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MetaCyc Polypeptide: predicted carbon-phosphorous lyase subunit

Gene: phnK Accession Numbers: EG10720 (MetaCyc), b4097, ECK4090

Species: Escherichia coli K-12 substr. MG1655

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

Summary:
PhnK is a component of a protein complex that may be a carbon-phosphorous lyase [Jochimsen11].

phnK is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Metcalf91, Chen90]. PhnK appears to be required for carbon-phosphorous lyase activity [Metcalf93a]. A phnK mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

Locations: cytosol

Map Position: [4,316,029 <- 4,316,787]

Molecular Weight of Polypeptide: 27.831 kD (from nucleotide sequence), 29.0 kD (experimental) [Jochimsen11 ]

Unification Links: ASAP:ABE-0013424 , CGSC:34532 , DIP:DIP-10490N , EchoBASE:EB0714 , EcoGene:EG10720 , EcoliWiki:b4097 , ModBase:P16678 , OU-Microarray:b4097 , PortEco:phnK , Pride:P16678 , Protein Model Portal:P16678 , RefSeq:YP_026282 , RegulonDB:EG10720 , SMR:P16678 , String:511145.b4097 , UniProt:P16678

Relationship Links: InterPro:IN-FAMILY:IPR003439 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR012700 , InterPro:IN-FAMILY:IPR013563 , InterPro:IN-FAMILY:IPR017871 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00005 , Pfam:IN-FAMILY:PF08352 , Prosite:IN-FAMILY:PS00211 , Prosite:IN-FAMILY:PS50893 , Smart:IN-FAMILY:SM00382

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment [Metcalf93a]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
GO:0015833 - peptide transport Inferred by computational analysis [GOA01a]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016887 - ATPase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Credits:
Imported from EcoCyc 20-Dec-2011 by Caspi R , SRI International


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 27-Jan-2015 by Paley S , SRI International


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 6 -> 246
[UniProt09]
UniProt: ABC transporter;
Nucleotide-Phosphate-Binding-Region 38 -> 45
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;
Sequence-Conflict 47
[Burland95, UniProt10a]
UniProt: (in Ref. 3; AAA96996);

History:
10/20/97 Gene b4097 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10720; confirmed by SwissProt match.


References

Burland95: Burland V, Plunkett G, Sofia HJ, Daniels DL, Blattner FR (1995). "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes." Nucleic Acids Res 23(12);2105-19. PMID: 7610040

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

GOA01a: 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

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

Metcalf93a: 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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: 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


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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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