Escherichia coli K-12 substr. MG1655 Polypeptide: PhnH subunit of methylphosphonate degradation complex

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

Regulation Summary Diagram: ?

Regulation summary diagram for phnH

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

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].

Gene Citations: [Wanner92a]

Locations: cytosol

Map Position: [4,318,686 <- 4,319,270] (93.08 centisomes, 335°)
Length: 585 bp / 194 aa

Molecular Weight of Polypeptide: 21.027 kD (from nucleotide sequence), 28.0 kD (experimental) [Jochimsen11 ]

Unification Links: ASAP:ABE-0013430 , CGSC:34541 , DIP:DIP-10487N , EchoBASE:EB0711 , EcoGene:EG10717 , EcoliWiki:b4100 , OU-Microarray:b4100 , PortEco:phnH , PR:PRO_000023534 , Protein Model Portal:P16686 , RefSeq:NP_418524 , RegulonDB:EG10717 , SMR:P16686 , String:511145.b4100 , UniProt:P16686

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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for phnH

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]
GO:0061693 - alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism metabolism of other compounds phosphorous metabolism

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 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 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: methylphosphonate degradation complex

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)

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: methylphosphonate degradation complex

EC Number:

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

Kinetic Parameters:

Km (μM)
kcat (sec-1)

Subunit of: 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)

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]

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

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4100 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10717.


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."

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

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

Wanner92a: 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
Page generated by SRI International Pathway Tools version 19.0 on Wed Oct 7, 2015, biocyc13.