Escherichia coli K-12 substr. MG1655 Enzyme: phosphatidylglycerophosphatase C

Gene: pgpC Accession Numbers: EG11371 (EcoCyc), b2560, ECK2558

Synonyms: yfhB, PGPC-ase

Regulation Summary Diagram: ?

Regulation summary diagram for pgpC

E.coli contains three phosphatidylglycerophosphatases - PgpA, PgpB and PgpC - which catalyse the dephosphorylation of phosphatidylglycerol phosphate (PGP) to phosphatidylglycerol (PG), an essential phospholipid of the inner and outer membrane in E. coli. PgpA and PgpC appear to be specific for PGP [Icho83, Lu11] whereas PgpB is a multifunctional enzyme that is also active on undecaprenyl diphosphate, phosphatidicic acid and lysophosphatidic acid [El05, Dillon96].

pgpC is essential for growth in a pgpApgpB mutant [Lu11] but not in wild type cells [Baba06]. A pgpApgpBpgpC triple mutant is not viable but can be generated with a complementing plasmid containing any one of the three phosphatidylglycerophosphatases. A triple mutant complemented with any one of pgpA, pgpB or pgpC expressed on a temperature sensitive plasmid is viable at 30°C but not at 42°C [Lu11]. Lipid profiling of these strains showed accumulation of PGP and disappearance of PG when shifted from 30°C to 42°C [Lu11]. Overexpression of pgpC from a plasmid results in increased phosphatidylglycerophosphatase activity compared to the wild type [Lu11]. The activity of PgpC is temperature sensitive with significant reduction observed at 42°C compared to 30°C [Funk92, Lu11]. PgpC activity accounts for up to 50% of the total phosphatidylglycerophosphatase activity in wild type cells [Funk92].

PgpC contains a single predicted transmembrane segment and an active site that faces the cytoplasm [Lu11].

Locations: inner membrane

Map Position: [2,695,937 <- 2,696,572] (58.11 centisomes, 209°)
Length: 636 bp / 211 aa

Molecular Weight of Polypeptide: 24.439 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008421 , EchoBASE:EB1345 , EcoGene:EG11371 , EcoliWiki:b2560 , OU-Microarray:b2560 , PortEco:yfhB , Protein Model Portal:P0AD42 , RefSeq:NP_417055 , RegulonDB:EG11371 , String:511145.b2560 , UniProt:P0AD42

Relationship Links: InterPro:IN-FAMILY:IPR006435 , InterPro:IN-FAMILY:IPR023214

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for pgpC

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01, Lu11]
GO:0046474 - glycerophospholipid biosynthetic process Inferred from experiment [Lu11]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0006655 - phosphatidylglycerol biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0009395 - phospholipid catabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0016042 - lipid catabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008962 - phosphatidylglycerophosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, Lu11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005887 - integral component of plasma membrane Inferred from experiment Inferred by computational analysis [Lu11]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of macromolecules (cellular constituents) phospholipid

Essentiality data for pgpC 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 10-Apr-2008 by Keseler I , SRI International
Last-Curated ? 04-Jan-2011 by Mackie A , Macquarie University

Enzymatic reaction of: phosphatidylglycerophosphatase

Synonyms: phosphatidylglycerophosphate phosphohydrolase

EC Number:

an L-1-phosphatidylglycerol-phosphate + H2O <=> an L-1-phosphatidyl-glycerol + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: superpathway of phospholipid biosynthesis I (bacteria) , cardiolipin biosynthesis III , cardiolipin biosynthesis I

Cofactors or Prosthetic Groups: Mg2+ [Funk92]

Inhibitors (Unknown Mechanism): Hg2+ [Funk92] , NaF [Funk92] , phosphate [Funk92]

Kinetic Parameters:

Km (μM)
an L-1-phosphatidylglycerol-phosphate
[Dowhan92, BRENDA14]
an L-1-phosphatidylglycerol-phosphate
[Chang67, BRENDA14]

pH(opt): 7 [BRENDA14, Dowhan92]

Sequence Features

Protein sequence of phosphatidylglycerophosphatase C with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 34 -> 54
UniProt: Helical.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b2560 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11371; 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Chang67: Chang YY, Kennedy EP (1967). "Phosphatidyl glycerophosphate phosphatase." J Lipid Res 8(5);456-62. PMID: 4292860

Dillon96: Dillon DA, Wu WI, Riedel B, Wissing JB, Dowhan W, Carman GM (1996). "The Escherichia coli pgpB gene encodes for a diacylglycerol pyrophosphate phosphatase activity." J Biol Chem 271(48);30548-53. PMID: 8940025

Dowhan92: Dowhan W, Funk CR (1992). "Phosphatidylglycerophosphate phosphatase from Escherichia coli." Methods Enzymol 209;224-30. PMID: 1323035

El05: El Ghachi M, Derbise A, Bouhss A, Mengin-Lecreulx D (2005). "Identification of multiple genes encoding membrane proteins with undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia coli." J Biol Chem 280(19);18689-95. PMID: 15778224

Funk92: Funk CR, Zimniak L, Dowhan W (1992). "The pgpA and pgpB genes of Escherichia coli are not essential: evidence for a third phosphatidylglycerophosphate phosphatase." J Bacteriol 1992;174(1);205-13. PMID: 1309518

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.

Icho83: Icho T, Raetz CR (1983). "Multiple genes for membrane-bound phosphatases in Escherichia coli and their action on phospholipid precursors." J Bacteriol 153(2);722-30. PMID: 6296050

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

Lu11: Lu YH, Guan Z, Zhao J, Raetz CR (2011). "Three phosphatidylglycerol-phosphate phosphatases in the inner membrane of Escherichia coli." J Biol Chem 286(7);5506-18. PMID: 21148555

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

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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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