EC |
1.1.1.428 |
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] |
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|
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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] |
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|
|
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] |
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[EC 2.3.1.228 created 2013] |
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|
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, 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] |
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[EC 2.3.1.229 created 2013] |
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|
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] |
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|
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, PDB |
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] |
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[EC 2.4.2.44 created 2011] |
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EC
|
2.5.1.4
|
Transferred entry: | adenosylmethionine cyclotransferase. Now classified as EC 4.4.1.42, S-adenosyl-L-methionine lyase
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[EC 2.5.1.4 created 1965, deleted 2022] |
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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] |
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[EC 2.5.1.16 created 1972, modified 1982, modified 2013] |
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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] |
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|
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, 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] |
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[EC 2.5.1.23 created 1983, modified 2013] |
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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] |
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[EC 2.5.1.24 created 1984] |
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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] |
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|
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, 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 |
2.5.1.104 |
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, 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 |
2.5.1.108 |
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, PDB |
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, PDB |
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, 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 |
2.5.1.127 |
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, 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 |
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, PDB |
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 |
2.5.1.157 |
Accepted name: |
rRNA small subunit aminocarboxypropyltransferase |
Reaction: |
S-adenosyl-L-methionine + an N1-methylpseudouridine in rRNA = S-methyl-5′-thioadenosine + an N1-methyl-N3-[(3S)-3-aminocarboxypropyl]-pseudouridine in rRNA |
Other name(s): |
TSR3 (gene name) |
Systematic name: |
S-adenosyl-L-methionine:rRNA N1-methylpseudouridine 3-[(3S)-3-amino-3-carboxypropyl]transferase |
Comments: |
The enzyme, found in all eukaryotes and some archaea, catalyses the final step in production of the modified rRNA nucleotide N1-methyl-N3-[(3S)-aminocarboxypropyl]-pseudouridine (m1acp3ψ). This modified nucleotide is present in the small subunit of ribosomal RNA (18S in eukaryotes and 16S in archaea). cf. EC 2.5.1.114, tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase, and EC 2.5.1.108, 2-(3-amino-3-carboxypropyl)histidine synthase. |
Links to other databases: |
BRENDA, EXPASY, KEGG, MetaCyc |
References: |
1. |
Meyer, B., Wurm, J.P., Sharma, S., Immer, C., Pogoryelov, D., Kotter, P., Lafontaine, D.L., Wohnert, J. and Entian, K.D. Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans. Nucleic Acids Res. 44 (2016) 4304–4316. [DOI] [PMID: 27084949] |
|
[EC 2.5.1.157 created 2023] |
|
|
|
|
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, 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 |
2.8.4.6 |
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 |
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] |
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[EC 3.2.2.9 created 1972, modified 2004, modified 2020] |
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|
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] |
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[EC 3.2.2.16 created 1983, modified 2004] |
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EC
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3.3.1.2
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Transferred entry: | S-adenosyl-L-methionine hydrolase (L-homoserine-forming), now classified as EC 3.13.2.2, S-adenosyl-L-methionine hydrolase (L-homoserine-forming)
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[EC 3.3.1.2 created 1972, modified 1976, modified 2018, deleted 2022] |
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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, PDB |
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] |
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[EC 3.5.4.31 created 2011] |
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EC
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3.13.2.2
|
Transferred entry: | S-adenosyl-L-methionine hydrolase (L-homoserine-forming). Now classified as EC 4.4.1.42, S-adenosyl-L-methionine lyase
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[EC 3.13.2.2 created 1972 as EC 3.3.1.2, modified 1976, modified 2018, transferred 2022 to EC 3.13.2.2, deleted 2022] |
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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] |
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[EC 4.1.2.62 created 2020] |
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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] |
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[EC 4.4.1.14 created 1984, modified 2021] |
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EC |
4.4.1.42 |
Accepted name: |
S-adenosyl-L-methionine lyase |
Reaction: |
S-adenosyl-L-methionine = L-homoserine lactone + S-methyl-5′-thioadenosine |
Other name(s): |
T3p01 (gene name); SAM lyase; SAMase; adenosylmethionine cyclotransferase; S-adenosyl-L-methionine alkyltransferase (cyclizing) |
Systematic name: |
S-adenosyl-L-methionine S-methyl-5′-thioadenosine-lyase (cyclizing; L-homoserine lactone-forming) |
Comments: |
The enzyme was originally described from the yeast Saccharomyces cerevisiae (as EC 2.5.1.4), though it had not been well characterized. It was also incorrectly described from several bacteriophages as a hydrolase (EC 3.13.2.2). Later work has shown the bacteriophage enzyme to be a lyase. The enzyme binds its substrate at the border between two subunits of a trimeric complex in a position that prevents it from interacting with water. Instead, the substrate reacts with itself and splits in two. The product, L-homoserine lactone, spontaneously hydrolyses to L-homoserine. |
Links to other databases: |
BRENDA, EXPASY, KEGG, MetaCyc |
References: |
1. |
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] |
2. |
Mudd, S.H. Enzymatic cleavage of S-adenosylmethionine. J. Biol. Chem. 234 (1959) 87–92. [PMID: 13610898] |
3. |
Hausmann, R. Synthesis of an S-adenosylmethionine-cleaving enzyme in T3-infected Escherichia coli and its disturbance by co-infection with enzymatically incompetent bacteriophage. J. Virol. 1 (1967) 57–63. [DOI] [PMID: 4918233] |
4. |
Studier, F.W. and Movva, N.R. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J. Virol. 19 (1976) 136–145. [DOI] [PMID: 781304] |
5. |
Guo, X., Soderholm, A., Kanchugal, P., S., Isaksen, G.V., Warsi, O., Eckhard, U., Triguis, S., Gogoll, A., Jerlstrom-Hultqvist, J., Aqvist, J., Andersson, D.I. and Selmer, M. Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family. Elife 10 (2021) . [DOI] [PMID: 33567250] |
|
[EC 4.4.1.42 created 2022 (EC 2.5.1.4 created 1965, incorporated 2022, EC 3.13.2.2 created 1972 as EC 3.3.1.2, modified 1976, modified 2018, transferred 2022 to EC 3.13.2.2, incorporated 2022)] |
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|
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] |
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[EC 5.3.3.23 created 2021] |
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