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MetaCyc Polypeptide: PhnI subunit of methylphosphonate degradation complex

Gene: phnI Accession Numbers: EG10718 (MetaCyc), b4099, ECK4092

Species: Escherichia coli K-12 substr. MG1655

Component of:
methylphosphonate degradation complex (summary available)
predicted carbon-phosphorous lyase complex (summary available)

Summary:
The PhnI protein alone has nucleosidase activity, producing D-ribose-5-triphosphate and the free base from GTP and ATP. However, in a mixture together with PhnG, PhnH and PhnL, it catalyzes the nucleophilic attack of methylphosphonate on the anomeric carbon of ATP to form adenine and α-D-ribose-1-methylphosphonate-5-triphosphate [Kamat11a].

PhnI was also found to be a component of a protein complex that was thought to function as a carbon-phosphorous lyase [Jochimsen11].

phnI is part of an operon that is phosphate starvation inducible and required for use of phosphonate and phosphite as phosphorus sources [Yakovleva98, Metcalf91, Chen90]. phnI is required for use of phosphonates but not for uptake [Metcalf93]. A phnI mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

Locations: cytosol

Map Position: [4,317,622 <- 4,318,686]

Molecular Weight of Polypeptide: 38.853 kD (from nucleotide sequence), 43.0 kD (experimental) [Jochimsen11 ]

Unification Links: ASAP:ABE-0013428 , CGSC:34538 , DIP:DIP-10488N , EchoBASE:EB0712 , EcoGene:EG10718 , EcoliWiki:b4099 , OU-Microarray:b4099 , PortEco:phnI , PR:PRO_000023535 , Protein Model Portal:P16687 , RefSeq:NP_418523 , RegulonDB:EG10718 , String:511145.b4099 , UniProt:P16687

Relationship Links: InterPro:IN-FAMILY:IPR008773 , Pfam:IN-FAMILY:PF05861

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment [Metcalf93]
GO:0019634 - organic phosphonate metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

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


Subunit of: methylphosphonate degradation complex

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of methylphosphonate degradation complex = [PhnL][PhnH][PhnG][PhnI]
         PhnL subunit of methylphosphonate degradation complex = PhnL (summary available)
         PhnH subunit of methylphosphonate degradation complex = PhnH (summary available)
         PhnG subunit of methylphosphonate degradation complex = PhnG (summary available)
         PhnI subunit of methylphosphonate degradation complex = PhnI (summary available)

Summary:
A mixture of the purified PhnI, PhnG, PhnH and PhnL polypeptides catalyzes the nucleophilic attack of methylphosphonate on the anomeric carbon of ATP to form adenine and α-D-ribose-1-methylphosphonate-5-triphosphate. The subunit stoichiometry of this complex is unknown [Kamat11a].

Credits:
Created in EcoCyc 22-Nov-2011 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: methylphosphonate degradation complex

EC Number: 2.7.8.37

methylphosphonate + ATP <=> α-D-ribose-1-methylphosphonate-5-triphosphate + adenine

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.

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)
Citations
methylphosphonate
20.0
[Kamat11a]
ATP
56.0
[Kamat11a]


Subunit of: predicted carbon-phosphorous lyase complex

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of predicted carbon-phosphorous lyase complex = [PhnG]4[PhnH]2[PhnI]2[PhnK][PhnJ]2
         PhnG subunit of methylphosphonate degradation complex = PhnG (summary available)
         PhnH subunit of methylphosphonate degradation complex = PhnH (summary available)
         PhnI subunit of methylphosphonate degradation complex = PhnI (summary available)
         predicted carbon-phosphorous lyase subunit = PhnK (summary available)
         carbon-phosphorous lyase = PhnJ (summary available)

Summary:
The PhnGHIJK complex is predicted to perform a catalytic activity during utilization of phosphonates. However, using a variety of possible substrates and cofactors, no activity was found [Jochimsen11].

The utilization of phosphonates as the sole source of phosphate is "cryptic" in E. coli K-12 [Wanner90]. This is due to an 8 bp insertion in the phnE ORF that leads to a frameshift and premature termination of translation of PhnE. Spontanteous revertants have lost the 8 bp insertion [Makino91].

The genes encoding proteins of this complex are members of the 14-gene phnCDEFGHIJKLMNOP operon which is involved in phosphonate uptake and metabolism and is a member of the phosphate regulon [Metcalf91].

Molecular Weight: 260.0 kD (experimental) [Jochimsen11]

Credits:
Created in EcoCyc 07-Jul-2011 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Sequence Features

Feature Class Location Citations Comment
Extrinsic-Sequence-Variant 264
[UniProt10]
Alternate sequence: D; UniProt: (in strain: B);
Extrinsic-Sequence-Variant 351
[UniProt10]
Alternate sequence: K; UniProt: (in strain: B);

History:
10/20/97 Gene b4099 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10718; confirmed by SwissProt match.


References

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

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

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

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

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

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

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

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."

Wanner90: Wanner BL, Boline JA (1990). "Mapping and molecular cloning of the phn (psiD) locus for phosphonate utilization in Escherichia coli." J Bacteriol 172(3);1186-96. PMID: 2155195

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 Mon Dec 22, 2014, biocyc13.