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/Assimilation → Inorganic Nutrients Metabolism → Phosphorus Compounds Metabolism → Methylphosphonate Degradation|
Some taxa known to possess this pathway include : Escherichia coli K-12 substr. MG1655
Expected Taxonomic Range:
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 184.108.40.206, 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 220.127.116.11, 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 18.104.22.168, 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 22.214.171.124, 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
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
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
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
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
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
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
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