.4.1.23 [2-hydroxypropyl-CoM lyase; component I], EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV]) that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 244301-33-5
References:
1.  Allen, J.R., Clark, D.D., Krum, J.G. and Ensign, S.A. A role for coenzyme M (2-mercaptoethanesulfonic acid) in a bacterial pathway of aliphatic epoxide carboxylation. Proc. Natl. Acad. Sci. USA 96 (1999) 8432–8437. [DOI] [PMID: 10411892]
[EC 1.1.1.268 created 2001]
 
 
EC 2.6.1.117     Relevance: 77.1%
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).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
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 4.2.1.109     Relevance: 73%
Accepted name: methylthioribulose 1-phosphate dehydratase
Reaction: 5-(methylsulfanyl)-D-ribulose 1-phosphate = 5-(methylsulfanyl)-2,3-dioxopentyl phosphate + H2O
For diagram of methionine salvage, click here
Other name(s): 1-PMT-ribulose dehydratase; S-methyl-5-thio-D-ribulose-1-phosphate hydro-lyase; S-methyl-5-thio-D-ribulose-1-phosphate 4-hydro-lyase [5-(methylthio)-2,3-dioxopentyl-phosphate-forming]
Systematic name: 5-(methylsulfanyl)-D-ribulose-1-phosphate 4-hydro-lyase [5-(methylsulfanyl)-2,3-dioxopentyl-phosphate-forming]
Comments: This enzyme forms part of the methionine-salvage pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1114239-22-3
References:
1.  Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5′-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598–9606. [PMID: 2838472]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [DOI] [PMID: 7852397]
[EC 4.2.1.109 created 2006]
 
 
EC 2.5.1.23     Relevance: 72.9%
Accepted name: sym-norspermidine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + propane-1,3-diamine = S-methyl-5′-thioadenosine + bis(3-aminopropyl)amine
Glossary: S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): S-adenosylmethioninamine:propane-1,3-diamine 3-aminopropyltransferase; S-adenosyl 3-(methylthio)propylamine:propane-1,3-diamine 3-aminopropyltransferase
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:propane-1,3-diamine 3-aminopropyltransferase
Comments: The enzyme has been originally characterized from the protist Euglena gracilis [1,2]. The enzyme from the archaeon Sulfolobus solfataricus can transfer the propylamine moiety from S-adenosyl 3-(methylsulfanyl)propylamine to putrescine, sym-norspermidine and spermidine with lower efficiency [3]. cf. EC 2.5.1.16 (spermidine synthase) and EC 2.5.1.22 (spermine synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Aleksijevic, A., Grove, J. and Schuber, F. Studies on polyamine biosynthesis in Euglena gracilis. Biochim. Biophys. Acta 565 (1979) 199–207. [DOI] [PMID: 116684]
2.  Villanueva, V.R., Adlakha, R.C. and Calbayrac, R. Biosynthesis of polyamines in Euglena gracilis. Phytochemistry 19 (1980) 787–790.
3.  Cacciapuoti, G., Porcelli, M., Carteni-Farina, M., Gambacorta, A. and Zappia, V. Purification and characterization of propylamine transferase from Sulfolobus solfataricus, an extreme thermophilic archaebacterium. Eur. J. Biochem. 161 (1986) 263–271. [DOI] [PMID: 3096734]
[EC 2.5.1.23 created 1983, modified 2013]
 
 
EC 6.2.1.44     Relevance: 72%
Accepted name: 3-(methylthio)propionyl—CoA ligase
Reaction: ATP + 3-(methylsulfanyl)propanoate + CoA = AMP + diphosphate + 3-(methylsulfanyl)propanoyl-CoA
For diagram of 3-(dimethylsulfonio)propanoate metabolism, click here
Other name(s): DmdB; MMPA-CoA ligase; methylmercaptopropionate-coenzyme A ligase; 3-methylmercaptopropionyl-CoA ligase; 3-(methylthio)propanoate:CoA ligase (AMP-forming)
Systematic name: 3-(methylsulfanyl)propanoate:CoA ligase (AMP-forming)
Comments: The enzyme is part of a dimethylsulfoniopropanoate demethylation pathway in the marine bacteria Ruegeria pomeroyi and Pelagibacter ubique. It also occurs in some nonmarine bacteria capable of metabolizing dimethylsulfoniopropionate (e.g. Burkholderia thailandensis, Pseudomonas aeruginosa, and Silicibacter lacuscaerulensis). It requires Mg2+ [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Reisch, C.R., Stoudemayer, M.J., Varaljay, V.A., Amster, I.J., Moran, M.A. and Whitman, W.B. Novel pathway for assimilation of dimethylsulphoniopropionate widespread in marine bacteria. Nature 473 (2011) 208–211. [DOI] [PMID: 21562561]
2.  Bullock, H.A., Reisch, C.R., Burns, A.S., Moran, M.A. and Whitman, W.B. Regulatory and functional diversity of methylmercaptopropionate coenzyme A ligases from the dimethylsulfoniopropionate demethylation pathway in Ruegeria pomeroyi DSS-3 and other proteobacteria. J. Bacteriol. 196 (2014) 1275–1285. [DOI] [PMID: 24443527]
[EC 6.2.1.44 created 2014]
 
 
EC 2.1.1.373     Relevance: 71.8%
Accepted name: 2-hydroxy-4-(methylsulfanyl)butanoate S-methyltransferase
Reaction: S-adenosyl-L-methionine + (2R)-2-hydroxy-4-(methylsulfanyl)butanoate = S-adenosyl-L-homocysteine + (2R)-4-(dimethylsulfaniumyl)-2-hydroxybutanoate
Other name(s): dsyB (gene name); methylthiohydroxybutyrate methyltransferase; MTHB methyltransferase
Systematic name: S-adenosyl-L-methionine:(2R)-2-hydroxy-4-(methylsulfanyl)butanoate S-methyltransferase
Comments: The enzyme, characterized from the marine bacterium Labrenzia aggregata, participates in the biosynthesis of dimethylsulfoniopropanoate (DMSP). A eukaryotic enzyme that shares little sequence similarity with the bacterial enzyme was identified in many marine phytoplankton species.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Summers, P.S., Nolte, K.D., Cooper, A.J.L., Borgeas, H., Leustek, T., Rhodes, D. and Hanson, A.D. Identification and stereospecificity of the first three enzymes of 3-dimethylsulfoniopropionate biosynthesis in a chlorophyte alga. Plant Physiol. 116 (1998) 369–378. [DOI]
2.  Curson, A.R., Liu, J., Bermejo Martinez, A., Green, R.T., Chan, Y., Carrion, O., Williams, B.T., Zhang, S.H., Yang, G.P., Bulman Page, P.C., Zhang, X.H. and Todd, J.D. Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process. Nat. Microbiol. 2:17009 (2017). [DOI] [PMID: 28191900]
3.  Kageyama, H., Tanaka, Y., Shibata, A., Waditee-Sirisattha, R. and Takabe, T. Dimethylsulfoniopropionate biosynthesis in a diatom Thalassiosira pseudonana: Identification of a gene encoding MTHB-methyltransferase. Arch. Biochem. Biophys. 645 (2018) 100–106. [DOI] [PMID: 29574051]
4.  Curson, A.RJ., Williams, B.T., Pinchbeck, B.J., Sims, L.P., Martinez, A.B., Rivera, P.PL., Kumaresan, D., Mercade, E., Spurgin, L.G., Carrion, O., Moxon, S., Cattolico, R.A., Kuzhiumparambil, U., Guagliardo, P., Clode, P.L., Raina, J.B. and Todd, J.D. DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nat. Microbiol. 3 (2018) 430–439. [DOI] [PMID: 29483657]
[EC 2.1.1.373 created 2020]
 
 
EC 2.5.1.79     Relevance: 71.4%
Accepted name: thermospermine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + spermidine = S-methyl-5′-thioadenosine + thermospermine + H+
Glossary: thermospermine = N1-[3-(3-aminopropylamino)propyl]butane-1,4-diamine
S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): TSPMS; ACL5; SAC51; S-adenosyl 3-(methylthio)propylamine:spermidine 3-aminopropyltransferase (thermospermine synthesizing)
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:spermidine 3-aminopropyltransferase (thermospermine-forming)
Comments: This plant enzyme is crucial for the proper functioning of xylem vessel elements in the vascular tissues of plants [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Romer, P., Faltermeier, A., Mertins, V., Gedrange, T., Mai, R. and Proff, P. Investigations about N-aminopropyl transferases probably involved in biomineralization. J. Physiol. Pharmacol. 59 Suppl 5 (2008) 27–37. [PMID: 19075322]
2.  Knott, J.M., Romer, P. and Sumper, M. Putative spermine synthases from Thalassiosira pseudonana and Arabidopsis thaliana synthesize thermospermine rather than spermine. FEBS Lett. 581 (2007) 3081–3086. [DOI] [PMID: 17560575]
3.  Muniz, L., Minguet, E.G., Singh, S.K., Pesquet, E., Vera-Sirera, F., Moreau-Courtois, C.L., Carbonell, J., Blazquez, M.A. and Tuominen, H. ACAULIS5 controls Arabidopsis xylem specification through the prevention of premature cell death. Development 135 (2008) 2573–2582. [DOI] [PMID: 18599510]
[EC 2.5.1.79 created 2010, modified 2013]
 
 
EC 2.5.1.128     Relevance: 70.6%
Accepted name: N4-bis(aminopropyl)spermidine synthase
Reaction: 2 S-adenosyl 3-(methylsulfanyl)propylamine + spermidine = 2 S-methyl-5′-thioadenosine + N4-bis(aminopropyl)spermidine (overall reaction)
(1a) S-adenosyl 3-(methylsulfanyl)propylamine + spermidine = S-methyl-5′-thioadenosine + N4-aminopropylspermidine
(1b) S-adenosyl 3-(methylsulfanyl)propylamine + N4-aminopropylspermidine = S-methyl-5′-thioadenosine + N4-bis(aminopropyl)spermidine
Glossary: spermidine = N-(3-aminopropyl)butane-1,4-diamine
N4-aminopropylspermidine = N,N′-bis(3-aminopropyl)butane-1,4-diamine
N4-bis(aminopropyl)spermidine = N,N,N′-tris(3-aminopropyl)butane-1,4-diamine
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:spermidine 3-aminopropyltransferase [N4-bis(aminopropyl)spermidine synthesizing]
Comments: The enzyme, characterized from the thermophilic archaeon Thermococcus kodakarensis, synthesizes the branched-chain polyamine N4-bis(aminopropyl)spermidine, which is required for cell growth at high-temperature. When spermine is used as substrate, the enzyme forms N4-aminopropylspermine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Okada, K., Hidese, R., Fukuda, W., Niitsu, M., Takao, K., Horai, Y., Umezawa, N., Higuchi, T., Oshima, T., Yoshikawa, Y., Imanaka, T. and Fujiwara, S. Identification of a novel aminopropyltransferase involved in the synthesis of branched-chain polyamines in hyperthermophiles. J. Bacteriol. 196 (2014) 1866–1876. [DOI] [PMID: 24610711]
[EC 2.5.1.128 created 2014]
 
 
EC 5.3.2.5     Relevance: 69.5%
Accepted name: 2,3-diketo-5-methylthiopentyl-1-phosphate enolase
Reaction: 5-(methylsulfanyl)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylsulfanyl)-3-oxopent-1-enyl phosphate
Other name(s): DK-MTP-1-P enolase; MtnW; YkrW; RuBisCO-like protein; RLP; 2,3-diketo-5-methylthiopentyl-1-phosphate keto—enol-isomerase
Systematic name: 5-(methylsulfanyl)-2,3-dioxopentyl phosphate keto—enol-isomerase
Comments: The enzyme participates in the methionine salvage pathway in Bacillus subtilis [2].In some species a single bifunctional enzyme, EC 3.1.3.77, acireductone synthase, catalyses both this reaction and EC 3.1.3.87, 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Myers, R.W., Wray, J.W., Fish, S. and Abeles, R.H. Purification and characterization of an enzyme involved in oxidative carbon-carbon bond cleavage reactions in the methionine salvage pathway of Klebsiella pneumoniae. J. Biol. Chem. 268 (1993) 24785–24791. [PMID: 8227039]
2.  Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N. and Yokota, A. A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO. Science 302 (2003) 286–290. [DOI] [PMID: 14551435]
[EC 5.3.2.5 created 2012]
 
 
EC 1.13.11.53     Relevance: 68.6%
Accepted name: acireductone dioxygenase (Ni2+-requiring)
Reaction: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 3-(methylsulfanyl)propanoate + formate + CO
For diagram of methionine salvage, click here and for diagram of reaction, click here
Glossary: acireductone = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Other name(s): ARD; 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase (ambiguous); acireductone dioxygenase (ambiguous); E-2; 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming)
Systematic name: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one:oxygen oxidoreductase (formate- and CO-forming)
Comments: Requires Ni2+. If iron(II) is bound instead of Ni2+, the reaction catalysed by EC 1.13.11.54, acireductone dioxygenase [iron(II)-requiring], occurs instead [1]. The enzyme from the bacterium Klebsiella oxytoca (formerly Klebsiella pneumoniae) ATCC strain 8724 is involved in the methionine salvage pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Wray, J.W. and Abeles, R.H. A bacterial enzyme that catalyzes formation of carbon monoxide. J. Biol. Chem. 268 (1993) 21466–21469. [PMID: 8407993]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [DOI] [PMID: 7852397]
3.  Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5′-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598–9606. [PMID: 2838472]
4.  Dai, Y., Wensink, P.C. and Abeles, R.H. One protein, two enzymes. J. Biol. Chem. 274 (1999) 1193–1195. [DOI] [PMID: 9880484]
5.  Mo, H., Dai, Y., Pochapsky, S.S. and Pochapsky, T.C. 1H, 13C and 15N NMR assignments for a carbon monoxide generating metalloenzyme from Klebsiella pneumoniae. J. Biomol. NMR 14 (1999) 287–288. [PMID: 10481280]
6.  Dai, Y., Pochapsky, T.C. and Abeles, R.H. Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry 40 (2001) 6379–6387. [DOI] [PMID: 11371200]
7.  Al-Mjeni, F., Ju, T., Pochapsky, T.C. and Maroney, M.J. XAS investigation of the structure and function of Ni in acireductone dioxygenase. Biochemistry 41 (2002) 6761–6769. [DOI] [PMID: 12022880]
8.  Pochapsky, T.C., Pochapsky, S.S., Ju, T., Mo, H., Al-Mjeni, F. and Maroney, M.J. Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat. Struct. Biol. 9 (2002) 966–972. [DOI] [PMID: 12402029]
[EC 1.13.11.53 created 2006]
 
 
EC 1.13.11.54     Relevance: 67.8%
Accepted name: acireductone dioxygenase [iron(II)-requiring]
Reaction: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one + O2 = 4-(methylsulfanyl)-2-oxobutanoate + formate
For diagram of methionine salvage, click here and for diagram of reaction, click here
Glossary: acireductone = 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Other name(s): ARD′; 2-hydroxy-3-keto-5-thiomethylpent-1-ene dioxygenase (ambiguous); acireductone dioxygenase (ambiguous); E-2′; E-3 dioxygenase; 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one:oxygen oxidoreductase (formate-forming)
Systematic name: 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one:oxygen oxidoreductase (formate-forming)
Comments: Requires iron(II). If Ni2+ is bound instead of iron(II), the reaction catalysed by EC 1.13.11.53, acireductone dioxygenase (Ni2+-requiring), occurs instead. The enzyme from the bacterium Klebsiella oxytoca (formerly Klebsiella pneumoniae) ATCC strain 8724 is involved in the methionine salvage pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Wray, J.W. and Abeles, R.H. A bacterial enzyme that catalyzes formation of carbon monoxide. J. Biol. Chem. 268 (1993) 21466–21469. [PMID: 8407993]
2.  Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147–3153. [DOI] [PMID: 7852397]
3.  Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5′-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598–9606. [PMID: 2838472]
4.  Dai, Y., Wensink, P.C. and Abeles, R.H. One protein, two enzymes. J. Biol. Chem. 274 (1999) 1193–1195. [DOI] [PMID: 9880484]
5.  Mo, H., Dai, Y., Pochapsky, S.S. and Pochapsky, T.C. 1H, 13C and 15N NMR assignments for a carbon monoxide generating metalloenzyme from Klebsiella pneumoniae. J. Biomol. NMR 14 (1999) 287–288. [PMID: 10481280]
6.  Dai, Y., Pochapsky, T.C. and Abeles, R.H. Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae. Biochemistry 40 (2001) 6379–6387. [DOI] [PMID: 11371200]
7.  Al-Mjeni, F., Ju, T., Pochapsky, T.C. and Maroney, M.J. XAS investigation of the structure and function of Ni in acireductone dioxygenase. Biochemistry 41 (2002) 6761–6769. [DOI] [PMID: 12022880]
8.  Pochapsky, T.C., Pochapsky, S.S., Ju, T., Mo, H., Al-Mjeni, F. and Maroney, M.J. Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae. Nat. Struct. Biol. 9 (2002) 966–972. [DOI] [PMID: 12402029]
[EC 1.13.11.54 created 2006]
 
 
EC 2.3.3.17     Relevance: 65.4%
Accepted name: methylthioalkylmalate synthase
Reaction: an ω-(methylsulfanyl)-2-oxoalkanoate + acetyl-CoA + H2O = a 2-[ω-(methylsulfanyl)alkyl]malate + CoA
For diagram of L-Homomethionine biosynthesis, click here
Other name(s): MAM1 (gene name); MAM3 (gene name); acetyl-CoA:ω-(methylthio)-2-oxoalkanoate C-acetyltransferase
Systematic name: acetyl-CoA:ω-(methylsulfanyl)-2-oxoalkanoate C-acetyltransferase
Comments: The enzyme, characterized from the plant Arabidopsis thaliana, is involved in the L-methionine side-chain elongation pathway, forming substrates for the biosynthesis of aliphatic glucosinolates. Two forms are known - MAM1 catalyses only only the first two rounds of methionine chain elongation, while MAM3 catalyses all six cycles, up to formation of L-hexahomomethionine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Textor, S., Bartram, S., Kroymann, J., Falk, K.L., Hick, A., Pickett, J.A. and Gershenzon, J. Biosynthesis of methionine-derived glucosinolates in Arabidopsis thaliana: recombinant expression and characterization of methylthioalkylmalate synthase, the condensing enzyme of the chain-elongation cycle. Planta 218 (2004) 1026–1035. [DOI] [PMID: 14740211]
2.  Textor, S., de Kraker, J.W., Hause, B., Gershenzon, J. and Tokuhisa, J.G. MAM3 catalyzes the formation of all aliphatic glucosinolate chain lengths in Arabidopsis. Plant Physiol. 144 (2007) 60–71. [DOI] [PMID: 17369439]
[EC 2.3.3.17 created 2016]
 
 
EC 1.1.1.428     Relevance: 64.7%
Accepted name: 4-methylthio 2-oxobutanoate reductase (NADH)
Reaction: (2R)-2-hydroxy-4-(methylsulfanyl)butanoate + NAD+ = 4-(methylsulfanyl)-2-oxobutanoate + NADH + H+
Other name(s): CTBP1 (gene name); C-terminal-binding protein 1; MTOB reductase; 4-methylthio 2-oxobutyrate reductase; 4-methylthio 2-oxobutyric acid reductase
Systematic name: (2R)-2-hydroxy-4-(methylsulfanyl)butanoate:NAD+ 2-oxidoreductase
Comments: The substrate of this enzyme is formed as an intermediate during L-methionine salvage from S-methyl-5′-thioadenosine, which is formed during the biosynthesis of polyamines. The human enzyme also functions as a transcriptional co-regulator that downregulates the expression of many tumor-suppressor genes, thus providing a link between gene repression and the methionine salvage pathway. A similar, but NADP-specific, enzyme is involved in dimethylsulfoniopropanoate biosynthesis in algae and phytoplankton.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kumar, V., Carlson, J.E., Ohgi, K.A., Edwards, T.A., Rose, D.W., Escalante, C.R., Rosenfeld, M.G. and Aggarwal, A.K. Transcription corepressor CtBP is an NAD+-regulated dehydrogenase. Mol. Cell 10 (2002) 857–869. [DOI] [PMID: 12419229]
2.  Achouri, Y., Noel, G. and Van Schaftingen, E. 2-Keto-4-methylthiobutyrate, an intermediate in the methionine salvage pathway, is a good substrate for CtBP1. Biochem. Biophys. Res. Commun. 352 (2007) 903–906. [DOI] [PMID: 17157814]
3.  Hilbert, B.J., Grossman, S.R., Schiffer, C.A. and Royer, W.E., Jr. Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design. FEBS Lett. 588 (2014) 1743–1748. [DOI] [PMID: 24657618]
4.  Korwar, S., Morris, B.L., Parikh, H.I., Coover, R.A., Doughty, T.W., Love, I.M., Hilbert, B.J., Royer, W.E., Jr., Kellogg, G.E., Grossman, S.R. and Ellis, K.C. Design, synthesis, and biological evaluation of substrate-competitive inhibitors of C-terminal Binding Protein (CtBP). Bioorg. Med. Chem. 24 (2016) 2707–2715. [DOI] [PMID: 27156192]
[EC 1.1.1.428 created 2022]
 
 
EC 2.5.1.22     Relevance: 62.6%
Accepted name: spermine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + spermidine = S-methyl-5′-thioadenosine + spermine
For diagram of spermine biosynthesis, click here
Glossary: spermidine = N-(3-aminopropyl)butane-1,4-diamine
spermine = N,N′-bis(3-aminopropyl)butane-1,4-diamine
S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): spermidine aminopropyltransferase; spermine synthetase; S-adenosylmethioninamine:spermidine 3-aminopropyltransferase; S-adenosyl 3-(methylthio)propylamine:spermidine 3-aminopropyltransferase
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:spermidine 3-aminopropyltransferase
Comments: The enzyme from mammalia is highly specific for spermidine [2,3]. cf. EC 2.5.1.16 (spermidine synthase) and EC 2.5.1.23 (sym-norspermidine synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 74812-43-4
References:
1.  Hibasami, H., Borchardt, R.T., Chen, S.-Y., Coward, J.K. and Pegg, A.E. Studies of inhibition of rat spermidine synthase and spermine synthase. Biochem. J. 187 (1980) 419–428. [PMID: 7396856]
2.  Pajula, R.-L., Raina, A. and Eloranta, T. Polyamine synthesis in mammalian tissues. Isolation and characterization of spermine synthase from bovine brain. Eur. J. Biochem. 101 (1979) 619–626. [DOI] [PMID: 520313]
3.  Pegg, A.E., Shuttleworth, K. and Hibasami, H. Specificity of mammalian spermidine synthase and spermine synthase. Biochem. J. 197 (1981) 315–320. [PMID: 6798961]
[EC 2.5.1.22 created 1982, modified 2013]
 
 
EC 4.1.1.50     Relevance: 60.9%
Accepted name: adenosylmethionine decarboxylase
Reaction: S-adenosyl-L-methionine = S-adenosyl 3-(methylsulfanyl)propylamine + CO2
For diagram of spermidine biosynthesis, click here and for diagram of spermine biosynthesis, click here
Glossary: S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): S-adenosylmethionine decarboxylase; S-adenosyl-L-methionine decarboxylase; S-adenosyl-L-methionine carboxy-lyase; S-adenosyl-L-methionine carboxy-lyase [(5-deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium-salt-forming]
Systematic name: S-adenosyl-L-methionine carboxy-lyase [S-adenosyl 3-(methylsulfanyl)propylamine-forming]
Comments: The Escherichia coli enzyme contains a pyruvoyl group.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9036-20-8
References:
1.  Anton, D.L. and Kutny, R. Escherichia coli S-adenosylmethionine decarboxylase. Subunit structure, reductive amination, and NH2-terminal sequences. J. Biol. Chem. 262 (1987) 2817–2822. [PMID: 3546296]
2.  Tabor, C.W. Adenosylmethionine decarboxylase. Methods Enzymol. 5 (1962) 756–760. [DOI]
[EC 4.1.1.50 created 1972]
 
 
EC 1.14.11.17     Relevance: 59%
Accepted name: taurine dioxygenase
Reaction: taurine + 2-oxoglutarate + O2 = sulfite + aminoacetaldehyde + succinate + CO2
Other name(s): 2-aminoethanesulfonate dioxygenase; α-ketoglutarate-dependent taurine dioxygenase
Systematic name: taurine, 2-oxoglutarate:oxygen oxidoreductase (sulfite-forming)
Comments: Requires FeII. The enzyme from Escherichia coli also acts on pentanesulfonate, 3-(N-morpholino)propanesulfonate and 2-(1,3-dioxoisoindolin-2-yl)ethanesulfonate, but at lower rates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 197809-75-9
References:
1.  Eichhorn, E., Van Der Poeg, J.R., Kertesz, M.A. and Leisinger, T. Characterization of α-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J. Biol. Chem. 272 (1997) 23031–23036. [DOI] [PMID: 9287300]
[EC 1.14.11.17 created 2000]
 
 
EC 2.5.1.104     Relevance: 58.1%
Accepted name: N1-aminopropylagmatine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + agmatine = S-methyl-5′-thioadenosine + N1-(3-aminopropyl)agmatine
For diagram of spermidine biosynthesis, click here
Glossary: S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): agmatine/cadaverine aminopropyl transferase; ACAPT; PF0127 (gene name); triamine/agmatine aminopropyltransferase; SpeE (ambiguous); agmatine aminopropyltransferase; S-adenosyl 3-(methylthio)propylamine:agmatine 3-aminopropyltransferase
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:agmatine 3-aminopropyltransferase
Comments: The enzyme is involved in the biosynthesis of spermidine from agmatine in some archaea and bacteria. The enzyme from the Gram-negative bacterium Thermus thermophilus accepts agmatine, spermidine and norspermidine with similar catalytic efficiency. The enzymes from the archaea Pyrococcus furiosus and Thermococcus kodakarensis prefer agmatine, but can utilize cadaverine, putrescine and propane-1,3-diamine with much lower catalytic efficiency. cf. EC 2.5.1.16, spermidine synthase, and EC 2.5.1.23, sym-norspermidine synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ohnuma, M., Terui, Y., Tamakoshi, M., Mitome, H., Niitsu, M., Samejima, K., Kawashima, E. and Oshima, T. N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus. J. Biol. Chem. 280 (2005) 30073–30082. [DOI] [PMID: 15983049]
2.  Cacciapuoti, G., Porcelli, M., Moretti, M.A., Sorrentino, F., Concilio, L., Zappia, V., Liu, Z.J., Tempel, W., Schubot, F., Rose, J.P., Wang, B.C., Brereton, P.S., Jenney, F.E. and Adams, M.W. The first agmatine/cadaverine aminopropyl transferase: biochemical and structural characterization of an enzyme involved in polyamine biosynthesis in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 189 (2007) 6057–6067. [DOI] [PMID: 17545282]
3.  Morimoto, N., Fukuda, W., Nakajima, N., Masuda, T., Terui, Y., Kanai, T., Oshima, T., Imanaka, T. and Fujiwara, S. Dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon Thermococcus kodakarensis. J. Bacteriol. 192 (2010) 4991–5001. [DOI] [PMID: 20675472]
4.  Ohnuma, M., Ganbe, T., Terui, Y., Niitsu, M., Sato, T., Tanaka, N., Tamakoshi, M., Samejima, K., Kumasaka, T. and Oshima, T. Crystal structures and enzymatic properties of a triamine/agmatine aminopropyltransferase from Thermus thermophilus. J. Mol. Biol. 408 (2011) 971–986. [DOI] [PMID: 21458463]
[EC 2.5.1.104 created 2013]
 
 
EC 2.5.1.16     Relevance: 58%
Accepted name: spermidine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + putrescine = S-methyl-5′-thioadenosine + spermidine
For diagram of spermine biosynthesis, click here
Glossary: spermidine = N-(3-aminopropyl)butane-1,4-diamine
spermine = N,N′-bis(3-aminopropyl)butane-1,4-diamine
putrescine = butane-1,4-diamine
S-adenosyl 3-(methylsulfanyl)propylamine = (3-aminopropyl){[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}methylsulfonium
Other name(s): aminopropyltransferase; putrescine aminopropyltransferase; spermidine synthetase; SpeE (ambiguous); S-adenosylmethioninamine:putrescine 3-aminopropyltransferase; S-adenosyl 3-(methylthio)propylamine:putrescine 3-aminopropyltransferase
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:putrescine 3-aminopropyltransferase
Comments: The enzymes from the plant Glycine max and from mammalia are highly specific for putrescine as the amine acceptor [2,7]. The enzymes from the bacteria Escherichia coli and Thermotoga maritima prefer putrescine but are more tolerant towards other amine acceptors, such as spermidine and cadaverine [5,6]. cf. EC 2.5.1.22 (spermine synthase) and EC 2.5.1.23 (sym-norspermidine synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37277-82-0
References:
1.  Hannonen, P., Janne, J. and Raina, A. Partial purification and characterization of spermine synthase from rat brain. Biochim. Biophys. Acta 289 (1972) 225–231. [DOI] [PMID: 4564056]
2.  Pegg, A.E., Shuttleworth, K. and Hibasami, H. Specificity of mammalian spermidine synthase and spermine synthase. Biochem. J. 197 (1981) 315–320. [PMID: 6798961]
3.  Tabor, C.W. Propylamine transferase (spermidine synthesis). Methods Enzymol. 5 (1962) 761–765.
4.  Tabor, H. and Tabor, C.W. Biosynthesis and metabolism of 1,4-diaminobutane, spermidine, spermine, and related amines. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 203–268. [PMID: 4628436]
5.  Bowman, W.H., Tabor, C.W. and Tabor, H. Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli. J. Biol. Chem. 248 (1973) 2480–2486. [PMID: 4572733]
6.  Korolev, S., Ikeguchi, Y., Skarina, T., Beasley, S., Arrowsmith, C., Edwards, A., Joachimiak, A., Pegg, A.E. and Savchenko, A. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat. Struct. Biol. 9 (2002) 27–31. [DOI] [PMID: 11731804]
7.  Yoon, S.O., Lee, Y.S., Lee, S.H. and Cho, Y.D. Polyamine synthesis in plants: isolation and characterization of spermidine synthase from soybean (Glycine max) axes. Biochim. Biophys. Acta 1475 (2000) 17–26. [DOI] [PMID: 10806333]
[EC 2.5.1.16 created 1972, modified 1982, modified 2013]
 
 
EC 4.1.1.57     Relevance: 56.3%
Accepted name: methionine decarboxylase
Reaction: L-methionine = 3-(methylsulfanyl)propanamine + CO2
Other name(s): L-methionine decarboxylase; L-methionine carboxy-lyase; L-methionine carboxy-lyase (3-methylthiopropanamine-forming)
Systematic name: L-methionine carboxy-lyase [3-(methylsulfanyl)propanamine-forming]
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37290-50-9
References:
1.  Hagion, H. and Nakayama, K. Amino acid metabolism in microorganisms. Part IV. L-Methionine decarboxylase produced by Streptomyces strain. Agric. Biol. Chem. 32 (1968) 727–733.
[EC 4.1.1.57 created 1972]
 
 
EC 1.14.14.42     Relevance: 55.2%
Accepted name: homomethionine N-monooxygenase
Reaction: an L-polyhomomethionine + 2 [reduced NADPH—hemoprotein reductase] + 2 O2 = an (E)-ω-(methylsulfanyl)alkanal oxime + 2 [oxidized NADPH—hemoprotein reductase] + CO2 + 3 H2O (overall reaction)
(1a) an L-polyhomomethionine + [reduced NADPH—hemoprotein reductase] + O2 = an L-N-hydroxypolyhomomethionine + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) an L-N-hydroxypolyhomomethionine + [reduced NADPH—hemoprotein reductase] + O2 = an L-N,N-dihydroxypolyhomomethionine + [oxidized NADPH—hemoprotein reductase] + H2O
(1c) an L-N,N-dihydroxypolyhomomethionine = an (E)-ω-(methylsulfanyl)alkanal oxime + CO2 + H2O
Glossary: homomethionine = (2S)-2-amino-5-(methylsulfanyl)pentanoate
an L-polyhomomethionine = analogs of L-methionine that contain additional methylene groups in the side chain prior to the sulfur atom.
Other name(s): CYP79F1 (gene name); CYP79F2 (gene name)
Systematic name: L-polyhomomethionine,[NADPH—hemoprotein reductase]:oxygen oxidoreductase
Comments: This plant cytochrome P-450 (heme thiolate) enzyme is involved in methionine-derived aliphatic glucosinolates biosynthesis. It catalyses two successive N-hydroxylations, which are followed by dehydration and decarboxylation. CYP79F1 from Arabidopsis thaliana can metabolize mono-, di-, tri-, tetra-, penta-, and hexahomomethionine to their corresponding aldoximes, while CYP79F2 from the same plant can only metabolize penta- and hexahomomethionine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hansen, C.H., Wittstock, U., Olsen, C.E., Hick, A.J., Pickett, J.A. and Halkier, B.A. Cytochrome p450 CYP79F1 from arabidopsis catalyzes the conversion of dihomomethionine and trihomomethionine to the corresponding aldoximes in the biosynthesis of aliphatic glucosinolates. J. Biol. Chem. 276 (2001) 11078–11085. [DOI] [PMID: 11133994]
2.  Chen, S., Glawischnig, E., Jørgensen, K., Naur, P., Jorgensen, B., Olsen, C.E., Hansen, C.H., Rasmussen, H., Pickett, J.A. and Halkier, B.A. CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant J. 33 (2003) 923–937. [DOI] [PMID: 12609033]
[EC 1.14.14.42 created 2017]
 
 
EC 2.8.4.4     Relevance: 53.6%
Accepted name: [ribosomal protein uS12] (aspartate89-C3)-methylthiotransferase
Reaction: L-aspartate89-[ribosomal protein uS12] + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced acceptor = 3-(methylsulfanyl)-L-aspartate89-[ribosomal protein uS12] + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5′-deoxyadenosine + oxidized acceptor (overall reaction)
(1a) S-adenosyl-L-methionine + L-aspartate89-[ribosomal protein uS12] + sulfur-(sulfur carrier) = S-adenosyl-L-homocysteine + L-aspartate89-[ribosomal protein uS12]-methanethiol + (sulfur carrier)
(1b) L-aspartate89-[ribosomal protein uS12]-methanethiol + S-adenosyl-L-methionine + reduced acceptor = 3-(methylsulfanyl)-L-aspartate89-[ribosomal protein uS12] + L-methionine + 5′-deoxyadenosine + oxidized acceptor
Other name(s): RimO; [ribosomal protein S12]-Asp89:sulfur-(sulfur carrier),S-adenosyl-L-methionine C3-methylthiotransferase; [ribosomal protein S12]-L-aspartate89:sulfur-(sulfur carrier),S-adenosyl-L-methionine C3-methylthiotransferase
Systematic name: [ribosomal protein uS12]-L-aspartate89:sulfur-(sulfur carrier),S-adenosyl-L-methionine C3-(methylsulfanyl)transferase
Comments: This bacterial enzyme binds two [4Fe-4S] clusters [2,3]. A bridge of five sulfur atoms is formed between the free Fe atoms of the two [4Fe-4S] clusters [6]. In the first reaction the enzyme transfers a methyl group from AdoMet to the external sulfur ion of the sulfur bridge. In the second reaction the enzyme catalyses the reductive fragmentation of a second molecule of AdoMet, yielding a 5′-deoxyadenosine radical, which then attacks the methylated sulfur atom of the polysulfide bridge, resulting in the transfer of a methylsulfanyl group to aspartate89 [5,6]. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Anton, B.P., Saleh, L., Benner, J.S., Raleigh, E.A., Kasif, S. and Roberts, R.J. RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc. Natl. Acad. Sci. USA 105 (2008) 1826–1831. [DOI] [PMID: 18252828]
2.  Lee, K.H., Saleh, L., Anton, B.P., Madinger, C.L., Benner, J.S., Iwig, D.F., Roberts, R.J., Krebs, C. and Booker, S.J. Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry 48 (2009) 10162–10174. [DOI] [PMID: 19736993]
3.  Arragain, S., Garcia-Serres, R., Blondin, G., Douki, T., Clemancey, M., Latour, J.M., Forouhar, F., Neely, H., Montelione, G.T., Hunt, J.F., Mulliez, E., Fontecave, M. and Atta, M. Post-translational modification of ribosomal proteins: structural and functional characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine methylthiotransferase. J. Biol. Chem. 285 (2010) 5792–5801. [DOI] [PMID: 20007320]
4.  Strader, M.B., Costantino, N., Elkins, C.A., Chen, C.Y., Patel, I., Makusky, A.J., Choy, J.S., Court, D.L., Markey, S.P. and Kowalak, J.A. A proteomic and transcriptomic approach reveals new insight into β-methylthiolation of Escherichia coli ribosomal protein S12. Mol. Cell. Proteomics 10:M110.005199 (2011). [DOI] [PMID: 21169565]
5.  Landgraf, B.J., Arcinas, A.J., Lee, K.H. and Booker, S.J. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. J. Am. Chem. Soc. 135 (2013) 15404–15416. [DOI] [PMID: 23991893]
6.  Forouhar, F., Arragain, S., Atta, M., Gambarelli, S., Mouesca, J.M., Hussain, M., Xiao, R., Kieffer-Jaquinod, S., Seetharaman, J., Acton, T.B., Montelione, G.T., Mulliez, E., Hunt, J.F. and Fontecave, M. Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases. Nat. Chem. Biol. 9 (2013) 333–338. [DOI] [PMID: 23542644]
[EC 2.8.4.4 created 2014, modified 2014, modified 2023]
 
 
EC 2.5.1.126     Relevance: 52.5%
Accepted name: norspermine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + norspermidine = S-methyl-5′-thioadenosine + norspermine
Glossary: norspermidine = bis(3-aminopropyl)amine
norspermine = N,N′-bis(3-aminopropyl)-1,3-propanediamine
spermidine = N-(3-aminopropyl)-1,4-butanediamine
thermospermine = N-{3-[(3-aminopropyl)amino]propyl}-1,4-butanediamine
Other name(s): long-chain polyamine synthase (ambiguous)
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:norspermidine 3-aminopropyltransferase
Comments: The enzyme, characterized from the thermophilic archaeon Pyrobaculum aerophilum, can also synthesize norspermidine from propane-1,3-diamine and thermospermine from spermidine (with lower activity). The long-chain polyamines stabilize double-stranded DNA at high temperatures. In contrast to EC 2.5.1.127, caldopentamine synthase, this enzyme does not accept norspermine as a substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Knott, J.M. Biosynthesis of long-chain polyamines by crenarchaeal polyamine synthases from Hyperthermus butylicus and Pyrobaculum aerophilum. FEBS Lett. 583 (2009) 3519–3524. [DOI] [PMID: 19822146]
[EC 2.5.1.126 created 2014]
 
 
EC 2.8.4.5     Relevance: 51%
Accepted name: tRNA (N6-L-threonylcarbamoyladenosine37-C2)-methylthiotransferase
Reaction: N6-L-threonylcarbamoyladenine37 in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = 2-(methylsulfanyl)-N6-L-threonylcarbamoyladenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5′-deoxyadenosine + electron acceptor (overall reaction)
(1a) N6-L-threonylcarbamoyladenine37 in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = 2-sulfanyl-N6-L-threonylcarbamoyladenine37 in tRNA + (sulfur carrier) + L-methionine + 5′-deoxyadenosine + electron acceptor
(1b) S-adenosyl-L-methionine + 2-sulfanyl-N6-L-threonylcarbamoyladenine37 in tRNA = S-adenosyl-L-homocysteine + 2-(methylsulfanyl)-N6-L-threonylcarbamoyladenine37 in tRNA
For diagram of N6-L-Threonylcarbamoyladenosine37 modified tRNA biosynthesis, click here
Glossary: N6-L-threonylcarbamoyladenine37 = t6A37
2-sulfanyl-N6-L-threonylcarbamoyladenine37 = ms2t6A37
Other name(s): MtaB; methylthio-threonylcarbamoyl-adenosine transferase B; CDKAL1 (gene name); tRNA (N6-L-threonylcarbamoyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-methylthiotransferase
Systematic name: tRNA (N6-L-threonylcarbamoyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-(methylsulfanyl)transferase
Comments: The enzyme, which is a member of the S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes superfamily, binds two [4Fe-4S] clusters as well as the transferred sulfur. The sulfur donor is believed to be one of the [4Fe-4S] clusters, which is sacrificed in the process, so that in vitro the reaction is a single turnover. The identity of the electron donor is not known.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Arragain, S., Handelman, S.K., Forouhar, F., Wei, F.Y., Tomizawa, K., Hunt, J.F., Douki, T., Fontecave, M., Mulliez, E. and Atta, M. Identification of eukaryotic and prokaryotic methylthiotransferase for biosynthesis of 2-methylthio-N6-threonylcarbamoyladenosine in tRNA. J. Biol. Chem. 285 (2010) 28425–28433. [DOI] [PMID: 20584901]
[EC 2.8.4.5 created 2014, modified 2015]
 
 
EC 2.8.4.3     Relevance: 49.6%
Accepted name: tRNA-2-methylthio-N6-dimethylallyladenosine synthase
Reaction: N6-(3-methylbut-2-en-1-yl)-adenine37 in tRNA + sulfur-(sulfur carrier) + 2 S-adenosyl-L-methionine + reduced electron acceptor = N6-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenine37 in tRNA + S-adenosyl-L-homocysteine + (sulfur carrier) + L-methionine + 5′-deoxyadenine + electron acceptor (overall reaction)
(1a) N6-(3-methylbut-2-en-1-yl)-adenine37 in tRNA + sulfur-(sulfur carrier) + S-adenosyl-L-methionine + reduced electron acceptor = N6-(3-methylbut-2-en-1-yl)-2-thioadenine37 in tRNA + (sulfur carrier) + L-methionine + 5′-deoxyadenine + electron acceptor
(1b) S-adenosyl-L-methionine + N6-(3-methylbut-2-en-1-yl)-2-thioadenine37 in tRNA = S-adenosyl-L-homocysteine + N6-(3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenine37 in tRNA
For diagram of N6-(dimethylallyl)adenosine37 modified tRNA biosynthesis, click here
Glossary: N6-(3-methylbut-2-en-1-yl)-adenine37 in tRNA = N6-dimethylallyladenine37 in tRNA
Other name(s): MiaB; 2-methylthio-N-6-isopentenyl adenosine synthase; tRNA-i6A37 methylthiotransferase; tRNA (N6-dimethylallyladenosine37):sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-methylthiotransferase
Systematic name: tRNA N6-(3-methylbut-2-en-1-yl)-adenine37:sulfur-(sulfur carrier),S-adenosyl-L-methionine C2-(methylsulfanyl)transferase
Comments: This bacterial enzyme binds two [4Fe-4S] clusters as well as the transferred sulfur [3]. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. The sulfur donor is believed to be one of the [4Fe-4S] clusters, which is sacrificed in the process, so that in vitro the reaction is a single turnover. The identity of the electron donor is not known.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Pierrel, F., Bjork, G.R., Fontecave, M. and Atta, M. Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. J. Biol. Chem. 277 (2002) 13367–13370. [DOI] [PMID: 11882645]
2.  Pierrel, F., Hernandez, H.L., Johnson, M.K., Fontecave, M. and Atta, M. MiaB protein from Thermotoga maritima. Characterization of an extremely thermophilic tRNA-methylthiotransferase. J. Biol. Chem. 278 (2003) 29515–29524. [DOI] [PMID: 12766153]
3.  Pierrel, F., Douki, T., Fontecave, M. and Atta, M. MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme involved in thiolation and methylation of tRNA. J. Biol. Chem. 279 (2004) 47555–47563. [DOI] [PMID: 15339930]
4.  Hernandez, H.L., Pierrel, F., Elleingand, E., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Fontecave, M. and Atta, M. MiaB, a bifunctional radical-S-adenosylmethionine enzyme involved in the thiolation and methylation of tRNA, contains two essential [4Fe-4S] clusters. Biochemistry 46 (2007) 5140–5147. [DOI] [PMID: 17407324]
5.  Landgraf, B.J., Arcinas, A.J., Lee, K.H. and Booker, S.J. Identification of an intermediate methyl carrier in the radical S-adenosylmethionine methylthiotransferases RimO and MiaB. J. Am. Chem. Soc. 135 (2013) 15404–15416. [DOI] [PMID: 23991893]
[EC 2.8.4.3 created 2014, modified 2015]
 
 
EC 2.5.1.127     Relevance: 48.5%
Accepted name: caldopentamine synthase
Reaction: S-adenosyl 3-(methylsulfanyl)propylamine + norspermine = S-methyl-5′-thioadenosine + caldopentamine
Glossary: caldopentamine = N-(3-aminopropyl)-N′-{3-[(3-aminopropyl)amino]propyl}-1,3-propanediamine
norspermidine = N-(3-aminopropyl)-1,4-butanediamine
norspermine = N,N′-bis(3-aminopropyl)-1,3-propanediamine
spermidine = N-(3-aminopropyl)-1,4-butanediamine
thermospermine = N-{3-[(3-aminopropyl)amino]propyl}-1,4-butanediamine
Other name(s): long-chain polyamine synthase (ambiguous)
Systematic name: S-adenosyl 3-(methylsulfanyl)propylamine:norspermine 3-aminopropyltransferase
Comments: The enzyme, characterized from the thermophilic archaeon Hyperthermus butylicus, can also synthesize norspermine from norspermidine and thermospermine from spermidine (with lower activity). The long-chain polyamines stabilize double-stranded DNA at high temperatures. In contrast to EC 2.5.1.23, sym-norspermidine synthase and EC 2.5.1.126, norspermine synthase, this enzyme shows no activity with propane-1,3-diamine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Knott, J.M. Biosynthesis of long-chain polyamines by crenarchaeal polyamine synthases from Hyperthermus butylicus and Pyrobaculum aerophilum. FEBS Lett. 583 (2009) 3519–3524. [DOI] [PMID: 19822146]
[EC 2.5.1.127 created 2014]
 
 
EC 3.4.19.16     Relevance: 48.2%
Accepted name: glucosinolate γ-glutamyl hydrolase
Reaction: (1) an (E)-1-(glutathion-S-yl)-N-hydroxy-ω-(methylsulfanyl)alkan-1-imine + H2O = an (E)-1-(L-cysteinylglycin-S-yl)-N-hydroxy-ω-(methylsulfanyl)alkan-1-imine + L-glutamate
(2) (E)-1-(glutathion-S-yl)-N-hydroxy-2-(1H-indol-3-yl)ethan-1-imine + H2O = (E)-1-(L-cysteinylglycin-S-yl)-N-hydroxy-2-(1H-indol-3-yl)ethan-1-imine + L-glutamate
(3) (glutathion-S-yl)(1H-indol-3-yl)acetonitrile + H2O = (L-cysteinylglycin-S-yl)(1H-indol-3-yl)acetonitrile + L-glutamate
(4) (Z)-1-(glutathion-S-yl)-N-hydroxy-2-phenylethan-1-imine + H2O = (Z)-1-(L-cysteinyglycin-S-yl)-N-hydroxy-2-phenylethan-1-imine + L-glutamate
Other name(s): GGP1 (gene name); GGP3 (gene name)
Comments: This enzyme, characterized from the plant Arabidopsis thaliana, participates in the biosynthesis of the plant defense compounds glucosinolates and camalexin. It is the only known plant enzyme capable of hydrolysing the γ-glutamyl residue of glutathione in the cytosol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Geu-Flores, F., Møldrup, M.E., Böttcher, C., Olsen, C.E., Scheel, D. and Halkier, B.A. Cytosolic γ-glutamyl peptidases process glutathione conjugates in the biosynthesis of glucosinolates and camalexin in Arabidopsis. Plant Cell 23 (2011) 2456–2469. [DOI] [PMID: 21712415]
[EC 3.4.19.16 created 2017]
 
 
EC 2.4.1.195     Relevance: 48.2%
Accepted name: N-hydroxythioamide S-β-glucosyltransferase
Reaction: (1) UDP-α-D-glucose + (Z)-2-phenyl-1-thioacetohydroximate = UDP + desulfoglucotropeolin
(2) UDP-α-D-glucose + an (E)-ω-(methylsulfanyl)alkyl-thiohydroximate = UDP + an aliphatic desulfoglucosinolate
(3) UDP-α-D-glucose + (E)-2-(1H-indol-3-yl)-1-thioacetohydroximate = UDP + desulfoglucobrassicin
For diagram of glucotropeolin biosynthesis, click here
Glossary: an aliphatic desulfoglucosinolate = an ω-(methylsulfanyl)alkylhydroximate S-glucoside
Other name(s): UGT74B1 (gene name); desulfoglucosinolate-uridine diphosphate glucosyltransferase; uridine diphosphoglucose-thiohydroximate glucosyltransferase; thiohydroximate β-D-glucosyltransferase; UDPG:thiohydroximate glucosyltransferase; thiohydroximate S-glucosyltransferase; thiohydroximate glucosyltransferase; UDP-glucose:thiohydroximate S-β-D-glucosyltransferase; UDP-glucose:N-hydroxy-2-phenylethanethioamide S-β-D-glucosyltransferase
Systematic name: UDP-α-D-glucose:N-hydroxy-2-phenylethanethioamide S-β-D-glucosyltransferase
Comments: The enzyme specifically glucosylates the thiohydroximate functional group. It is involved in the biosynthesis of glucosinolates in cruciferous plants, and acts on aliphatic, aromatic, and indolic substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9068-14-8
References:
1.  Jain, J.C., Reed, D.W., Groot Wassink, J.W.D. and Underhill, E.W. A radioassay of enzymes catalyzing the glucosylation and sulfation steps of glucosinolate biosynthesis in Brassica species. Anal. Biochem. 178 (1989) 137–140. [DOI] [PMID: 2524977]
2.  Reed, D.W., Davin, L., Jain, J.C., Deluca, V., Nelson, L. and Underhill, E.W. Purification and properties of UDP-glucose:thiohydroximate glucosyltransferase from Brassica napus L. seedlings. Arch. Biochem. Biophys. 305 (1993) 526–532. [DOI] [PMID: 8373190]
3.  Marillia, E.F., MacPherson, J.M., Tsang, E.W., Van Audenhove, K., Keller, W.A. and GrootWassink, J.W. Molecular cloning of a Brassica napus thiohydroximate S-glucosyltransferase gene and its expression in Escherichia coli. Physiol. Plant. 113 (2001) 176–184. [PMID: 12060294]
4.  Fahey, J.W., Zalcmann, A.T. and Talalay, P. The chemical diversity and distribution of glucosinolates and isothiocyanates among plants. Phytochemistry 56 (2001) 5–51. [DOI] [PMID: 11198818]
5.  Grubb, C.D., Zipp, B.J., Ludwig-Muller, J., Masuno, M.N., Molinski, T.F. and Abel, S. Arabidopsis glucosyltransferase UGT74B1 functions in glucosinolate biosynthesis and auxin homeostasis. Plant J. 40 (2004) 893–908. [DOI] [PMID: 15584955]
[EC 2.4.1.195 created 1992, modified 2006, modified 2018]
 
 
EC 1.8.1.5     Relevance: 41.9%
Accepted name: 2-oxopropyl-CoM reductase (carboxylating)
Reaction: CoM + acetoacetate + NADP+ = 2-oxopropyl-CoM + CO2 + NADPH
For diagram of epoxide carboxylation, click here
Glossary: coenzyme M (CoM) = 2-sulfanylethane-1-sulfonate = 2-mercaptoethanesulfonate (deprecated)
Other name(s): NADPH:2-(2-ketopropylthio)ethanesulfonate oxidoreductase/carboxylase; NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase; 2-mercaptoethanesulfonate,acetoacetate:NADP+ oxidoreductase (decarboxylating)
Systematic name: 2-sulfanylethane-1-sulfonate,acetoacetate:NADP+ oxidoreductase (decarboxylating)
Comments: Also acts on thioethers longer in chain length on the oxo side, e.g. 2-oxobutyl-CoM, but this portion must be attached to CoM (2-sulfanylethane-1-sulfonate); no CoM analogs will substitute. This enzyme forms component II of a four-component enzyme system EC 4.4.1.23 (2-hydroxypropyl-CoM lyase; component I), EC 1.8.1.5 [2-oxopropyl-CoM reductase (carboxylating); component II], EC 1.1.1.268 [2-(R)-hydroxypropyl-CoM dehydrogenase; component III] and EC 1.1.1.269 [2-(S)-hydroxypropyl-CoM dehydrogenase; component IV].html">click here that is involved in epoxyalkane carboxylation in Xanthobacter sp. strain Py2.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 244301-63-1
References:
1.  Allen, J.R., Clark, D.D., Krum, J.G. and Ensign, S.A. A role for coenzyme M (2-mercaptoethanesulfonic acid) in a bacterial pathway of aliphatic epoxide carboxylation. Proc. Natl. Acad. Sci. USA 96 (1999) 8432–8437. [DOI] [PMID: 10411892]
2.  Clark, D.D., Allen, J.R. and Ensign, S.A. Characterization of five catalytic activities associated with the NADPH:2-ketopropyl-coenzyme M [2-(2-ketopropylthio)ethanesulfonate] oxidoreductase/carboxylase of the Xanthobacter strain Py2 epoxide carboxylase system. Biochemistry 39 (2000) 1294–1304. [DOI] [PMID: 10684609]
[EC 1.8.1.5 created 2001]
 
 
EC 2.6.1.73     Relevance: 41.1%
Accepted name: methionine—glyoxylate transaminase
Reaction: L-methionine + glyoxylate = 4-(methylsulfanyl)-2-oxobutanoate + glycine
For diagram of EC 2.6.1, click here
Other name(s): methionine-glyoxylate aminotransferase; MGAT
Systematic name: L-methionine:glyoxylate aminotransferase
Comments: L-Glutamate can also act as donor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 116155-75-0
References:
1.  Glover, J.R., Chapple, C.C.S., Rothwell, S., Tober, I. and Ellis, B.E. Allylglucosinolate biosynthesis in Brassica carinata. Phytochemistry 27 (1988) 1345–1348.
[EC 2.6.1.73 created 1992]
 
 
EC 3.2.2.16     Relevance: 38.9%
Accepted name: methylthioadenosine nucleosidase
Reaction: S-methyl-5′-thioadenosine + H2O = 5-(methylsulfanyl)-D-ribose + adenine
For diagram of the methionine-salvage pathway, click here
Other name(s): 5′-methylthioadenosine nucleosidase; MTA nucleosidase; MeSAdo nucleosidase; methylthioadenosine methylthioribohydrolase; MTN1 (gene name)
Systematic name: S-methyl-5′-thioadenosine adeninehyrolase
Comments: Unlike EC 3.2.2.9, adenosylhomocysteine nucleosidase, this plant enzyme has little or no activity with S-adenosyl-L-homocysteine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 50812-28-7
References:
1.  Guranowski, A.B., Chiang, P.K. and Cantoni, G.L. 5′-Methylthioadenosine nucleosidase. Purification and characterization of the enzyme from Lupinus luteus seeds. Eur. J. Biochem. 114 (1981) 293–299. [DOI] [PMID: 6783408]
2.  Rzewuski, G., Cornell, K.A., Rooney, L., Burstenbinder, K., Wirtz, M., Hell, R. and Sauter, M. OsMTN encodes a 5′-methylthioadenosine nucleosidase that is up-regulated during submergence-induced ethylene synthesis in rice (Oryza sativa L.). J. Exp. Bot. 58 (2007) 1505–1514. [PMID: 17339651]
3.  Siu, K.K., Lee, J.E., Sufrin, J.R., Moffatt, B.A., McMillan, M., Cornell, K.A., Isom, C. and Howell, P.L. Molecular determinants of substrate specificity in plant 5′-methylthioadenosine nucleosidases. J. Mol. Biol. 378 (2008) 112–128. [PMID: 18342331]
4.  Park, E.Y., Choi, W.S., Oh, S.I., Kim, K.N., Shin, J.S. and Song, H.K. Biochemical and structural characterization of 5′-methylthioadenosine nucleosidases from Arabidopsis thaliana. Biochem. Biophys. Res. Commun. 381 (2009) 619–624. [PMID: 19249293]
[EC 3.2.2.16 created 1983, modified 2004]
 
 
EC 2.6.1.41     Relevance: 38.5%
Accepted name: D-methionine—pyruvate transaminase
Reaction: D-methionine + pyruvate = 4-(methylsulfanyl)-2-oxobutanoate + L-alanine
Other name(s): D-methionine transaminase; D-methionine aminotransferase
Systematic name: D-methionine:pyruvate aminotransferase
Comments: Oxaloacetate can replace pyruvate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37277-93-3
References:
1.  Mapson, L.W., March, J.F. and Wardale, D.A. Biosynthesis of ethylene. 4-Methylmercapto-2-oxobutyric acid: an intermediate in the formation from methionine. Biochem. J. 115 (1969) 653–661. [PMID: 5357015]
[EC 2.6.1.41 created 1972, modified 1982]
 
 
EC 2.1.1.3     Relevance: 37.7%
Accepted name: thetin—homocysteine S-methyltransferase
Reaction: dimethylsulfonioacetate + L-homocysteine = (methylsulfanyl)acetate + L-methionine
Glossary: thetin = sulfobetaine = dimethylsulfonioacetate
Other name(s): dimethylthetin-homocysteine methyltransferase; thetin-homocysteine methylpherase
Systematic name: dimethylsulfonioacetate:L-homocysteine S-methyltransferase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9029-76-9
References:
1.  Klee, W.A., Richards, H.H. and Cantoni, G.L. The synthesis of methionine by enzymic transmethylation. VII. Existence of two separate homocysteine methylpherases on mammalian liver. Biochim. Biophys. Acta 54 (1961) 157–164. [DOI] [PMID: 14456704]
2.  Maw, G.A. Thetin-homocysteine transmethylase. A preliminary manometric study of the enzyme from rat liver. Biochem. J. 63 (1956) 116–124. [PMID: 13315256]
3.  Maw, G.A. Thetin-homocysteine transmethylase. Some further characteristics of the enzyme from rat liver. Biochem. J. 70 (1958) 168–173. [PMID: 13584318]
[EC 2.1.1.3 created 1961]
 
 
EC 1.14.13.92     Relevance: 36%
Accepted name: phenylacetone monooxygenase
Reaction: phenylacetone + NADPH + H+ + O2 = benzyl acetate + NADP+ + H2O
For diagram of reaction, click here
Other name(s): PAMO
Systematic name: phenylacetone,NADPH:oxygen oxidoreductase
Comments: A flavoprotein (FAD). NADH cannot replace NADPH as coenzyme. In addition to phenylacetone, which is the best substrate found to date, this Baeyer-Villiger monooxygenase can oxidize other aromatic ketones [1-(4-hydroxyphenyl)propan-2-one, 1-(4-hydroxyphenyl)propan-2-one and 3-phenylbutan-2-one], some alipatic ketones (e.g. dodecan-2-one) and sulfides (e.g. 1-methyl-4-(methylsulfanyl)benzene).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 1005768-90-0
References:
1.  Malito, E., Alfieri, A., Fraaije, M.W. and Mattevi, A. Crystal structure of a Baeyer-Villiger monooxygenase. Proc. Natl. Acad. Sci. USA 101 (2004) 13157–13162. [DOI] [PMID: 15328411]
2.  Fraaije, M.W., Wu, J., Heuts, D.P., van Hellemond, E.W., Spelberg, J.H. and Janssen, D.B. Discovery of a thermostable Baeyer-Villiger monooxygenase by genome mining. Appl. Microbiol. Biotechnol. 66 (2005) 393–400. [DOI] [PMID: 15599520]
[EC 1.14.13.92 created 2005]
 
 
EC 2.8.4.6     Relevance: 34.8%
Accepted name: S-methyl-1-thioxylulose 5-phosphate methylthiotransferase
Reaction: S-methyl-1-thio-D-xylulose 5-phosphate + glutathione = 1-deoxy-D-xylulose 5-phosphate + S-(methylsulfanyl)glutathione
Other name(s): 1-methylthioxylulose 5-phosphate sulfurylase (incorrect)
Systematic name: S-methyl-1-thio-D-xylulose 5-phosphate:glutathione methylthiotransferase
Comments: The enzyme, characterized from the bacterium Rhodospirillum rubrum, belongs to the cupin superfamily and contains a manganese ion. It participates in an anaerobic salvage pathway that restores methionine from S-methyl-5′-thioadenosine. The enzyme was assayed in vitro using L-dithiothreitol instead of glutathione.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Erb, T.J., Evans, B.S., Cho, K., Warlick, B.P., Sriram, J., Wood, B.M., Imker, H.J., Sweedler, J.V., Tabita, F.R. and Gerlt, J.A. A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat. Chem. Biol. 8 (2012) 926–932. [DOI] [PMID: 23042035]
2.  Warlick, B.P., Evans, B.S., Erb, T.J., Ramagopal, U.A., Sriram, J., Imker, H.J., Sauder, J.M., Bonanno, J.B., Burley, S.K., Tabita, F.R., Almo, S.C., Sweedler, J.S. and Gerlt, J.A. 1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum. Biochemistry 51 (2012) 8324–8326. [DOI] [PMID: 23035785]
3.  Cho, K., Evans, B.S., Wood, B.M., Kumar, R., Erb, T.J., Warlick, B.P., Gerlt, J.A. and Sweedler, J.V. Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways. Metabolomics 2014 (2014) . [DOI] [PMID: 25705145]
[EC 2.8.4.6 created 2021]
 
 
EC 2.3.1.229     Relevance: 34.6%
Accepted name: 4-coumaroyl-homoserine lactone synthase
Reaction: 4-coumaroyl-CoA + S-adenosyl-L-methionine = CoA + S-methyl-5′-thioadenosine + N-(4-coumaroyl)-L-homoserine lactone
Glossary: S-methyl-5′-thioadenosine = 5′-deoxy-5′-(methylsulfanyl)adenosine
Other name(s): p-coumaryl-homoserine lactone synthase; RpaI
Systematic name: 4-coumaroyl-CoA:S-adenosyl-L-methionine trans-4-coumaroyltranserase (lactone-forming, methylthioadenosine-releasing)
Comments: The enzyme is found in the bacterium Rhodopseudomonas palustris, which produces N-(4-coumaroyl)-L-homoserine lactone as a quorum-sensing signal.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schaefer, A.L., Greenberg, E.P., Oliver, C.M., Oda, Y., Huang, J.J., Bittan-Banin, G., Peres, C.M., Schmidt, S., Juhaszova, K., Sufrin, J.R. and Harwood, C.S. A new class of homoserine lactone quorum-sensing signals. Nature 454 (2008) 595–599. [DOI] [PMID: 18563084]
[EC 2.3.1.229 created 2013]
 
 
EC 2.1.1.269     Relevance: 34.6%
Accepted name: dimethylsulfoniopropionate demethylase
Reaction: S,S-dimethyl-β-propiothetin + tetrahydrofolate = 3-(methylsulfanyl)propanoate + 5-methyltetrahydrofolate
For diagram of 3-(dimethylsulfonio)propanoate metabolism, click here
Glossary: S,S-dimethyl-β-propiothetin = 3-(S,S-dimethylsulfonio)propanoate
Other name(s): dmdA (gene name); dimethylsulfoniopropionate-dependent demethylase A
Systematic name: S,S-dimethyl-β-propiothetin:tetrahydrofolate S-methyltransferase
Comments: The enzyme from the marine bacteria Pelagibacter ubique and Ruegeria pomeroyi are specific towards S,S-dimethyl-β-propiothetin. They do not demethylate glycine-betaine [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Jansen, M. and Hansen, T.A. Tetrahydrofolate serves as a methyl acceptor in the demethylation of dimethylsulfoniopropionate in cell extracts of sulfate-reducing bacteria. Arch. Microbiol. 169 (1998) 84–87. [PMID: 9396840]
2.  Reisch, C.R., Moran, M.A. and Whitman, W.B. Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J. Bacteriol. 190 (2008) 8018–8024. [DOI] [PMID: 18849431]
3.  Schuller, D.J., Reisch, C.R., Moran, M.A., Whitman, W.B. and Lanzilotta, W.N. Structures of dimethylsulfoniopropionate-dependent demethylase from the marine organism Pelagibacter ubique. Protein Sci. 21 (2012) 289–298. [DOI] [PMID: 22162093]
[EC 2.1.1.269 created 2013]
 
 
EC 2.6.1.88     Relevance: 34%
Accepted name: methionine transaminase
Reaction: L-methionine + a 2-oxo carboxylate = 4-(methylsulfanyl)-2-oxobutanoate + an L-amino acid
Other name(s): methionine-oxo-acid transaminase
Systematic name: L-methionine:2-oxo-acid aminotransferase
Comments: The enzyme is most active with L-methionine. It participates in the L-methionine salvage pathway from S-methyl-5′-thioadenosine, a by-product of polyamine biosynthesis. The enzyme from the bacterium Klebsiella pneumoniae can use several different amino acids as amino donor, with aromatic amino acids being the most effective [1]. The enzyme from the plant Arabidopsis thaliana is also a part of the chain elongation pathway in the biosynthesis of methionine-derived glucosinolates [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Heilbronn, J., Wilson, J. and Berger, B.J. Tyrosine aminotransferase catalyzes the final step of methionine recycling in Klebsiella pneumoniae. J. Bacteriol. 181 (1999) 1739–1747. [PMID: 10074065]
2.  Dolzan, M., Johansson, K., Roig-Zamboni, V., Campanacci, V., Tegoni, M., Schneider, G. and Cambillau, C. Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function. FEBS Lett. 571 (2004) 141–146. [DOI] [PMID: 15280032]
3.  Schuster, J., Knill, T., Reichelt, M., Gershenzon, J. and Binder, S. Branched-chain aminotransferase4 is part of the chain elongation pathway in the biosynthesis of methionine-derived glucosinolates in Arabidopsis. Plant Cell 18 (2006) 2664–2679. [DOI] [PMID: 17056707]
[EC 2.6.1.88 created 2011]
 
 
EC 2.3.1.228     Relevance: 33.8%
Accepted name: isovaleryl-homoserine lactone synthase
Reaction: isovaleryl-CoA + S-adenosyl-L-methionine = CoA + S-methyl-5′-thioadenosine + N-isovaleryl-L-homoserine lactone
Glossary: S-methyl-5′-thioadenosine = 5′-deoxy-5′-(methylsulfanyl)adenosine
Other name(s): IV-HSL synthase; BjaI
Systematic name: isovaleryl-CoA:S-adenosyl-L-methionine isovaleryltranserase (lactone-forming, methylthioadenosine-releasing)
Comments: The enzyme, found in the bacterium Bradyrhizobium japonicum, does not accept isovaleryl-[acyl-carrier protein] as acyl donor (cf. EC 2.3.1.184, acyl-homoserine-lactone synthase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lindemann, A., Pessi, G., Schaefer, A.L., Mattmann, M.E., Christensen, Q.H., Kessler, A., Hennecke, H., Blackwell, H.E., Greenberg, E.P. and Harwood, C.S. Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum. Proc. Natl. Acad. Sci. USA 108 (2011) 16765–16770. [DOI] [PMID: 21949379]
[EC 2.3.1.228 created 2013]
 
 
EC 4.1.2.62     Relevance: 32.5%
Accepted name: 5-deoxyribulose 1-phosphate aldolase
Reaction: (1) 5-deoxy-D-ribulose 1-phosphate = glycerone phosphate + acetaldehyde
(2) S-methyl-5-thio-D-ribulose 1-phosphate = glycerone phosphate + (2-methylsulfanyl)acetaldehyde
Other name(s): 5-(methylthio)ribulose-1-phosphate aldolase; ald2 (gene name)
Systematic name: 5-deoxy-D-ribulose 1-phosphate acetaldehyde-lyase (glycerone-phosphate-forming)
Comments: The enzyme, originally characterized from the bacterium Rhodospirillum rubrum, is involved in degradation pathways for 5′-deoxyadenosine and S-methyl-5′-thioadenosine, which are formed from S-adenosyl-L-methionine (SAM, AdoMet) by radical SAM enzymes and other types of SAM-dependent enzymes, respectively. The enzyme requires a divalent metal cation, with Co2+ producing the highest activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  North, J.A., Miller, A.R., Wildenthal, J.A., Young, S.J. and Tabita, F.R. Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation. Proc. Natl. Acad. Sci. USA 114 (2017) E10455–E10464. [PMID: 29133429]
2.  North, J.A., Wildenthal, J.A., Erb, T.J., Evans, B.S., Byerly, K.M., Gerlt, J.A. and Tabita, F.R. A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. Mol. Microbiol. (2020) . [PMID: 31950558]
[EC 4.1.2.62 created 2020]
 
 
EC 2.6.1.62     Relevance: 31.8%
Accepted name: adenosylmethionine—8-amino-7-oxononanoate transaminase
Reaction: S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-(methylsulfanyl)-2-oxobutanoate + 7,8-diaminononanoate
Other name(s): 7,8-diaminonanoate transaminase; 7,8-diaminononanoate transaminase; DAPA transaminase (ambiguous); 7,8-diaminopelargonic acid aminotransferase; DAPA aminotransferase (ambiguous); 7-keto-8-aminopelargonic acid; diaminopelargonate synthase; 7-keto-8-aminopelargonic acid aminotransferase
Systematic name: S-adenosyl-L-methionine:8-amino-7-oxononanoate aminotransferase
Comments: A pyridoxal 5′-phosphate enzyme. S-adenosylhomocysteine can also act as donor.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37259-71-5
References:
1.  Izumi, Y., Sato, K., Tani, Y. and Ogata, K. Purification of 7-keto-8-aminopelargonic acid-7,8-diaminopelargonic acid aminotransferase, an enzyme involved in biotin synthesis, from Brevibacterium divaricatum. Agric. Biol. Chem. 37 (1973) 2683–2684.
2.  Izumi, Y., Sato, K., Tani, Y. and Ogata, K. 7,8-Diaminopelargonic acid aminotransferase, an enzyme involved in biotin synthesis by microorganisms. Agric. Biol. Chem. 39 (1975) 175–181.
3.  Stoner, G.L. and Eisenberg, M.A. Purification and properties of 7,8-diaminopelargonic acid aminotransferase. An enzyme in the biotin biosynthetic pathway. J. Biol. Chem. 250 (1973) 4029–4036. [PMID: 1092681]
[EC 2.6.1.62 created 1983]
 
 
EC 5.1.99.5     Relevance: 31.3%
Accepted name: hydantoin racemase
Reaction: D-5-monosubstituted hydantoin = L-5-monosubstituted hydantoin
Glossary: hydantoin = imidazolidine-2,4-dione
Other name(s): 5′-monosubstituted-hydantoin racemase; HyuA; HyuE
Systematic name: D-5-monosubstituted-hydantoin racemase
Comments: This enzyme, along with N-carbamoylase (EC 3.5.1.77 and EC 3.5.1.87) and hydantoinase, forms part of the reaction cascade known as the "hydantoinase process", which allows the total conversion of D,L-5-monosubstituted hydantoins into optically pure D- or L-amino acids [7]. The enzyme from Pseudomonas sp. (HyuE) has a preference for hydantoins with aliphatic substituents, e.g. D- and L-5-[2-(methylsulfanyl)ethyl]hydantoin, whereas that from Arthrobacter aurescens shows highest activity with arylalkyl substituents, especially 5-benzylhydantoin, at the 5-position [2]. In the enzyme from Sinorhizobium meliloti, Cys76 is responsible for recognition and proton retrieval of D-isomers, while Cys181 is responsible for L-isomer recognition and racemization [6].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Watabe, K., Ishikawa, T., Mukohara, Y. and Nakamura, H. Purification and characterization of the hydantoin racemase of Pseudomonas sp. strain NS671 expressed in Escherichia coli. J. Bacteriol. 174 (1992) 7989–7995. [DOI] [PMID: 1459947]
2.  Wiese, A., Pietzsch, M., Syldatk, C., Mattes, R. and Altenbuchner, J. Hydantoin racemase from Arthrobacter aurescens DSM 3747: heterologous expression, purification and characterization. J. Biotechnol. 80 (2000) 217–230. [DOI] [PMID: 10949312]
3.  Martínez-Rodríguez, S., Las Heras-Vázquez, F.J., Mingorance-Cazorla, L., Clemente-Jiménez, J.M. and Rodríguez-Vico, F. Molecular cloning, purification, and biochemical characterization of hydantoin racemase from the legume symbiont Sinorhizobium meliloti CECT 4114. Appl. Environ. Microbiol. 70 (2004) 625–630. [DOI] [PMID: 14711700]
4.  Martínez-Rodríguez, S., Las Heras-Vázquez, F.J., Clemente-Jiménez, J.M. and Rodríguez-Vico, F. Biochemical characterization of a novel hydantoin racemase from Agrobacterium tumefaciens C58. Biochimie 86 (2004) 77–81. [DOI] [PMID: 15016445]
5.  Suzuki, S., Onishi, N. and Yokozeki, K. Purification and characterization of hydantoin racemase from Microbacterium liquefaciens AJ 3912. Biosci. Biotechnol. Biochem. 69 (2005) 530–536. [DOI] [PMID: 15784981]
6.  Martínez-Rodríguez, S., Andújar-Sánchez, M., Neira, J.L., Clemente-Jiménez, J.M., Jara-Pérez, V., Rodríguez-Vico, F. and Las Heras-Vázquez, F.J. Site-directed mutagenesis indicates an important role of cysteines 76 and 181 in the catalysis of hydantoin racemase from Sinorhizobium meliloti. Protein Sci. 15 (2006) 2729–2738. [DOI] [PMID: 17132860]
7.  Altenbuchner, J., Siemann-Herzberg, M. and Syldatk, C. Hydantoinases and related enzymes as biocatalysts for the synthesis of unnatural chiral amino acids. Curr. Opin. Biotechnol. 12 (2001) 559–563. [DOI] [PMID: 11849938]
[EC 5.1.99.5 created 2008]
 
 


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