The Enzyme Database

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EC 2.3.1.184     
Accepted name: acyl-homoserine-lactone synthase
Reaction: an acyl-[acyl-carrier protein] + S-adenosyl-L-methionine = an [acyl-carrier protein] + S-methyl-5′-thioadenosine + an N-acyl-L-homoserine lactone
For diagram of reaction, click here
Other name(s): acyl-homoserine lactone synthase; acyl homoserine lactone synthase; acyl-homoserinelactone synthase; acylhomoserine lactone synthase; AHL synthase; AHS; AHSL synthase; AhyI; AinS; AinS protein; autoinducer synthase; autoinducer synthesis protein rhlI; EsaI; ExpISCC1; ExpISCC3065; LasI; LasR; LuxI; LuxI protein; LuxM; N-acyl homoserine lactone synthase; RhlI; YspI ; acyl-[acyl carrier protein]:S-adenosyl-L-methionine acyltranserase (lactone-forming, methylthioadenosine-releasing)
Systematic name: acyl-[acyl-carrier protein]:S-adenosyl-L-methionine acyltranserase (lactone-forming, methylthioadenosine-releasing)
Comments: Acyl-homoserine lactones (AHLs) are produced by a number of bacterial species and are used by them to regulate the expression of virulence genes in a process known as quorum-sensing. Each bacterial cell has a basal level of AHL and, once the population density reaches a critical level, it triggers AHL-signalling which, in turn, initiates the expression of particular virulence genes [5]. N-(3-Oxohexanoyl)-[acyl-carrier protein] and hexanoyl-[acyl-carrier protein] are the best substrates [1]. The fatty-acyl substrate is derived from fatty-acid biosynthesis through acyl-[acyl-carrier protein] rather than from fatty-acid degradation through acyl-CoA [1]. S-Adenosyl-L-methionine cannot be replaced by methionine, S-adenosylhomocysteine, homoserine or homoserine lactone [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 176023-66-8
References:
1.  Schaefer, A.L., Val, D.L., Hanzelka, B.L., Cronan, J.E., Jr. and Greenberg, E.P. Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. Proc. Natl. Acad. Sci. USA 93 (1996) 9505–9509. [DOI] [PMID: 8790360]
2.  Watson, W.T., Murphy, F.V., 4th, Gould, T.A., Jambeck, P., Val, D.L., Cronan, J.E., Jr., Beck von Bodman, S. and Churchill, M.E. Crystallization and rhenium MAD phasing of the acyl-homoserinelactone synthase EsaI. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 1945–1949. [PMID: 11717525]
3.  Chakrabarti, S. and Sowdhamini, R. Functional sites and evolutionary connections of acylhomoserine lactone synthases. Protein Eng. 16 (2003) 271–278. [PMID: 12736370]
4.  Hanzelka, B.L., Parsek, M.R., Val, D.L., Dunlap, P.V., Cronan, J.E., Jr. and Greenberg, E.P. Acylhomoserine lactone synthase activity of the Vibrio fischeri AinS protein. J. Bacteriol. 181 (1999) 5766–5770. [PMID: 10482519]
5.  Parsek, M.R., Val, D.L., Hanzelka, B.L., Cronan, J.E., Jr. and Greenberg, E.P. Acyl homoserine-lactone quorum-sensing signal generation. Proc. Natl. Acad. Sci. USA 96 (1999) 4360–4365. [DOI] [PMID: 10200267]
6.  Ulrich, R.L. Quorum quenching: enzymatic disruption of N-acylhomoserine lactone-mediated bacterial communication in Burkholderia thailandensis. Appl. Environ. Microbiol. 70 (2004) 6173–6180. [DOI] [PMID: 15466564]
7.  Gould, T.A., Schweizer, H.P. and Churchill, M.E. Structure of the Pseudomonas aeruginosa acyl-homoserinelactone synthase LasI. Mol. Microbiol. 53 (2004) 1135–1146. [DOI] [PMID: 15306017]
8.  Raychaudhuri, A., Jerga, A. and Tipton, P.A. Chemical mechanism and substrate specificity of RhlI, an acylhomoserine lactone synthase from Pseudomonas aeruginosa. Biochemistry 44 (2005) 2974–2981. [DOI] [PMID: 15723540]
9.  Gould, T.A., Herman, J., Krank, J., Murphy, R.C. and Churchill, M.E. Specificity of acyl-homoserine lactone synthases examined by mass spectrometry. J. Bacteriol. 188 (2006) 773–783. [DOI] [PMID: 16385066]
[EC 2.3.1.184 created 2007]
 
 
EC 2.3.1.228     
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 2.3.1.229     
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
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 2.4.2.28     
Accepted name: S-methyl-5′-thioadenosine phosphorylase
Reaction: S-methyl-5′-thioadenosine + phosphate = adenine + S-methyl-5-thio-α-D-ribose 1-phosphate
For diagram of methionine salvage, click here
Other name(s): 5′-deoxy-5′-methylthioadenosine phosphorylase; MTA phosphorylase; MeSAdo phosphorylase; MeSAdo/Ado phosphorylase; methylthioadenosine phosphorylase; methylthioadenosine nucleoside phosphorylase; 5′-methylthioadenosine:phosphate methylthio-D-ribosyl-transferase; S-methyl-5-thioadenosine phosphorylase; S-methyl-5-thioadenosine:phosphate S-methyl-5-thio-α-D-ribosyl-transferase
Systematic name: S-methyl-5′-thioadenosine:phosphate S-methyl-5-thio-α-D-ribosyl-transferase
Comments: Also acts on 5′-deoxyadenosine and other analogues having 5′-deoxy groups.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 61970-06-7
References:
1.  Carteni-Farina, M., Oliva, A., Romeo, G., Napolitano, G., De Rosa, M., Gambacorta, A. and Zappia, V. 5′-Methylthioadenosine phosphorylase from Caldariella acidophila. Purification and properties. Eur. J. Biochem. 101 (1979) 317–324. [DOI] [PMID: 118001]
2.  Garbers, D.L. Demonstration of 5′-methylthioadenosine phosphorylase activity in various rat tissues. Some properties of the enzyme from rat lung. Biochim. Biophys. Acta 523 (1978) 82–93. [DOI] [PMID: 415762]
3.  Pegg, A.E. and Williams-Ashman, H.G. Phosphate-stimulated breakdown of 5′-methylthioadenosine by rat ventral prostate. Biochem. J. 115 (1969) 241–247. [PMID: 5378381]
[EC 2.4.2.28 created 1983]
 
 
EC 2.4.2.44     
Accepted name: S-methyl-5′-thioinosine phosphorylase
Reaction: S-methyl-5′-thioinosine + phosphate = hypoxanthine + S-methyl-5-thio-α-D-ribose 1-phosphate
Other name(s): MTIP; MTI phosphorylase; methylthioinosine phosphorylase
Systematic name: S-methyl-5′-thioinosine:phosphate S-methyl-5-thio-α-D-ribosyl-transferase
Comments: No activity with S-methyl-5′-thioadenosine. The catabolism of of 5′-methylthioadenosine in Pseudomonas aeruginosa involves deamination to S-methyl-5′-thioinosine (EC 3.5.4.31, S-methyl-5′-thioadenosine deaminase) and phosphorolysis to hypoxanthine [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Guan, R., Ho, M.C., Almo, S.C. and Schramm, V.L. Methylthioinosine phosphorylase from Pseudomonas aeruginosa. Structure and annotation of a novel enzyme in quorum sensing. Biochemistry 50 (2011) 1247–1254. [DOI] [PMID: 21197954]
[EC 2.4.2.44 created 2011]
 
 
EC 2.5.1.4     
Accepted name: adenosylmethionine cyclotransferase
Reaction: S-adenosyl-L-methionine = S-methyl-5′-thioadenosine + 2-aminobutan-4-olide
Other name(s): adenosylmethioninase
Systematic name: S-adenosyl-L-methionine alkyltransferase (cyclizing)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9030-34-6
References:
1.  Mudd, S.H. Enzymatic cleavage of S-adenosylmethionine. J. Biol. Chem. 234 (1959) 87–92. [PMID: 13610898]
2.  Mudd, S.H. The mechanism of the enzymatic cleavage of S-adenosylmethionine to α-amino-γ-butyrolactone. J. Biol. Chem. 234 (1959) 1784–1786. [PMID: 13672964]
[EC 2.5.1.4 created 1965]
 
 
EC 2.5.1.16     
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 2.5.1.22     
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 2.5.1.23     
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
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 2.5.1.24     
Accepted name: discadenine synthase
Reaction: S-adenosyl-L-methionine + N6-(Δ2-isopentenyl)-adenine = S-methyl-5′-thioadenosine + discadenine
Glossary: discadenine = 3-(3-amino-3-carboxypropyl)-N6-(Δ2-isopentenyl)-adenine
Other name(s): discadenine synthetase; S-adenosyl-L-methionine:6-N-(Δ2-isopentenyl)-adenine 3-(3-amino-3-carboxypropyl)-transferase
Systematic name: S-adenosyl-L-methionine:N6-(Δ2-isopentenyl)-adenine 3-(3-amino-3-carboxypropyl)-transferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 74082-52-3
References:
1.  Taya, Y., Tanaka, Y. and Nishimura, S. Cell-free biosynthesis of discadenine, a spore germination inhibitor of Dictyostelium discoideum. FEBS Lett. 89 (1978) 326–328. [DOI] [PMID: 566219]
[EC 2.5.1.24 created 1984]
 
 
EC 2.5.1.25     
Accepted name: tRNA-uridine aminocarboxypropyltransferase
Reaction: S-adenosyl-L-methionine + a uridine in tRNA = S-methyl-5′-thioadenosine + a 3-[(3S)-3-amino-3-carboxypropyl]uridine in tRNA
Other name(s): S-adenosyl-L-methionine:tRNA-uridine 3-(3-amino-3-carboxypropyl)transferase; tapT (gene name); DTWD1 (gene name); DTWD2 (gene name); S-adenosyl-L-methionine:uridine47 in tRNAPhe 3-[(3S)-3-amino-3-carboxypropyl]transferase
Systematic name: S-adenosyl-L-methionine:uridine in tRNA 3-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: 3-[(3S)-3-amino-3-carboxypropyl]uridine (acp3U) is a highly conserved modification found in tRNA core region in bacteria and eukaryotes that confers thermal stability on tRNA. The enzyme from the bacterium Escherichia coli catalyses the modification of uridine47 in the V-loop of tRNAs for Arg2, Ile1, Ile2, Ile2v, Lys, Met, Phe, Val2A, and Val2B. The human homologs DTWD1 and DTWD2 are responsible for acp3U formation at positions 20 and 20a, respectively, in the D-loop of several cytoplasmic tRNAs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Nishimura, S., Taya, Y., Kuchino, Y. and Ohashi, Z. Enzymatic synthesis of 3-(3-amino-3-carboxypropyl)uridine in Escherichia coli phenylalanine transfer RNA: transfer of the 3-amino-acid-3-carboxypropyl group from S-adenosylmethionine. Biochem. Biophys. Res. Commun. 57 (1974) 702–708. [DOI] [PMID: 4597321]
2.  Takakura, M., Ishiguro, K., Akichika, S., Miyauchi, K. and Suzuki, T. Biogenesis and functions of aminocarboxypropyluridine in tRNA. Nat. Commun. 10:5542 (2019). [DOI] [PMID: 31804502]
3.  Meyer, B., Immer, C., Kaiser, S., Sharma, S., Yang, J., Watzinger, P., Weiss, L., Kotter, A., Helm, M., Seitz, H.M., Kotter, P., Kellner, S., Entian, K.D. and Wohnert, J. Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs. Nucleic Acids Res. 48 (2020) 1435–1450. [DOI] [PMID: 31863583]
[EC 2.5.1.25 created 1984, modified 2014, modified 2020]
 
 
EC 2.5.1.38     
Accepted name: isonocardicin synthase
Reaction: S-adenosyl-L-methionine + nocardicin G = S-methyl-5′-thioadenosine + isonocardicin C
For diagram of nocardicin biosynthesis, click here
Other name(s): nocardicin aminocarboxypropyltransferase; S-adenosyl-L-methionine:nocardicin-E 3-amino-3-carboxypropyltransferase
Systematic name: S-adenosyl-L-methionine:nocardicin-G 3-amino-3-carboxypropyltransferase
Comments: The enzyme, characterized from the bacterium Nocardia uniformis, is involved in the biosynthesis of the β-lactam antibiotic nocardicin A. The enzyme can act on nocardicin E, F, and G, producing isonocardicin A, B, and C, respectively. However, the in vivo substrate is believed to be nocardicin G [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 118246-74-5
References:
1.  Wilson, B.A., Bantia, S., Salituro, G.M., Reeve, A.M. and Townsend, C.A. Cell-free biosynthesis of nocardicin A from nocardicin E and S-adenosylmethionine. J. Am. Chem. Soc. 110 (1988) 8238–8239.
2.  Reeve, A.M., Breazeale, S.D. and Townsend, C.A. Purification, characterization, and cloning of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyltransferase in nocardicin biosynthesis. J. Biol. Chem. 273 (1998) 30695–30703. [DOI] [PMID: 9804844]
3.  Kelly, W.L. and Townsend, C.A. Mutational analysis of nocK and nocL in the nocardicin a producer Nocardia uniformis. J. Bacteriol. 187 (2005) 739–746. [DOI] [PMID: 15629944]
[EC 2.5.1.38 created 1992, modified 2016]
 
 
EC 2.5.1.43     
Accepted name: nicotianamine synthase
Reaction: 3 S-adenosyl-L-methionine = 3 S-methyl-5′-thioadenosine + nicotianamine
For diagram of nicotianamine biosynthesis, click here
Systematic name: S-adenosyl-L-methionine:S-adenosyl-L-methionine:S-adenosyl-L-methionine 3-amino-3-carboxypropyltransferase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 161515-44-2
References:
1.  Higuchi, K., Kanazawa, K., Nishizawa, N.-K., Chino, M., Mori, S. Purification and characterization of nicotianamine synthase from Fe-deficient barley root. Plant Soil 165 (1994) 173–179.
[EC 2.5.1.43 created 1999]
 
 
EC 2.5.1.79     
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
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 2.5.1.104     
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
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 2.5.1.108     
Accepted name: 2-(3-amino-3-carboxypropyl)histidine synthase
Reaction: S-adenosyl-L-methionine + L-histidine-[translation elongation factor 2] = S-methyl-5′-thioadenosine + 2-[(3S)-3-amino-3-carboxypropyl]-L-histidine-[translation elongation factor 2]
For diagram of diphthamide biosynthesis, click here
Other name(s): Dph2
Systematic name: S-adenosyl-L-methionine:L-histidine-[translation elongation factor 2] 2-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: A [4Fe-4S] enzyme that modifies a histidine residue of the translation elongation factor 2 (EF2) via a 3-amino-3-carboxypropyl radical. The enzyme is present in archae and eukaryotes but not in eubacteria. The enzyme is a member of the ’AdoMet radical’ (radical SAM) family and generates the 3-amino-3-carboxypropyl radical by an uncanonical clevage of S-adenosyl-L-methionine. The relevant histidine of EF2 is His715 in mammals, His699 in yeast and His600 in Pyrococcus horikoshii. Part of diphthamide biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Liu, S., Milne, G.T., Kuremsky, J.G., Fink, G.R. and Leppla, S.H. Identification of the proteins required for biosynthesis of diphthamide, the target of bacterial ADP-ribosylating toxins on translation elongation factor 2. Mol. Cell Biol. 24 (2004) 9487–9497. [DOI] [PMID: 15485916]
2.  Zhang, Y., Zhu, X., Torelli, A.T., Lee, M., Dzikovski, B., Koralewski, R.M., Wang, E., Freed, J., Krebs, C., Ealick, S.E. and Lin, H. Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme. Nature 465 (2010) 891–896. [DOI] [PMID: 20559380]
3.  Zhu, X., Dzikovski, B., Su, X., Torelli, A.T., Zhang, Y., Ealick, S.E., Freed, J.H. and Lin, H. Mechanistic understanding of Pyrococcus horikoshii Dph2, a [4Fe-4S] enzyme required for diphthamide biosynthesis. Mol. Biosyst. 7 (2011) 74–81. [DOI] [PMID: 20931132]
4.  Dong, M., Horitani, M., Dzikovski, B., Pandelia, M.E., Krebs, C., Freed, J.H., Hoffman, B.M. and Lin, H. Organometallic complex formed by an unconventional radical S-adenosylmethionine enzyme. J. Am. Chem. Soc. 138 (2016) 9755–9758. [DOI] [PMID: 27465315]
[EC 2.5.1.108 created 2013]
 
 
EC 2.5.1.114     
Accepted name: tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase
Reaction: S-adenosyl-L-methionine + 4-demethylwyosine37 in tRNAPhe = S-methyl-5′-thioadenosine + 7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: 4-demethylwyosine = imG-14 = 6-methyl-3-(β-D-ribofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
7-[(3S)-3-amino-3-carboxypropyl]-4-demethylwyosine = yW-89
Other name(s): TYW2; tRNA-yW synthesizing enzyme-2; TRM12 (gene name); taw2 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNAPhe (4-demethylwyosine37-C7)-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: The enzyme, which is found in all eukaryotes and in the majority of Euryarchaeota (but not in the Crenarchaeota), is involved in the hypermodification of the guanine nucleoside at position 37 of tRNA leading to formation of assorted wye bases. This modification is essential for translational reading-frame maintenance. The eukaryotic enzyme is involved in biosynthesis of the tricyclic base wybutosine, which is found only in tRNAPhe.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Umitsu, M., Nishimasu, H., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc. Natl. Acad. Sci. USA 106 (2009) 15616–15621. [DOI] [PMID: 19717466]
2.  Rodriguez, V., Vasudevan, S., Noma, A., Carlson, B.A., Green, J.E., Suzuki, T. and Chandrasekharappa, S.C. Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PLoS One 7:e39297 (2012). [DOI] [PMID: 22761755]
3.  de Crecy-Lagard, V., Brochier-Armanet, C., Urbonavicius, J., Fernandez, B., Phillips, G., Lyons, B., Noma, A., Alvarez, S., Droogmans, L., Armengaud, J. and Grosjean, H. Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol. Biol. Evol. 27 (2010) 2062–2077. [DOI] [PMID: 20382657]
[EC 2.5.1.114 created 2013]
 
 
EC 2.5.1.126     
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
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 2.5.1.127     
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 2.5.1.128     
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
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 2.5.1.152     
Accepted name: D-histidine 2-aminobutanoyltransferase
Reaction: S-adenosyl-L-methionine + D-histidine = N-[(3S)-3-amino-3-carboxypropyl]-D-histidine + S-methyl-5′-thioadenosine
For diagram of staphylopine biosynthesis, click here
Glossary: staphylopine = N-[(3S)-3-{[(1S)-1-carboxyethyl]amino}-3-carboxypropyl]-D-histidine
Other name(s): cntL (gene name)
Systematic name: S-adenosyl-L-methionine:D-histidine N-[(3S)-3-amino-3-carboxypropyl]-transferase
Comments: The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the metallophore staphylopine, which is involved in the acquisition of nickel, copper, and cobalt.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ghssein, G., Brutesco, C., Ouerdane, L., Fojcik, C., Izaute, A., Wang, S., Hajjar, C., Lobinski, R., Lemaire, D., Richaud, P., Voulhoux, R., Espaillat, A., Cava, F., Pignol, D., Borezee-Durant, E. and Arnoux, P. Biosynthesis of a broad-spectrum nicotianamine-like metallophore in Staphylococcus aureus. Science 352 (2016) 1105–1109. [PMID: 27230378]
[EC 2.5.1.152 created 2019]
 
 
EC 2.6.1.88     
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
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 3.2.2.9     
Accepted name: adenosylhomocysteine nucleosidase
Reaction: (1) S-adenosyl-L-homocysteine + H2O = S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine
(2) 5′-deoxyadenosine + H2O = 5-deoxy-D-ribose + adenine
(3) S-methyl-5′-thioadenosine + H2O = 5-(methylsulfanyl)-D-ribose + adenine
For diagram of autoinducer AI-2 biosynthesis, click here and for diagram of the methionine-salvage pathway, click here
Other name(s): S-adenosylhomocysteine hydrolase (ambiguous); S-adenosylhomocysteine nucleosidase; 5′-methyladenosine nucleosidase; S-adenosylhomocysteine/5′-methylthioadenosine nucleosidase; AdoHcy/MTA nucleosidase; MTN2 (gene name); mtnN (gene name)
Systematic name: S-adenosyl-L-homocysteine homocysteinylribohydrolase
Comments: This enzyme, found in bacteria and plants, acts on three different substrates. It is involved in the S-adenosyl-L-methionine (SAM, AdoMet) cycle, which recycles S-adenosyl-L-homocysteine back to SAM, and in salvage pathways for 5′-deoxyadenosine and S-methyl-5′-thioadenosine, which are produced from SAM during the action of many enzymes. cf. the plant enzyme EC 3.2.2.16, methylthioadenosine nucleosidase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9055-10-1
References:
1.  Duerre, J.A. A hydrolytic nucleosidase acting on S-adenosylhomocysteine and on 5-methylthioadenosine. J. Biol. Chem. 237 (1962) 3737–3741.
2.  Ferro, A.J., Barrett, A. and Shapiro, S.K. Kinetic properties and the effect of substrate analogues on 5′-methylthioadenosine nucleosidase from Escherichia coli. Biochim. Biophys. Acta 438 (1976) 487–494. [DOI] [PMID: 782530]
3.  Cornell, K.A., Swarts, W.E., Barry, R.D. and Riscoe, M.K. Characterization of recombinant Eschericha coli 5′-methylthioadenosine/S-adenosylhomocysteine nucleosidase: analysis of enzymatic activity and substrate specificity. Biochem. Biophys. Res. Commun. 228 (1996) 724–732. [PMID: 8941345]
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]
5.  Farrar, C.E., Siu, K.K., Howell, P.L. and Jarrett, J.T. Biotin synthase exhibits burst kinetics and multiple turnovers in the absence of inhibition by products and product-related biomolecules. Biochemistry 49 (2010) 9985–9996. [PMID: 20961145]
6.  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 3.2.2.9 created 1972, modified 2004, modified 2020]
 
 
EC 3.2.2.16     
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 3.3.1.2     
Accepted name: S-adenosyl-L-methionine hydrolase (L-homoserine-forming)
Reaction: S-adenosyl-L-methionine + H2O = L-homoserine + S-methyl-5′-thioadenosine
Glossary: S-methyl-L-methionine sulfonium salt = (S)-3-amino-3-carboxypropyldi(methyl)sulfonium salt
Other name(s): S-adenosylmethionine cleaving enzyme; methylmethionine-sulfonium-salt hydrolase; adenosylmethionine lyase; adenosylmethionine hydrolase; S-adenosylmethionine hydrolase; S-adenosyl-L-methionine hydrolase
Systematic name: S-adenosyl-L-methionine hydrolase (L-homoserine-forming)
Comments: Also hydrolyses S-methyl-L-methionine to dimethyl sulfide and homoserine. cf. EC 3.13.1.8, S-adenosyl-L-methionine hydrolase (adenosine-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37288-62-3
References:
1.  Mazelis, M., Levin, B. and Mallinson, N. Decomposition of methyl methionine sulfonium salts by a bacterial enzyme. Biochim. Biophys. Acta 105 (1965) 106–114. [PMID: 5849106]
[EC 3.3.1.2 created 1972, modified 1976, modified 2018]
 
 
EC 3.5.4.31     
Accepted name: S-methyl-5′-thioadenosine deaminase
Reaction: S-methyl-5′-thioadenosine + H2O = S-methyl-5′-thioinosine + NH3
Other name(s): MTA deaminase; 5-methylthioadenosine deaminase
Systematic name: S-methyl-5′-thioadenosine amidohydrolase
Comments: The enzyme from Thermotoga maritima also functions as S-adenosylhomocysteine deaminase (EC 3.5.4.28) and has some activity against adenosine. Adenosine 5′-phosphate and S-adenosyl-L-methionine (SAM) are not substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hermann, J.C., Marti-Arbona, R., Fedorov, A.A., Fedorov, E., Almo, S.C., Shoichet, B.K. and Raushel, F.M. Structure-based activity prediction for an enzyme of unknown function. Nature 448 (2007) 775–779. [DOI] [PMID: 17603473]
[EC 3.5.4.31 created 2011]
 
 
EC 4.1.2.62     
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 4.4.1.14     
Accepted name: 1-aminocyclopropane-1-carboxylate synthase
Reaction: S-adenosyl-L-methionine = 1-aminocyclopropane-1-carboxylate + S-methyl-5′-thioadenosine
For diagram of ethylene biosynthesis, click here
Glossary: S-methyl-5′-thioadenosine = 5′-deoxy-5′-(methylsulfanyl)adenosine
Other name(s): 1-aminocyclopropanecarboxylate synthase; 1-aminocyclopropane-1-carboxylic acid synthase; 1-aminocyclopropane-1-carboxylate synthetase; aminocyclopropanecarboxylic acid synthase; aminocyclopropanecarboxylate synthase; ACC synthase; S-adenosyl-L-methionine methylthioadenosine-lyase; S-adenosyl-L-methionine methylthioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Systematic name: S-adenosyl-L-methionine S-methyl-5′-thioadenosine-lyase (1-aminocyclopropane-1-carboxylate-forming)
Comments: A pyridoxal 5′-phosphate protein. The enzyme catalyses an α,γ-elimination.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 72506-68-4
References:
1.  Boller, T., Herner, R.C. and Kende, H. Assay for and enzymatic formation of an ethylene precursor, 1-aminocyclopropane-1-carboxylic acid. Planta 145 (1979) 293–303. [DOI] [PMID: 24317737]
2.  Yu, Y.-B., Adams, D.O. and Yang, S.F. 1-Aminocyclopropanecarboxylate synthase, a key enzyme in ethylene biosynthesis. Arch. Biochem. Biophys. 198 (1979) 280–296. [DOI] [PMID: 507845]
[EC 4.4.1.14 created 1984, modified 2021]
 
 
EC 5.3.3.23     
Accepted name: S-methyl-5-thioribulose 1-phosphate isomerase
Reaction: (1) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-xylulose 5-phosphate
(2) S-methyl-5-thio-D-ribulose 1-phosphate = S-methyl-1-thio-D-ribulose 5-phosphate
Other name(s): rlp (gene name); 5-methylthioribulose-1-phosphate isomerase (incorrect)
Systematic name: S-methyl-5-thio-D-ribulose 1-phosphate 1,3-isomerase
Comments: The enzyme, characterized from the bacterium Rhodospirillum rubrum, participates in methionine salvage from S-methyl-5′-thioadenosine. It is a RuBisCO-like protein (RLP) that is not capable of carbon fixation, and catalyses an isomerization reaction that converts S-methyl-5-thio-D-ribulose 1-phosphate to a 3:1 mixture of S-methyl-1-thioxylulose 5-phosphate and S-methyl-1-thioribulose 5-phosphate. The reaction is an overall 1,3-proton transfer, which likely consists of two 1,2-proton transfer events.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Imker, H.J., Singh, J., Warlick, B.P., Tabita, F.R. and Gerlt, J.A. Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum. Biochemistry 47 (2008) 11171–11173. [DOI] [PMID: 18826254]
2.  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]
[EC 5.3.3.23 created 2021]
 
 


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