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Escherichia coli K-12 substr. MG1655 Enzyme: phosphatidylglycerophosphatase [multifunctional]



Gene: pgpB Accession Numbers: EG10705 (EcoCyc), b1278, ECK1273

Regulation Summary Diagram: ?

Summary:
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].

The main physiological activity of PgpB may be its diacylglycerol pyrophosphate (DGPP) phosphatase activity. Phosphatidate (PA), lyso-PA, and phosphatidylglycerophosphate are alternative substrates for the enzyme [Dillon96]. PgpB is unusual in that it appears to be located in both the outer and cytoplasmic membranes [Icho88]. Topological studies shows that PgpB is constituted by six transmembrane segments, with the N- and C-terminal regions localized in the cytoplasm and the active site located on the outer side of the cytoplasmic membrane [Touze08]. Its activity varies according to the subcellular location. PGP phosphatase activity is higher in the cytoplasmic membrane, while PA and LPA phosphatase activities are higher in the outer membrane [Icho88].

A pgpB null mutant has no obvious growth defect [Funk92]. Simultaneous inactivation of pgpB, bacA, and ybjG is lethal. Depletion of BacA in the triple mutant strain causes changes in cell morphology and lysis. Overexpression of pgpB, yeiU, bacA, and ybjG leads to increased undecaprenyl pyrophosphate (C55PP) phosphatase activity in crude membrane extracts. Expression of C55PP phosphatase activity from any one of the three genes pgpB, bacA, and ybjG appears to be sufficient for synthesis of undecaprenyl phosphate and survival [El05].

Locations: inner membrane, outer membrane

Map Position: [1,337,354 -> 1,338,118] (28.82 centisomes)
Length: 765 bp / 254 aa

Molecular Weight of Polypeptide: 29.021 kD (from nucleotide sequence), 28 kD (experimental) [Icho88 ]

pI: 10.3

Unification Links: ASAP:ABE-0004294 , CGSC:17641 , EchoBASE:EB0699 , EcoGene:EG10705 , EcoliWiki:b1278 , ModBase:P0A924 , OU-Microarray:b1278 , PortEco:pgpB , PR:PRO_000023526 , Protein Model Portal:P0A924 , RefSeq:NP_415794 , RegulonDB:EG10705 , String:511145.b1278 , UniProt:P0A924

Relationship Links: InterPro:IN-FAMILY:IPR000326 , InterPro:IN-FAMILY:IPR016118 , Pfam:IN-FAMILY:PF01569 , Smart:IN-FAMILY:SM00014

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009252 - peptidoglycan biosynthetic process Inferred from experiment [El05]
GO:0016311 - dephosphorylation Inferred by computational analysis Inferred from experiment [Icho83, GOA01a]
GO:0046474 - glycerophospholipid biosynthetic process Inferred from experiment [Icho83]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006655 - phosphatidylglycerol biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0009395 - phospholipid catabolic process Inferred by computational analysis [UniProtGOA11]
GO:0016042 - lipid catabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008962 - phosphatidylglycerophosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, Icho83]
GO:0050380 - undecaprenyl-diphosphatase activity Inferred from experiment Inferred by computational analysis [GOA01a, Touze08, El05]
GO:0000810 - diacylglycerol diphosphate phosphatase activity Inferred by computational analysis [GOA01a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0008195 - phosphatidate phosphatase activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Zhang07, Daley05, Touze08, Icho88]
GO:0005887 - integral component of plasma membrane Inferred from experiment [Touze08]
GO:0009279 - cell outer membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Icho88]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

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

Essentiality data for pgpB 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 05-Jan-2011 by Mackie A , Macquarie University


Enzymatic reaction of: phosphatidylglycerophosphatase

Synonyms: phosphatidylglycerophosphate phosphohydrolase B, PGPB-ase

EC Number: 3.1.3.27

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 of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for an L-1-phosphatidylglycerol-phosphate: 1-oleyl-2-lyso-phosphatidate [Icho88 ] , a 1,2-diacyl-sn-glycerol 3-phosphate [Icho88 ]

In Pathways: phospholipid biosynthesis I , cardiolipin biosynthesis III , cardiolipin biosynthesis I


Enzymatic reaction of: diacylglycerol pyrophosphate phosphatase

a 1,2-diacyl-sn-glycerol 3-diphosphate[periplasmic space] + H2O[periplasmic space] <=> a 1,2-diacyl-sn-glycerol 3-phosphate[periplasmic space] + phosphate[periplasmic space] + H+[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a 1,2-diacyl-sn-glycerol 3-diphosphate: an L-1-phosphatidylglycerol-phosphate [Dillon96 ] , a 1,2-diacyl-sn-glycerol 3-phosphate [Dillon96 ] , 1-oleyl-2-lyso-phosphatidate [Dillon96 ]

Summary:
The Vmax/Km for DGPP is 942, Vmax/Km for PA is 101 [Dillon96].

Activators (Unknown Mechanism): EDTA [Dillon96]

Inhibitors (Unknown Mechanism): Mn2+ [Dillon96]

pH(opt): 6.5 [Dillon96]


Enzymatic reaction of: undecaprenyl pyrophosphate phosphatase

EC Number: 3.6.1.27

di-trans,octa-cis-undecaprenyl diphosphate + H2O <=> di-trans,octa-cis-undecaprenyl phosphate + phosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Touze08]
 
Chain 2 -> 254
[UniProt12]
UniProt: Phosphatidylglycerophosphatase B.
Transmembrane-Region 9 -> 29
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 48 -> 68
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 72 -> 92
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 97 -> 105
[UniProt12]
UniProt: Phosphatase sequence motif I; Sequence Annotation Type: region of interest.
Transmembrane-Region 159 -> 179
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 160 -> 163
[UniProt12]
UniProt: Phosphatase sequence motif II; Sequence Annotation Type: region of interest.
Transmembrane-Region 185 -> 205
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Protein-Segment 200 -> 211
[UniProt12]
UniProt: Phosphatase sequence motif III; Sequence Annotation Type: region of interest.
Transmembrane-Region 211 -> 231
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1278 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10705; confirmed by SwissProt match.


References

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

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

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

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: 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

Icho88: Icho T (1988). "Membrane-bound phosphatases in Escherichia coli: sequence of the pgpB gene and dual subcellular localization of the pgpB product." J Bacteriol 1988;170(11);5117-24. PMID: 2846511

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

Touze08: Touze T, Blanot D, Mengin-Lecreulx D (2008). "Substrate specificity and membrane topology of Escherichia coli PgpB, an undecaprenyl pyrophosphate phosphatase." J Biol Chem 283(24);16573-83. PMID: 18411271

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

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

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

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

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Other References Related to Gene Regulation

Klein14: Klein G, Kobylak N, Lindner B, Stupak A, Raina S (2014). "Assembly of lipopolysaccharide in Escherichia coli requires the essential LapB heat shock protein." J Biol Chem. PMID: 24722986


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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 18.5 on Mon Dec 22, 2014, biocyc13.