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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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MetaCyc Enzyme: RPnTP hydrolase

Gene: phnM Accession Numbers: EG10722 (MetaCyc), b4095, ECK4088

Species: Escherichia coli K-12 substr. MG1655

Summary:
PhnM catalyzes hydrolysis of α-D-ribose-1-methylphosphonate-5-triphosphate, generating α-D-ribose-1-methylphosphonate 5-phosphate and pyrophosphate [Kamat11a]. PhnM is a member of the amidohydrolase superfamily [Seibert05].

phnM is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90c]. PhnM appeared to be required for carbon-phosphorous lyase activity [Metcalf93].

Locations: cytosol, inner membrane

Map Position: [4,314,105 <- 4,315,241]

Molecular Weight of Polypeptide: 42.01 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013419 , CGSC:34526 , EchoBASE:EB0716 , EcoGene:EG10722 , EcoliWiki:b4095 , ModBase:P16689 , OU-Microarray:b4095 , PortEco:phnM , Protein Model Portal:P16689 , RefSeq:NP_418519 , RegulonDB:EG10722 , SMR:P16689 , String:511145.b4095 , UniProt:P16689

Relationship Links: InterPro:IN-FAMILY:IPR011059 , InterPro:IN-FAMILY:IPR012696 , Pfam:IN-FAMILY:PF01979

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment Inferred by computational analysis [GOA01, Metcalf93]
Molecular Function: GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005886 - plasma membrane

MultiFun Terms: cell structure membrane
metabolism metabolism of other compounds phosphorous metabolism

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: RPnTP hydrolase

EC Number: 3.6.1.63

α-D-ribose-1-methylphosphonate-5-triphosphate + H2O <=> α-D-ribose-1-methylphosphonate 5-phosphate + diphosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for α-D-ribose-1-methylphosphonate-5-triphosphate: ribose triphosphate [Kamat11a ]

In Pathways: methylphosphonate degradation I

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
α-D-ribose-1-methylphosphonate-5-triphosphate
56.0
6.4
[Kamat11a]


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 318
[UniProt10]
Alternate sequence: E; UniProt: (in strain: B);

History:
10/20/97 Gene b4095 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10722; confirmed by SwissProt match.


References

Chen90c: 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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Kamat11a: Kamat SS, Williams HJ, Raushel FM (2011). "Intermediates in the transformation of phosphonates to phosphate by bacteria." Nature 480(7378);570-3. PMID: 22089136

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Yakovleva98: Yakovleva GM, Kim SK, Wanner BL (1998). "Phosphate-independent expression of the carbon-phosphorus lyase activity of Escherichia coli." Appl Microbiol Biotechnol 49(5);573-8. PMID: 9650256


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, BIOCYC13A.