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Escherichia coli K-12 substr. MG1655 Protein: carbon-phosphorus lyase core complex
Inferred from experiment

Synonyms: C-P lyase core complex

Subunit composition of carbon-phosphorus lyase core complex = [PhnJ]2[PhnI]2[PhnH]2[PhnG]2
         carbon-phosphorus lyase core complex, PhnJ subunit = PhnJ (summary available)
         carbon-phosphorus lyase core complex, PhnI subunit = PhnI (summary available)
         carbon-phosphorus lyase core complex, PhnH subunit = PhnH (summary available)
         carbon-phosphorus lyase core complex, PhnG subunit = PhnG (summary available)

Summary:
The carbon-phosphorus lyase core complex consists of the PhnG, PhnH, PhnI and PhnJ subunits [Ren15]. A crystal structure of the complex has been solved at 1.7 Å resolution. A PhnI homodimer forms the core of the complex, serving as a hub for attachment of the other subunits [Seweryn15]. The core complex stably associates with PhnK [Jochimsen11, Ren15].

A zinc binding site shared between PhnI (His328 and His333) and PhnJ (His108) observed in the crystal structure is functionally important [Seweryn15].

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].

Citations: [He09]

Molecular Weight: 260.0 kD (experimental) [Jochimsen11]

Relationship Links: PDB:Structure:4XB6

Gene-Reaction Schematic

Gene-Reaction Schematic

Credits:
Created 07-Jul-2011 by Keseler I, SRI International
Last-Curated 26-Aug-2015 by Keseler I, SRI International


Component enzyme of carbon-phosphorus lyase core complex : carbon-phosphorus lyase core complex, PhnJ subunit

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:
Inferred from experimentInferred by computational analysisGO:0019700 - organic phosphonate catabolic process [GOA01a, Metcalf93]
Inferred by computational analysisGO:0042916 - alkylphosphonate transport [GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Ren15]
Inferred from experimentInferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a, GOA01a, Kamat11a]
Inferred from experimentInferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a, Kamat11a]
Inferred from experimentGO:0098848 - alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase activity [Kamat11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compoundsphosphorous metabolism

Unification Links: DIP:DIP-10489N, EcoliWiki:b4098, PR:PRO_000023536, Protein Model Portal:P16688, RefSeq:NP_418522, 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-phosphorus 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, Chen90a]. 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 LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of carbon-phosphorus lyase core complex: carbon-phosphorus lyase core complex, PhnI subunit

Synonyms: PhnI, PhnI subunit of methylphosphonate degradation complex

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:
Inferred from experimentGO:0019700 - organic phosphonate catabolic process [Metcalf93]
Inferred by computational analysisGO:0019634 - organic phosphonate metabolic process [GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Jochimsen11, Ren15]
Inferred from experimentInferred by computational analysisGO:0061693 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity [GOA01, Kamat11a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Cellular Component:
Inferred from experimentGO:0061694 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex [Kamat11a]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compoundsphosphorous metabolism

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

Immucillin-A triphosphate mimics the transition state structure for the nucleosidase reaction and inhibits PhnI activity [Kamat13].

PhnI is a component of the core carbon-phosphorus lyase complex [Jochimsen11, Ren15, Seweryn15].

phnI is part of an operon that is phosphate starvation inducible and required for use of phosphonate and phosphite as phosphorus sources [Yakovleva98, Metcalf91, Chen90a]. 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 enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of carbon-phosphorus lyase core complex: carbon-phosphorus lyase core complex, PhnH subunit

Synonyms: PhnH, PhnH subunit of methylphosphonate degradation complex

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:
Inferred from experimentGO:0019700 - organic phosphonate catabolic process [Metcalf93, Adams08]
Inferred by computational analysisGO:0019634 - organic phosphonate metabolic process [GOA01a]
Molecular Function:
Inferred from experimentGO:0042802 - identical protein binding [Jochimsen11, Adams08]
Inferred from experimentGO:0042803 - protein homodimerization activity [Adams08]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0061693 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity [GOA01]
Cellular Component:
Inferred from experimentGO:0061694 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex [Kamat11a]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compoundsphosphorous metabolism

Unification Links: DIP:DIP-10487N, EcoliWiki:b4100, PR:PRO_000023534, Protein Model Portal:P16686, RefSeq:NP_418524, SMR:P16686, 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, Chen90a]. 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 enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]

Subunit of carbon-phosphorus lyase core complex: carbon-phosphorus lyase core complex, PhnG subunit

Synonyms: PhnG, PhnG subunit of methylphosphonate degradation complex

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:
Inferred from experimentGO:0019700 - organic phosphonate catabolic process [Metcalf93]
Inferred by computational analysisGO:0015716 - organic phosphonate transport [GOA01a]
Inferred by computational analysisGO:0019634 - organic phosphonate metabolic process [GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Jochimsen11, Ren15, Rajagopala14]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0061693 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity [GOA01]
Cellular Component:
Inferred from experimentGO:0061694 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase complex [Kamat11a]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compoundsphosphorous metabolism

Unification Links: DIP:DIP-10486N, EcoliWiki:b4101, Protein Model Portal:P16685, RefSeq:NP_418525, 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, Chen90a]. 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 enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucoseYes 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

Chen90a: 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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

He09: He SM, Luo Y, Hove-Jensen B, Zechel DL (2009). "A fluorescent substrate for carbon-phosphorus lyase: towards the pathway for organophosphonate metabolism in bacteria." Bioorg Med Chem Lett 19(20);5954-7. PMID: 19733071

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

Kamat13: Kamat SS, Burgos ES, Raushel FM (2013). "Potent inhibition of the C-P lyase nucleosidase PhnI by Immucillin-A triphosphate." Biochemistry 52(42);7366-8. PMID: 24111876

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

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

Seweryn15: Seweryn P, Van LB, Kjeldgaard M, Russo CJ, Passmore LA, Hove-Jensen B, Jochimsen B, Brodersen DE (2015). "Structural insights into the bacterial carbon-phosphorus lyase machinery." Nature 525(7567);68-72. PMID: 26280334

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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