Escherichia coli K-12 substr. MG1655 Polypeptide: phosphonate ABC transporter - ATP binding subunit

Gene: phnC Accession Numbers: EG10713 (EcoCyc), b4106, ECK4099

Regulation Summary Diagram: ?

Regulation summary diagram for phnC

Component of: phosphonate ABC transporter (extended summary available)

PhnC is the ATP binding component of the alkylphosphonate ABC transporter.

Gene Citations: [Metcalf91, Wanner92, Metcalf93]

Locations: inner membrane, cytosol

Map Position: [4,322,400 <- 4,323,188] (93.16 centisomes, 335°)
Length: 789 bp / 262 aa

Molecular Weight of Polypeptide: 29.431 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013444 , CGSC:34553 , EchoBASE:EB0707 , EcoGene:EG10713 , EcoliWiki:b4106 , ModBase:P16677 , OU-Microarray:b4106 , PortEco:phnC , PR:PRO_000023532 , Pride:P16677 , Protein Model Portal:P16677 , RefSeq:NP_418530 , RegulonDB:EG10713 , SMR:P16677 , String:511145.b4106 , UniProt:P16677

Relationship Links: InterPro:IN-FAMILY:IPR003439 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR012693 , InterPro:IN-FAMILY:IPR017871 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00005 , Prosite:IN-FAMILY:PS00211 , Prosite:IN-FAMILY:PS50893 , Prosite:IN-FAMILY:PS51249 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 23 (75 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for phnC

GO Terms:

Biological Process: GO:0042916 - alkylphosphonate transport Inferred from experiment [Metcalf93]
GO:0006810 - transport Inferred by computational analysis [UniProtGOA11a]
GO:0008152 - metabolic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0015716 - organic phosphonate transport Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0015748 - organophosphate ester transport Inferred by computational analysis [GOA06, GOA01, GOA01a]
Molecular Function: GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0015416 - organic phosphonate transmembrane-transporting ATPase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016887 - ATPase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0043190 - ATP-binding cassette (ABC) transporter complex Inferred by computational analysis [GOA06]

MultiFun Terms: cell processes adaptations starvation
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases ABC superfamily ATP binding cytoplasmic component

Essentiality data for phnC 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]

Subunit of: phosphonate ABC transporter

Synonyms: PhnCDE

Subunit composition of phosphonate ABC transporter = [PhnC]2[PhnE_1]2[PhnD]
         phosphonate ABC transporter - ATP binding subunit = PhnC (summary available)
         phosphonate ABC transporter - membrane subunit = PhnE_1 (summary available)
         phosphonate ABC transporter - periplasmic binding protein = PhnD (summary available)

The PhnCDE phosphonate transporter belongs to the ATP Binding Cassette superfamily [Saurin94]. Phosphonates (e.g. methylphosphonate and 2-aminoethylphosphonate) are compounds with direct carbon-phosphorus bonds rather than the carbon-oxygen-phosphorus bonds of phosphates. They are used as phosphorus sources in E. coli [Metcalf91]; however, the ability to use certain phosphonates appears to be limited by the specificity of the PhnCDE transporter [Wanner92a, Wanner92].

The phnCDEFGHIJKLMNOP operon is a member of the PHO regulon and is induced many hundred-fold during phosphate limitation. The phnCDE genes were characterized by Tn insertion mutational analyses. Experiments with knockout mutants suggested the phnCDE gene products are responsible for the uptake of phosphonates, phosphite, phosphate, and certain phosphate esters such as phosphoserine [Wanner92]. Based on sequence similarity and mutational analysis, PhnC is the ATP-binding protein, PhnD is the periplasmic binding protein, and PhnE is the integral membrane protein [Metcalf91].

Escherichia coli K-12 is considered cryptic in its utilization of phosphonates despite containing the entire phn gene cluster. However, AFLP analysis has shown E. coli K-12 contains a high frequency (10-4 to >10-2) reversible gene switch that provides phase variable phosphonate utilization [Iqbal04, Wanner90]. The genetic basis was traced to a removable 8-bp insertion in the phnE coding region which results in truncation of the gene product when inserted into the gene [Makino91]. Variants of E.coli K-12 have been isolated that are capable of using methylphosphonate (MePn), 2-aminoethylphosphonate (2-AEPn), aminomethylphosphonate (AMePn), 3-aminopropylphosphonate, ethylphosphonate (EPn), phenylphosphonate (PhPn), and propylphosphonate as their sole P source, and these variants were found to have deletions of the octameric insertion except during phenylphosphonate utilization in which the deletion could not be detected [Makino91, Iqbal04]. Phn+ variants could not be isolated in media containing N-butanephosphonate, 1-aminoethylphosphonate, 1-ethylphosphonate, a-aminopropylphosphonate, phosphonoacetate, phosphonoformate or phosphonomycin [Iqbal04]. PhnD binding assays have shown the binding affinity for 2-AEPn is highest among tested phosphonates followed by EPn, MePn, phosphonoacetate, PhPn, AMePn, and inorganic phosphate [Rizk06]. Activation of PhnE also confers the ability to utilize the organophosphates diisopropyl phosphate and 5-bromo-4-chloro-3-indoxyl phosphate-p-toluidine as sole P sources in K-12 strain JA221 [Elashvili98].

Citations: [Wackett87, RochetteEgly90, Metcalf90, Metcalf93, Metcalf93a, Yakovleva98]

Locations: inner membrane

GO Terms:

Cellular Component: GO:0005886 - plasma membrane

Enzymatic reaction of: aminoalkylphosphonate ABC transporter

Transport reaction diagram for aminoalkylphosphonate ABC transporter

Enzymatic reaction of: alkylphosphonate ABC transporter

EC Number:

Transport reaction diagram for alkylphosphonate ABC transporter

Alternative Products for an alkylphosphonate: diisopropyl phosphate [Elashvili98 ] , 3-phospho-L-serine [Wanner92 ] , phosphinate [Wanner92 ] , phosphate [Wanner92 ]

Sequence Features

Protein sequence of phosphonate ABC transporter - ATP binding subunit with features indicated

Feature Class Location Citations Comment
Conserved-Region 5 -> 253
UniProt: ABC transporter;
Nucleotide-Phosphate-Binding-Region 37 -> 44
UniProt: ATP; Non-Experimental Qualifier: potential;
Extrinsic-Sequence-Variant 60
UniProt: In strain: B..
Extrinsic-Sequence-Variant 87
UniProt: In strain: B..
Extrinsic-Sequence-Variant 127
UniProt: In strain: B..
Extrinsic-Sequence-Variant 255
UniProt: In strain: B..

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b4106 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10713; 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

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

Elashvili98: Elashvili I, Defrank JJ, Culotta VC (1998). "phnE and glpT genes enhance utilization of organophosphates in Escherichia coli K-12." Appl Environ Microbiol 64(7);2601-8. PMID: 9647836

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Iqbal04: Iqbal S, Parker G, Davidson H, Moslehi-Rahmani E, Robson RL (2004). "Reversible phase variation in the phnE gene, which is required for phosphonate metabolism in Escherichia coli K-12." J Bacteriol 186(18);6118-23. PMID: 15342581

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

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

Metcalf90: Metcalf WW, Steed PM, Wanner BL (1990). "Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions." J Bacteriol 172(6);3191-200. PMID: 2160940

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

Metcalf93a: Metcalf WW, Wanner BL (1993). "Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli." Gene 129(1);27-32. PMID: 8335257

Rizk06: Rizk SS, Cuneo MJ, Hellinga HW (2006). "Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates." Protein Sci 15(7);1745-51. PMID: 16751609

RochetteEgly90: Rochette-Egly C, Fromental C, Chambon P (1990). "General repression of enhanson activity by the adenovirus-2 E1A proteins." Genes Dev 4(1);137-50. PMID: 2155159

Saurin94: Saurin W, Dassa E (1994). "Sequence relationships between integral inner membrane proteins of binding protein-dependent transport systems: evolution by recurrent gene duplications." Protein Sci 1994;3(2);325-44. PMID: 8003968

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wackett87: Wackett LP, Wanner BL, Venditti CP, Walsh CT (1987). "Involvement of the phosphate regulon and the psiD locus in carbon-phosphorus lyase activity of Escherichia coli K-12." J Bacteriol 169(4);1753-6. PMID: 3549702

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

Wanner92a: Wanner BL (1992). "Genes for phosphonate biodegradation in Escherichia coli." SAAS Bull Biochem Biotechnol 5;1-6. PMID: 1368181

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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