Escherichia coli K-12 substr. MG1655 Polypeptide: PhnL subunit of methylphosphonate degradation complex
Inferred from experiment

Gene: phnL Accession Numbers: EG10721 (EcoCyc), b4096, ECK4089

Regulation Summary Diagram

Regulation summary diagram for phnL

Component of: methylphosphonate degradation complex (summary available)

PhnL, in a mixture together with PhnG, 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].

phnL is part of an operon that is phosphate starvation-inducible and required for use of phosphonate and phosphite as phosphorous sources [Yakovleva98, Metcalf91, Chen90a]. PhnL appears to be required for carbon-phosphorous lyase activity [Metcalf93]. A phnL mutant accumulates presumed intermediates of the C-P lyase pathway of phosphonate degradation [HoveJensen10].

Gene Citations: [Wanner92a]

Locations: inner membrane, cytosol

Map Position: [4,315,238 <- 4,315,918] (93.01 centisomes, 335°)
Length: 681 bp / 226 aa

Molecular Weight of Polypeptide: 24.705 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013421, CGSC:34529, EchoBASE:EB0715, EcoGene:EG10721, EcoliWiki:b4096, ModBase:P16679, OU-Microarray:b4096, PortEco:phnL, PR:PRO_000023537, Pride:P16679, Protein Model Portal:P16679, RefSeq:NP_418520, RegulonDB:EG10721, SMR:P16679, String:511145.b4096, UniProt:P16679

Relationship Links: InterPro:IN-FAMILY:IPR003439, InterPro:IN-FAMILY:IPR003593, InterPro:IN-FAMILY:IPR012701, InterPro:IN-FAMILY:IPR017871, InterPro:IN-FAMILY:IPR027417, Pfam:IN-FAMILY:PF00005, Prosite:IN-FAMILY:PS00211, Prosite:IN-FAMILY:PS50893, Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 23 (75 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for phnL

GO Terms:
Biological Process:
Inferred from experimentGO:0019700 - organic phosphonate catabolic process [Metcalf93]
Molecular Function:
Inferred by computational analysisGO:0000166 - nucleotide binding [UniProtGOA11a]
Inferred by computational analysisGO:0005524 - ATP binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016887 - ATPase activity [GOA01a]
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]
GO:0005829 - cytosol []
Inferred by computational analysisGO:0005886 - plasma membrane [DiazMejia09]

MultiFun Terms: metabolismmetabolism of other compoundsphosphorous metabolism

Essentiality data for phnL 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]

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)
         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 PhnL subunit of methylphosphonate degradation complex with features indicated

Feature Class Location Attached Group Citations Comment
Conserved-Region 2 -> 226  
Inferred by computational analysis[UniProt15]
UniProt: ABC transporter.
Pfam PF00005 24 -> 178  
Inferred by computational analysis[Finn14]
ABC_tran : ABC transporter
Nucleotide-Phosphate-Binding-Region 41 -> 48 ATP
Inferred by computational analysis[UniProt15]
UniProt: ATP.

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

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4096 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10721; 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

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

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."

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

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

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

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."

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

Jiang95a: 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

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

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

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

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137

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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 19.5 on Mon Nov 30, 2015, BIOCYC14B.