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Protein

Phosphatidylglycerophosphatase B

Gene

pgpB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dephosphorylation of diacylglycerol diphosphate (DGPP) to phosphatidate (PA) and the subsequent dephosphorylation of PA to diacylglycerol (DAG). Also has undecaprenyl pyrophosphate phosphatase activity, required for the biosynthesis of the lipid carrier undecaprenyl phosphate. Can also use lysophosphatidic acid (LPA) and phosphatidylglycerophosphate as substrates. The pattern of activities varies according to subcellular location, PGP phosphatase activity is higher in the cytoplasmic membrane, whereas PA and LPA phosphatase activities are higher in the outer membrane. Activity is independent of a divalent cation ion and insensitive to inhibition by N-ethylmaleimide.4 Publications

Catalytic activityi

Phosphatidylglycerophosphate + H2O = phosphatidylglycerol + phosphate.
1,2-diacyl-sn-glycerol 3-diphosphate + H2O = 1,2-diacyl-sn-glycerol 3-phosphate + phosphate.
A 1,2-diacylglycerol 3-phosphate + H2O = a 1,2-diacyl-sn-glycerol + phosphate.
Ditrans,octacis-undecaprenyl diphosphate + H2O = ditrans,octacis-undecaprenyl phosphate + phosphate.

Enzyme regulationi

Inhibited by Mn2+ ions.

Kineticsi

  1. KM=530 µM for undecaprenyl pyrophosphate2 Publications
  2. KM=96 µM for farnesyl pyrophosphate2 Publications
  3. KM=80 µM for diacylglycerol pyrophosphate2 Publications
  4. KM=1700 µM for phosphatidate2 Publications
  1. Vmax=2167 nmol/min/mg enzyme with diacylglycerol pyrophosphate as substrate2 Publications
  2. Vmax=313 nmol/min/mg enzyme with phosphatidate as substrate2 Publications

pH dependencei

Optimum pH is 6.5 for DGPP phosphatase activity and 6.5-7.5 for undecaprenyl pyrophosphate phosphatase activity.2 Publications

Pathwayi: phosphatidylglycerol biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes phosphatidylglycerol from CDP-diacylglycerol.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgsA)
  2. Phosphatidylglycerophosphatase C (pgpC), Phosphatidylglycerophosphatase A (pgpA), Phosphatidylglycerophosphatase B (pgpB)
This subpathway is part of the pathway phosphatidylglycerol biosynthesis, which is itself part of Phospholipid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes phosphatidylglycerol from CDP-diacylglycerol, the pathway phosphatidylglycerol biosynthesis and in Phospholipid metabolism.

GO - Molecular functioni

  • diacylglycerol diphosphate phosphatase activity Source: UniProtKB-EC
  • phosphatidate phosphatase activity Source: UniProtKB-EC
  • phosphatidylglycerophosphatase activity Source: EcoCyc
  • undecaprenyl-diphosphatase activity Source: EcoCyc

GO - Biological processi

  • glycerophospholipid biosynthetic process Source: EcoCyc
  • peptidoglycan biosynthetic process Source: EcoCyc
  • phosphatidylglycerol biosynthetic process Source: UniProtKB-UniPathway
  • phospholipid catabolic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Lipid degradation, Lipid metabolism, Phospholipid degradation, Phospholipid metabolism

Enzyme and pathway databases

BioCyciEcoCyc:PGPPHOSPHAB-MONOMER.
ECOL316407:JW1270-MONOMER.
MetaCyc:PGPPHOSPHAB-MONOMER.
UniPathwayiUPA00084; UER00504.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphatidylglycerophosphatase B (EC:3.1.3.27)
Alternative name(s):
Diacylglycerol pyrophosphate phosphatase (EC:3.1.3.81)
Short name:
DGPP phosphatase
Phosphatidate phosphatase (EC:3.1.3.4)
Undecaprenyl pyrophosphate phosphatase (EC:3.6.1.27)
Undecaprenyl-diphosphatase
Gene namesi
Name:pgpB
Ordered Locus Names:b1278, JW1270
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10705. pgpB.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini2 – 8CytoplasmicSequence analysis7
Transmembranei9 – 29HelicalSequence analysisAdd BLAST21
Topological domaini30 – 47PeriplasmicSequence analysisAdd BLAST18
Transmembranei48 – 68HelicalSequence analysisAdd BLAST21
Topological domaini69 – 71CytoplasmicSequence analysis3
Transmembranei72 – 92HelicalSequence analysisAdd BLAST21
Topological domaini93 – 158PeriplasmicSequence analysisAdd BLAST66
Transmembranei159 – 179HelicalSequence analysisAdd BLAST21
Topological domaini180 – 184CytoplasmicSequence analysis5
Transmembranei185 – 205HelicalSequence analysisAdd BLAST21
Topological domaini206 – 210PeriplasmicSequence analysis5
Transmembranei211 – 231HelicalSequence analysisAdd BLAST21
Topological domaini232 – 254CytoplasmicSequence analysisAdd BLAST23

GO - Cellular componenti

  • cell outer membrane Source: EcoCyc
  • integral component of plasma membrane Source: EcoCyc
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Cell outer membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00000583622 – 254Phosphatidylglycerophosphatase BAdd BLAST253

Post-translational modificationi

The N-terminus is blocked.

Proteomic databases

PaxDbiP0A924.
PRIDEiP0A924.

Interactioni

Protein-protein interaction databases

BioGridi4262195. 212 interactors.
IntActiP0A924. 1 interactor.
STRINGi511145.b1278.

Structurei

Secondary structure

1254
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 25Combined sources23
Helixi35 – 46Combined sources12
Turni50 – 52Combined sources3
Helixi53 – 67Combined sources15
Helixi69 – 71Combined sources3
Helixi72 – 96Combined sources25
Turni97 – 99Combined sources3
Helixi105 – 113Combined sources9
Helixi118 – 122Combined sources5
Helixi126 – 139Combined sources14
Helixi145 – 154Combined sources10
Helixi162 – 178Combined sources17
Helixi179 – 181Combined sources3
Helixi184 – 203Combined sources20
Helixi209 – 234Combined sources26
Helixi241 – 254Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5JWYX-ray3.20A1-254[»]
ProteinModelPortaliP0A924.
SMRiP0A924.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni97 – 105Phosphatase sequence motif I9
Regioni160 – 163Phosphatase sequence motif II4
Regioni200 – 211Phosphatase sequence motif IIIAdd BLAST12

Sequence similaritiesi

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105EYK. Bacteria.
COG0671. LUCA.
HOGENOMiHOG000286191.
InParanoidiP0A924.
KOiK01096.
OMAiAQRLCGP.

Family and domain databases

Gene3Di1.20.144.10. 2 hits.
InterProiIPR000326. P_Acid_Pase_2/haloperoxidase.
[Graphical view]
PfamiPF01569. PAP2. 1 hit.
[Graphical view]
SMARTiSM00014. acidPPc. 1 hit.
[Graphical view]
SUPFAMiSSF48317. SSF48317. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A924-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRSIARRTAV GAALLLVMPV AVWISGWRWQ PGEQSWLLKA AFWVTETVTQ
60 70 80 90 100
PWGVITHLIL FGWFLWCLRF RIKAAFVLFA ILAAAILVGQ GVKSWIKDKV
110 120 130 140 150
QEPRPFVIWL EKTHHIPVDE FYTLKRAERG NLVKEQLAEE KNIPQYLRSH
160 170 180 190 200
WQKETGFAFP SGHTMFAASW ALLAVGLLWP RRRTLTIAIL LVWATGVMGS
210 220 230 240 250
RLLLGMHWPR DLVVATLISW ALVAVATWLA QRICGPLTPP AEENREIAQR

EQES
Length:254
Mass (Da):29,021
Last modified:July 19, 2005 - v1
Checksum:i9F4E6E88C34D458C
GO

Mass spectrometryi

Molecular mass is 30151 Da from positions 2 - 254. Determined by MALDI. Reported mass includes mass of a C-terminal His6 tag.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M23628 Unassigned DNA. Translation: AAB36618.1.
U00096 Genomic DNA. Translation: AAC74360.1.
AP009048 Genomic DNA. Translation: BAA14832.1.
PIRiA30193. PAECGB.
RefSeqiNP_415794.1. NC_000913.3.
WP_001256538.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74360; AAC74360; b1278.
BAA14832; BAA14832; BAA14832.
GeneIDi945863.
KEGGiecj:JW1270.
eco:b1278.
PATRICi32117818. VBIEscCol129921_1329.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M23628 Unassigned DNA. Translation: AAB36618.1.
U00096 Genomic DNA. Translation: AAC74360.1.
AP009048 Genomic DNA. Translation: BAA14832.1.
PIRiA30193. PAECGB.
RefSeqiNP_415794.1. NC_000913.3.
WP_001256538.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5JWYX-ray3.20A1-254[»]
ProteinModelPortaliP0A924.
SMRiP0A924.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262195. 212 interactors.
IntActiP0A924. 1 interactor.
STRINGi511145.b1278.

Proteomic databases

PaxDbiP0A924.
PRIDEiP0A924.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74360; AAC74360; b1278.
BAA14832; BAA14832; BAA14832.
GeneIDi945863.
KEGGiecj:JW1270.
eco:b1278.
PATRICi32117818. VBIEscCol129921_1329.

Organism-specific databases

EchoBASEiEB0699.
EcoGeneiEG10705. pgpB.

Phylogenomic databases

eggNOGiENOG4105EYK. Bacteria.
COG0671. LUCA.
HOGENOMiHOG000286191.
InParanoidiP0A924.
KOiK01096.
OMAiAQRLCGP.

Enzyme and pathway databases

UniPathwayiUPA00084; UER00504.
BioCyciEcoCyc:PGPPHOSPHAB-MONOMER.
ECOL316407:JW1270-MONOMER.
MetaCyc:PGPPHOSPHAB-MONOMER.

Miscellaneous databases

PROiP0A924.

Family and domain databases

Gene3Di1.20.144.10. 2 hits.
InterProiIPR000326. P_Acid_Pase_2/haloperoxidase.
[Graphical view]
PfamiPF01569. PAP2. 1 hit.
[Graphical view]
SMARTiSM00014. acidPPc. 1 hit.
[Graphical view]
SUPFAMiSSF48317. SSF48317. 2 hits.
ProtoNetiSearch...

Entry informationi

Entry nameiPGPB_ECOLI
AccessioniPrimary (citable) accession number: P0A924
Secondary accession number(s): P18201
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: November 2, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.