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Escherichia coli K-12 substr. MG1655 Protein: predicted carbon-phosphorous lyase complex

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

Gene-Reaction Schematic: ?

Credits:
Created 07-Jul-2011 by Keseler I , SRI International
Last-Curated ? 08-Jul-2011 by Keseler I , SRI International


Subunit of predicted carbon-phosphorous lyase complex: predicted carbon-phosphorous lyase subunit

Synonyms: PhnK

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

Locations: cytosol

Sequence Length: 252 AAs

Molecular Weight: 27.831 kD (from nucleotide sequence)

Molecular Weight: 29.0 kD (experimental) [Jochimsen11]

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment [Metcalf93]
GO:0006200 - ATP catabolic process Inferred by computational analysis [GOA01a]
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

Unification Links: DIP:DIP-10490N , EcoliWiki:b4097 , ModBase:P16678 , Pride:P16678 , Protein Model Portal:P16678 , RefSeq:YP_026282 , 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

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 [Metcalf93]. A phnK mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

Essentiality data for phnK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Component enzyme of predicted carbon-phosphorous lyase complex : carbon-phosphorous lyase

Synonyms: PhnJ

Gene: phnJ Accession Numbers: EG10719 (EcoCyc), b4098, ECK4091

Locations: cytosol

Sequence Length: 281 AAs

Molecular Weight: 31.845 kD (from nucleotide sequence)

Molecular Weight: 38.0 kD (experimental) [Jochimsen11]

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Metcalf93]
GO:0042916 - alkylphosphonate transport Inferred by computational analysis [GOA01a]
Molecular Function: GO:0016829 - lyase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Kamat11a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Kamat11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Unification Links: DIP:DIP-10489N , EcoliWiki:b4098 , PR:PRO_000023536 , Protein Model Portal:P16688 , RefSeq:NP_418522 , String:511145.b4098 , UniProt:P16688

Relationship Links: InterPro:IN-FAMILY:IPR010306 , Pfam:IN-FAMILY:PF06007

Catalyzes:
α-D-ribose-1-methylphosphonate 5-phosphate → 5-phospho-α-D-ribose 1,2-cyclic phosphate + methane

Summary:
PhnJ is a radical SAM enzyme that catalyzes the cleavage of α-D-ribose-1-methylphosphonate 5-phosphate (PRPn) to 5-phospho-α-D-ribose 1,2-cyclic phosphate (PRcP). Activity requires anaerobic reconstitution of a [4Fe-4S] cluster and the presence of dithionite [Kamat11a].

PhnJ was also found to be a component of a protein complex that was thought to catalyze the carbon-phosphorous lyase reaction [Jochimsen11].

phnJ is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90]. PhnJ appears to be required for carbon-phosphorous lyase activity [Metcalf93]. A phnJ mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

Essentiality data for phnJ knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of predicted carbon-phosphorous lyase complex: PhnI subunit of methylphosphonate degradation complex

Synonyms: PhnI

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

Locations: cytosol

Sequence Length: 354 AAs

Molecular Weight: 38.853 kD (from nucleotide sequence)

Molecular Weight: 43.0 kD (experimental) [Jochimsen11]

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment [Metcalf93]
GO:0019634 - organic phosphonate metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Unification Links: DIP:DIP-10488N , EcoliWiki:b4099 , PR:PRO_000023535 , Protein Model Portal:P16687 , RefSeq:NP_418523 , String:511145.b4099 , UniProt:P16687

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

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].

Essentiality data for phnI knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of predicted carbon-phosphorous lyase complex: PhnH subunit of methylphosphonate degradation complex

Synonyms: PhnH

Gene: phnH Accession Numbers: EG10717 (EcoCyc), b4100, ECK4093

Locations: cytosol

Sequence Length: 194 AAs

Molecular Weight: 21.027 kD (from nucleotide sequence)

Molecular Weight: 28.0 kD (experimental) [Jochimsen11]

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment [Metcalf93, Adams08]
GO:0019634 - organic phosphonate metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0042802 - identical protein binding Inferred from experiment [Adams08]
GO:0042803 - protein homodimerization activity Inferred from experiment [Adams08]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Unification Links: DIP:DIP-10487N , EcoliWiki:b4100 , PR:PRO_000023534 , Protein Model Portal:P16686 , RefSeq:NP_418524 , SMR:P16686 , String:511145.b4100 , UniProt:P16686

Relationship Links: InterPro:IN-FAMILY:IPR008772 , PDB:Structure:2FSU , Pfam:IN-FAMILY:PF05845

Summary:
PhnH, in a mixture together with PhnG, PhnL and PhnI, catalyzes the nucleophilic attack of methylphosphonate on the anomeric carbon of ATP to form adenine and α-D-ribose-1-methylphosphonate-5-triphosphate [Kamat11a].

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

phnH is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90]. PhnH is essential for C-P bond cleavage [Metcalf93, Adams08]. A phnH mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

A crystal structure of PhnH has been solved at 1.77 Å resolution. The purified protein is a dimer in solution [Adams08].

Essentiality data for phnH knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of predicted carbon-phosphorous lyase complex: PhnG subunit of methylphosphonate degradation complex

Synonyms: PhnG

Gene: phnG Accession Numbers: EG10716 (EcoCyc), b4101, ECK4094

Locations: cytosol

Sequence Length: 150 AAs

Molecular Weight: 16.54 kD (from nucleotide sequence)

Molecular Weight: 17.0 kD (experimental) [Jochimsen11]

GO Terms:

Biological Process: GO:0019700 - organic phosphonate catabolic process Inferred from experiment [Metcalf93]
GO:0015716 - organic phosphonate transport Inferred by computational analysis [GOA01a]
GO:0019634 - organic phosphonate metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

Unification Links: DIP:DIP-10486N , EcoliWiki:b4101 , Protein Model Portal:P16685 , RefSeq:NP_418525 , String:511145.b4101 , UniProt:P16685

Relationship Links: InterPro:IN-FAMILY:IPR009609 , Pfam:IN-FAMILY:PF06754

Summary:
PhnG, in a mixture together with PhnL, PhnH and PhnI, catalyzes the nucleophilic attack of methylphosphonate on the anomeric carbon of ATP to form adenine and α-D-ribose-1-methylphosphonate-5-triphosphate [Kamat11a].

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

phnG is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90]. PhnG appears to be required for carbon-phosphorous lyase activity [Metcalf93]. A phnG mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

Essentiality data for phnG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

References

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

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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 1991;173(8);2665-12. 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 1991;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

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

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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
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