Escherichia coli K-12 substr. MG1655 Polypeptide: carbon-phosphorus lyase core complex, PhnG subunit

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

Synonyms: PhnG subunit of methylphosphonate degradation complex

Regulation Summary Diagram

Regulation summary diagram for phnG

Component of:
carbon-phosphorus lyase core complex (extended summary available)
methylphosphonate degradation complex (summary available)

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].

Gene Citations: [Wanner92]

Locations: cytosol

Map Position: [4,321,244 <- 4,321,696] (93.1 centisomes, 335°)
Length: 453 bp / 150 aa

Molecular Weight of Polypeptide: 16.54 kD (from nucleotide sequence), 17.0 kD (experimental) [Jochimsen11]

Unification Links: ASAP:ABE-0013433, CGSC:34544, DIP:DIP-10486N, EchoBASE:EB0710, EcoGene:EG10716, EcoliWiki:b4101, OU-Microarray:b4101, PortEco:phnG, Protein Model Portal:P16685, RefSeq:NP_418525, RegulonDB:EG10716, String:511145.b4101, UniProt:P16685

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

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for phnG

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

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 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Curated 16-Mar-2006 by Shearer A, SRI International
Last-Curated 22-Nov-2011 by Keseler I, SRI International

Subunit of: 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)

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

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

Subunit of: methylphosphonate degradation complex

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

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].

Created 22-Nov-2011 by Keseler I, SRI International

Enzymatic reaction of: α-D-ribose 1-methylphosphonate 5-triphosphate synthase (methylphosphonate degradation complex)

Inferred from experiment

EC Number:

methylphosphonate + ATP → α-D-ribose-1-methylphosphonate-5-triphosphate + adenine

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: methylphosphonate degradation I

Kinetic Parameters:
Substrate Km (μM) kcat (sec-1) Citations
methylphosphonate 20.0 [Kamat11a]
ATP 56.0 [Kamat11a]

Sequence Features

Protein sequence of carbon-phosphorus lyase core complex, PhnG subunit with features indicated

Feature Class Location Citations Comment
Pfam PF06754 7 -> 147
Inferred by computational analysis[Finn14]
PhnG : Phosphonate metabolism protein PhnG [More...]
Extrinsic-Sequence-Variant 85
Author statement[UniProt15]
UniProt: In strain: B..

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Transcription Units

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4101 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10716; confirmed by SwissProt match.


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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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

Wanner92: Wanner BL, Metcalf WW (1992). "Molecular genetic studies of a 10.9-kb operon in Escherichia coli for phosphonate uptake and biodegradation." FEMS Microbiol Lett 79(1-3);133-9. PMID: 1335942

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

Other References Related to Gene Regulation

Jiang95: Jiang W, Metcalf WW, Lee KS, Wanner BL (1995). "Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2." J Bacteriol 1995;177(22);6411-21. PMID: 7592415

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

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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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