MetaCyc Pathway: methylphosphonate degradation I
Inferred from experiment

Pathway diagram: methylphosphonate degradation I

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: carbon-phosphorus lyase pathway

Superclasses: Degradation/Utilization/AssimilationInorganic Nutrients MetabolismPhosphorus Compounds MetabolismMethylphosphonate Degradation

Some taxa known to possess this pathway include : Escherichia coli K-12 substr. MG1655

Expected Taxonomic Range: Bacteria

Organophosphonates are organic compounds containing C-PO(OH)2 or C-PO(OR)2 groups (where R can be either an alkyl or an aryl group). Phosphonates are quite common among different organisms, including both prokaryotes and eukaryotes. They occur primarily as components of phosphonolipids ( (2-aminoethyl)phosphonate is a common phosphonate constituent of phospholipids, analogous to O-phosphoethanolamine). In addition, phosphonates are constituents of polysaccharides, glycoproteins, glycolipids, and several antibiotics.

Many bacterial species can utilize organophosphonates as the sole source of phosphorous [Huang05]. Breaking the C-P bond, which is much more stable than the C-O-P phosphoester bonds of phosphates, requires special enzymes [Wanner94].

The utilization of methylphosphonate, the most common organophosphonate, has been studied in detail. The pathway begins with a nucleophilic attack of methylphosphonate on the anomeric carbon of ATP to form adenine and α-D-ribose-1-methylphosphonate-5-triphosphate, a reaction catalyzed by EC, α-D-ribose 1-methylphosphonate 5-triphosphate synthase, an enzyme complex composed of four polypeptides encoded by the phnG, phnH, phnI and phnL genes.

The pathway continues by phosphohydrolysis of pyrophosphate (catalyzed by EC, α-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase) to form α-D-ribose-1-methylphosphonate 5-phosphate, the substrate of the enzyme that actually cleaves the C-P bond. The cleavage, performed by EC, α-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase in a SAM-requiring radical-based reaction, produces 5-phospho-α-D-ribose 1,2-cyclic phosphate and methane [Kamat11].

In the majority of organophosphonate-degrading bacteria the cyclic phosphate is cleaved by EC, phosphoribosyl 1,2-cyclic phosphate phosphodiesterase to form α-D-ribose 1,5-bisphosphate [Podzelinska09]. In a small number of organisms a different enzyme produced D-ribofuranose 5-phosphate (see methylphosphonate degradation II).

Variants: methylphosphonate degradation II

Unification Links: EcoCyc:PWY0-1533

Created in EcoCyc 22-Nov-2011 by Keseler I, SRI International
Imported from EcoCyc 20-Dec-2011 by Keseler I, SRI International
Revised 30-Oct-2013 by Caspi R, SRI International


Huang05: Huang J, Su Z, Xu Y (2005). "The evolution of microbial phosphonate degradative pathways." J Mol Evol 61(5);682-90. PMID: 16245012

Kamat11: Kamat SS, Williams HJ, Raushel FM (2011). "Intermediates in the transformation of phosphonates to phosphate by bacteria." Nature 480(7378);570-3. PMID: 22089136

Makino91: Makino K, Kim SK, Shinagawa H, Amemura M, Nakata A (1991). "Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12." J Bacteriol 173(8);2665-72. PMID: 1840580

Podzelinska09: Podzelinska K, He SM, Wathier M, Yakunin A, Proudfoot M, Hove-Jensen B, Zechel DL, Jia Z (2009). "Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation." J Biol Chem 284(25);17216-26. PMID: 19366688

Wanner94: Wanner BL (1994). "Molecular genetics of carbon-phosphorus bond cleavage in bacteria." Biodegradation 5(3-4);175-84. PMID: 7765831

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Adams08: Adams MA, Luo Y, Hove-Jensen B, He SM, van Staalduinen LM, Zechel DL, Jia Z (2008). "Crystal structure of PhnH: an essential component of carbon-phosphorus lyase in Escherichia coli." J Bacteriol 190(3);1072-83. PMID: 17993513

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Chen90: Chen CM, Ye QZ, Zhu ZM, Wanner BL, Walsh CT (1990). "Molecular biology of carbon-phosphorus bond cleavage. Cloning and sequencing of the phn (psiD) genes involved in alkylphosphonate uptake and C-P lyase activity in Escherichia coli B." J Biol Chem 265(8);4461-71. PMID: 2155230

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

He11: He SM, Wathier M, Podzelinska K, Wong M, McSorley FR, Asfaw A, Hove-Jensen B, Jia Z, Zechel DL (2011). "Structure and mechanism of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway." Biochemistry 50(40);8603-15. PMID: 21830807

HoveJensen10: Hove-Jensen B, Rosenkrantz TJ, Zechel DL, Willemoes M (2010). "Accumulation of intermediates of the carbon-phosphorus lyase pathway for phosphonate degradation in phn mutants of Escherichia coli." J Bacteriol 192(1);370-4. PMID: 19854894

HoveJensen11: Hove-Jensen B, McSorley FR, Zechel DL (2011). "Physiological role of phnP-specified phosphoribosyl cyclic phosphodiesterase in catabolism of organophosphonic acids by the carbon-phosphorus lyase pathway." J Am Chem Soc 133(10);3617-24. PMID: 21341651

Jochimsen11: Jochimsen B, Lolle S, McSorley FR, Nabi M, Stougaard J, Zechel DL, Hove-Jensen B (2011). "Five phosphonate operon gene products as components of a multi-subunit complex of the carbon-phosphorus lyase pathway." Proc Natl Acad Sci U S A 108(28);11393-8. PMID: 21705661

Kamat13: Kamat SS, Burgos ES, Raushel FM (2013). "Potent inhibition of the C-P lyase nucleosidase PhnI by Immucillin-A triphosphate." Biochemistry 52(42);7366-8. PMID: 24111876

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Metcalf91: Metcalf WW, Wanner BL (1991). "Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi." J Bacteriol 173(2);587-600. PMID: 1846145

Metcalf93: Metcalf WW, Wanner BL (1993). "Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements." J Bacteriol 175(11);3430-42. PMID: 8388873

Metcalf93a: Metcalf WW, Wanner BL (1993). "Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli." Gene 129(1);27-32. PMID: 8335257

Podzelinska08: Podzelinska K, He S, Soares A, Zechel D, Hove-Jensen B, Jia Z (2008). "Expression, purification and preliminary diffraction studies of PhnP." Acta Crystallogr Sect F Struct Biol Cryst Commun 64(Pt 6);554-7. PMID: 18540074

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Ren15: Ren Z, Ranganathan S, Zinnel NF, Russell WK, Russell DH, Raushel FM (2015). "Subunit Interactions within the Carbon-Phosphorus Lyase Complex from Escherichia coli." Biochemistry 54(21);3400-11. PMID: 25954983

Seibert05: Seibert CM, Raushel FM (2005). "Structural and catalytic diversity within the amidohydrolase superfamily." Biochemistry 44(17);6383-91. PMID: 15850372

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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