The Enzyme Database

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EC 1.1.1.309     
Accepted name: phosphonoacetaldehyde reductase (NADH)
Reaction: 2-hydroxyethylphosphonate + NAD+ = phosphonoacetaldehyde + NADH + H+
For diagram of phosphonate metabolism, click here
Other name(s): PhpC
Systematic name: 2-hydroxyethylphosphonate:NAD+ oxidoreductase
Comments: The enzyme from Streptomyces viridochromogenes catalyses a step in the biosynthesis of phosphinothricin tripeptide, the reduction of phosphonoacetaldehyde to 2-hydroxyethylphosphonate. The preferred cofactor is NADH, lower activity with NADPH [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Blodgett, J.A., Thomas, P.M., Li, G., Velasquez, J.E., van der Donk, W.A., Kelleher, N.L. and Metcalf, W.W. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nat. Chem. Biol. 3 (2007) 480–485. [DOI] [PMID: 17632514]
[EC 1.1.1.309 created 2011]
 
 
EC 1.13.11.72     
Accepted name: 2-hydroxyethylphosphonate dioxygenase
Reaction: 2-hydroxyethylphosphonate + O2 = hydroxymethylphosphonate + formate
For diagram of phosphonate metabolism, click here
Other name(s): HEPD; phpD (gene name); 2-hydroxyethylphosphonate:O2 1,2-oxidoreductase (hydroxymethylphosphonate forming)
Systematic name: 2-hydroxyethylphosphonate:oxygen 1,2-oxidoreductase (hydroxymethylphosphonate-forming)
Comments: Requires non-heme-Fe(II). Isolated from some bacteria including Streptomyces hygroscopicus and Streptomyces viridochromogenes. The pro-R hydrogen at C-2 of the ethyl group is retained by the formate ion. Any stereochemistry at C-1 of the ethyl group is lost. One atom from dioxygen is present in each product. Involved in phosphinothricin biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Cicchillo, R.M., Zhang, H., Blodgett, J.A., Whitteck, J.T., Li, G., Nair, S.K., van der Donk, W.A. and Metcalf, W.W. An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis. Nature 459 (2009) 871–874. [DOI] [PMID: 19516340]
2.  Whitteck, J.T., Malova, P., Peck, S.C., Cicchillo, R.M., Hammerschmidt, F. and van der Donk, W.A. On the stereochemistry of 2-hydroxyethylphosphonate dioxygenase. J. Am. Chem. Soc. 133 (2011) 4236–4239. [DOI] [PMID: 21381767]
3.  Peck, S.C., Cooke, H.A., Cicchillo, R.M., Malova, P., Hammerschmidt, F., Nair, S.K. and van der Donk, W.A. Mechanism and substrate recognition of 2-hydroxyethylphosphonate dioxygenase. Biochemistry 50 (2011) 6598–6605. [DOI] [PMID: 21711001]
[EC 1.13.11.72 created 2012]
 
 
EC 2.1.1.326     
Accepted name: N-acetyldemethylphosphinothricin P-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + N-acetyldemethylphosphinothricin + reduced acceptor = S-adenosyl-L-homocysteine + 5′-deoxyadenosine + L-methionine + N-acetylphosphinothricin + oxidized acceptor
Glossary: N-acetyldemethylphosphinothricin = (2S)-2-acetamido-4-phosphinatobutanoate
Other name(s): phpK (gene name); bcpD (gene name); P-methylase
Systematic name: S-adenosyl-L-methionine:N-acetyldemethylphosphinothricin P-methyltransferase
Comments: The enzyme was originally characterized from bacteria that produce the tripeptides bialaphos and phosalacine, which inhibit plant and bacterial glutamine synthetases. It is a radical S-adenosyl-L-methionine (SAM) enzyme that contains a [4Fe-4S] center and a methylcob(III)alamin cofactor. According to the proposed mechanism, the reduced iron-sulfur center donates an electron to SAM, resulting in homolytic cleavage of the carbon-sulfur bond to form a 5′-deoxyadenosyl radical that abstracts the hydrogen atom from the P-H bond of the substrate, forming a phosphinate-centered radical. This radical reacts with methylcob(III)alamin to produce the methylated product and cob(II)alamin, which is reduced by an unknown donor to cob(I)alamin. A potential route for restoring the latter back to methylcob(III)alamin is a nucleophilic attack on a second SAM molecule. The enzyme acts in vivo on N-acetyldemethylphosphinothricin-L-alanyl-L-alanine or N-acetyl-demethylphosphinothricin-L-alanyl-L-leucine, the intermediates in the biosynthesis of bialaphos and phosalacine, respectively. This transformation produces the only example of a carbon-phosphorus-carbon linkage known to occur in nature.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kamigiri, K., Hidaka, T., Imai, S., Murakami, T. and Seto, H. Studies on the biosynthesis of bialaphos (SF-1293) 12. C-P bond formation mechanism of bialaphos: discovery of a P-methylation enzyme. J. Antibiot. (Tokyo) 45 (1992) 781–787. [PMID: 1624380]
2.  Hidaka, T., Hidaka, M., Kuzuyama, T. and Seto, H. Sequence of a P-methyltransferase-encoding gene isolated from a bialaphos-producing Streptomyces hygroscopicus. Gene 158 (1995) 149–150. [DOI] [PMID: 7789803]
3.  Werner, W.J., Allen, K.D., Hu, K., Helms, G.L., Chen, B.S. and Wang, S.C. In vitro phosphinate methylation by PhpK from Kitasatospora phosalacinea. Biochemistry 50 (2011) 8986–8988. [DOI] [PMID: 21950770]
4.  Allen, K.D. and Wang, S.C. Spectroscopic characterization and mechanistic investigation of P-methyl transfer by a radical SAM enzyme from the marine bacterium Shewanella denitrificans OS217. Biochim. Biophys. Acta 1844 (2014) 2135–2144. [DOI] [PMID: 25224746]
5.  Hu, K., Werner, W.J., Allen, K.D. and Wang, S.C. Investigation of enzymatic C-P bond formation using multiple quantum HCP nuclear magnetic resonance spectroscopy. Magn. Reson. Chem. 53 (2015) 267–272. [DOI] [PMID: 25594737]
[EC 2.1.1.326 created 2016]
 
 
EC 2.3.1.183     
Accepted name: phosphinothricin acetyltransferase
Reaction: acetyl-CoA + phosphinothricin = CoA + N-acetylphosphinothricin
Glossary: phosphinothricin = glufosinate = 2-amino-4-[hydroxy(methyl)phosphoryl]butanoate
Other name(s): PAT (ambiguous); PPT acetyltransferase; Pt-N-acetyltransferase
Systematic name: acetyl-CoA:phosphinothricin N-acetyltransferase
Comments: The substrate phosphinothricin is used as a nonselective herbicide and is a potent inhibitor of EC 6.3.1.2, glutamine synthetase, a key enzyme of nitrogen metabolism in plants [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Botterman, J., Gosselé, V., Thoen, C. and Lauwereys, M. Characterization of phosphinothricin acetyltransferase and C-terminal enzymatically active fusion proteins. Gene 102 (1991) 33–37. [DOI] [PMID: 1864506]
2.  Dröge-Laser, W., Siemeling, U., Pühler, A. and Broer, I. The metabolites of the herbicide L-phosphinothricin (glufosinate) (identification, stability, and mobility in transgenic, herbicide-resistant, and untransformed plants). Plant Physiol. 105 (1994) 159–166. [PMID: 12232195]
[EC 2.3.1.183 created 2007]
 
 
EC 2.7.7.93     
Accepted name: phosphonoformate cytidylyltransferase
Reaction: CTP + phosphonoformate = CMP-5′-phosphonoformate + diphosphate
Other name(s): phpF (gene name)
Systematic name: CTP:phosphonoformate cytidylyltransferase
Comments: The enzyme, characterized from the bacterium Streptomyces viridochromogenes, participates in the biosynthesis of the herbicide antibiotic bialaphos. The enzyme from the bacterium Kitasatospora phosalacinea participates in the biosynthesis of the related compound phosalacine. Both compounds contain the nonproteinogenic amino acid L-phosphinothricin that acts as a potent inhibitor of EC 6.3.1.2, glutamine synthetase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Blodgett, J.A., Thomas, P.M., Li, G., Velasquez, J.E., van der Donk, W.A., Kelleher, N.L. and Metcalf, W.W. Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide. Nat. Chem. Biol. 3 (2007) 480–485. [DOI] [PMID: 17632514]
[EC 2.7.7.93 created 2016]
 
 
EC 4.2.1.166     
Accepted name: phosphinomethylmalate isomerase
Reaction: 2-(hydroxyphosphonoylmethyl)malate = 3-(hydroxyphosphonoylmethyl)malate (overall reaction)
(1a) 2-(hydroxyphosphonoylmethyl)malate = 2-(phosphinatomethylidene)butanedioate + H2O
(1b) 2-(phosphinatomethylidene)butanedioate + H2O = 3-(hydroxyphosphonoylmethyl)malate
Glossary: 2-(hydroxyphosphonoylmethyl)malate = 2-hydroxy-2-(hydroxyphosphonoylmethyl)butanedioate
3-(hydroxyphosphonoylmethyl)malate = 2-hydroxy-3-(hydroxyphosphonoylmethyl)butanedioate
Other name(s): pmi (gene name)
Systematic name: 2-(phosphinomethyl)malate hydro-lyase [3-(phosphinomethyl)malate-forming]
Comments: The enzyme, characterized from the bacterium Streptomyces viridochromogenes, is involved in bialaphos biosynthesis. The enzyme from the bacterium Kitasatospora phosalacinea participates in the biosynthesis of the related compound phosalacine. Both compounds contain the nonproteinogenic amino acid L-phosphinothricin that acts as a potent inhibitor of EC 6.3.1.2, glutamine synthetase. The similar enzyme EC 4.2.1.3, aconitate hydratase, cannot catalyse this reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Heinzelmann, E., Kienzlen, G., Kaspar, S., Recktenwald, J., Wohlleben, W. and Schwartz, D. The phosphinomethylmalate isomerase gene pmi, encoding an aconitase-like enzyme, is involved in the synthesis of phosphinothricin tripeptide in Streptomyces viridochromogenes. Appl. Environ. Microbiol. 67 (2001) 3603–3609. [DOI] [PMID: 11472937]
[EC 4.2.1.166 created 2016]
 
 
EC 6.2.1.67     
Accepted name: L-alanine—[L-alanyl-carrier protein] ligase
Reaction: ATP + L-alanine + holo-[L-alanyl-carrier protein] = AMP + diphosphate + L-alanyl-[L-alanyl-carrier protein] (overall reaction)
(1a) ATP + L-alanine = diphosphate + (L-alanyl)adenylate
(1b) (L-alanyl)adenylate + holo-[L-alanyl-carrier protein] = AMP + L-alanyl-[L-alanyl-carrier protein]
Other name(s): ambB (gene name); phsB (gene name)
Systematic name: L-alanine:[L-alanyl-carrier protein] ligase (AMP-forming)
Comments: The adenylation domain of the enzyme catalyses the activation of L-alanine to (L-alanyl)adenylate, followed by the transfer of the activated compound to the free thiol of a phosphopantetheine arm of a peptidyl-carrier protein domain. The peptidyl-carrier protein domain may be part of the same protein, or of a different protein. This activity is often found as part of a larger non-ribosomal peptide synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Schwartz, D., Grammel, N., Heinzelmann, E., Keller, U. and Wohlleben, W. Phosphinothricin tripeptide synthetases in Streptomyces viridochromogenes Tu494. Antimicrob. Agents Chemother. 49 (2005) 4598–4607. [DOI] [PMID: 16251301]
2.  Rojas Murcia, N., Lee, X., Waridel, P., Maspoli, A., Imker, H.J., Chai, T., Walsh, C.T. and Reimmann, C. The Pseudomonas aeruginosa antimetabolite L -2-amino-4-methoxy-trans-3-butenoic acid (AMB) is made from glutamate and two alanine residues via a thiotemplate-linked tripeptide precursor. Front. Microbiol. 6:170 (2015). [DOI] [PMID: 25814981]
[EC 6.2.1.67 created 2021]
 
 


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