PGPB_ECOLI
ID PGPB_ECOLI Reviewed; 254 AA.
AC P0A924; P18201;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Phosphatidylglycerophosphatase B;
DE EC=3.1.3.27;
DE AltName: Full=Diacylglycerol pyrophosphate phosphatase;
DE Short=DGPP phosphatase;
DE EC=3.1.3.81;
DE AltName: Full=Phosphatidate phosphatase;
DE EC=3.1.3.4;
DE AltName: Full=Undecaprenyl pyrophosphate phosphatase;
DE EC=3.6.1.27;
DE AltName: Full=Undecaprenyl-diphosphatase;
GN Name=pgpB; OrderedLocusNames=b1278, JW1270;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 19-28, AND DUAL
RP SUBCELLULAR LOCATION.
RC STRAIN=K12 / CS520;
RX PubMed=2846511; DOI=10.1128/jb.170.11.5117-5124.1988;
RA Icho T.;
RT "Membrane-bound phosphatases in Escherichia coli: sequence of the pgpB gene
RT and dual subcellular localization of the pgpB product.";
RL J. Bacteriol. 170:5117-5124(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12;
RX PubMed=8940025; DOI=10.1074/jbc.271.48.30548;
RA Dillon D.A., Wu W.I., Riedel B., Wissing J.B., Dowhan W., Carman G.M.;
RT "The Escherichia coli pgpB gene encodes for a diacylglycerol pyrophosphate
RT phosphatase activity.";
RL J. Biol. Chem. 271:30548-30553(1996).
RN [6]
RP FUNCTION.
RX PubMed=15778224; DOI=10.1074/jbc.m412277200;
RA El Ghachi M., Derbise A., Bouhss A., Mengin-Lecreulx D.;
RT "Identification of multiple genes encoding membrane proteins with
RT undecaprenyl pyrophosphate phosphatase (UppP) activity in Escherichia
RT coli.";
RL J. Biol. Chem. 280:18689-18695(2005).
RN [7]
RP SUBCELLULAR LOCATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15919996; DOI=10.1126/science.1109730;
RA Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G.;
RT "Global topology analysis of the Escherichia coli inner membrane
RT proteome.";
RL Science 308:1321-1323(2005).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND MASS SPECTROMETRY.
RX PubMed=18411271; DOI=10.1074/jbc.m800394200;
RA Touze T., Blanot D., Mengin-Lecreulx D.;
RT "Substrate specificity and membrane topology of Escherichia coli PgpB, an
RT undecaprenyl pyrophosphate phosphatase.";
RL J. Biol. Chem. 283:16573-16583(2008).
RN [9]
RP FUNCTION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=21148555; DOI=10.1074/jbc.m110.199265;
RA Lu Y.H., Guan Z., Zhao J., Raetz C.R.;
RT "Three phosphatidylglycerol-phosphate phosphatases in the inner membrane of
RT Escherichia coli.";
RL J. Biol. Chem. 286:5506-5518(2011).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS).
RC STRAIN=B / BL21-DE3;
RX PubMed=24821770; DOI=10.1073/pnas.1403097111;
RA Fan J., Jiang D., Zhao Y., Liu J., Zhang X.C.;
RT "Crystal structure of lipid phosphatase Escherichia coli
RT phosphatidylglycerophosphate phosphatase B.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:7636-7640(2014).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN COMPLEX WITH INHIBITOR, AND
RP ACTIVITY REGULATION.
RX PubMed=27405756; DOI=10.1074/jbc.m116.737874;
RA Tong S., Lin Y., Lu S., Wang M., Bogdanov M., Zheng L.;
RT "Structural insight into substrate selection and catalysis of lipid
RT phosphate phosphatase PgpB in the cell membrane.";
RL J. Biol. Chem. 291:18342-18352(2016).
CC -!- FUNCTION: Catalyzes the dephosphorylation of diacylglycerol diphosphate
CC (DGPP) to phosphatidate (PA) and the subsequent dephosphorylation of PA
CC to diacylglycerol (DAG). Also has undecaprenyl pyrophosphate
CC phosphatase activity, required for the biosynthesis of the lipid
CC carrier undecaprenyl phosphate. Can also use lysophosphatidic acid
CC (LPA) and phosphatidylglycerophosphate as substrates. The pattern of
CC activities varies according to subcellular location, PGP phosphatase
CC activity is higher in the cytoplasmic membrane, whereas PA and LPA
CC phosphatase activities are higher in the outer membrane. Activity is
CC independent of a divalent cation ion and insensitive to inhibition by
CC N-ethylmaleimide. {ECO:0000269|PubMed:15778224,
CC ECO:0000269|PubMed:18411271, ECO:0000269|PubMed:21148555,
CC ECO:0000269|PubMed:8940025}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycero-3'-phosphate) +
CC H2O = 1,2-diacyl-sn-glycero-3-phospho-(1'-sn-glycerol) + phosphate;
CC Xref=Rhea:RHEA:33751, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:60110, ChEBI:CHEBI:64716; EC=3.1.3.27;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = a 1,2-diacyl-
CC sn-glycero-3-phosphate + H(+) + phosphate; Xref=Rhea:RHEA:27449,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58608, ChEBI:CHEBI:59996; EC=3.1.3.81;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 1,2-diacyl-sn-glycero-3-phosphate + H2O = a 1,2-diacyl-sn-
CC glycerol + phosphate; Xref=Rhea:RHEA:27429, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:17815, ChEBI:CHEBI:43474, ChEBI:CHEBI:58608; EC=3.1.3.4;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=di-trans,octa-cis-undecaprenyl diphosphate + H2O = di-
CC trans,octa-cis-undecaprenyl phosphate + H(+) + phosphate;
CC Xref=Rhea:RHEA:28094, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58405, ChEBI:CHEBI:60392; EC=3.6.1.27;
CC -!- ACTIVITY REGULATION: Inhibited by Mn(2+) ions. Inhibited by
CC phosphatidylethanolamine (PE) (PubMed:27405756).
CC {ECO:0000269|PubMed:27405756}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=530 uM for undecaprenyl pyrophosphate
CC {ECO:0000269|PubMed:18411271, ECO:0000269|PubMed:8940025};
CC KM=96 uM for farnesyl pyrophosphate {ECO:0000269|PubMed:18411271,
CC ECO:0000269|PubMed:8940025};
CC KM=80 uM for diacylglycerol pyrophosphate
CC {ECO:0000269|PubMed:18411271, ECO:0000269|PubMed:8940025};
CC KM=1700 uM for phosphatidate {ECO:0000269|PubMed:18411271,
CC ECO:0000269|PubMed:8940025};
CC Vmax=2167 nmol/min/mg enzyme with diacylglycerol pyrophosphate as
CC substrate {ECO:0000269|PubMed:18411271, ECO:0000269|PubMed:8940025};
CC Vmax=313 nmol/min/mg enzyme with phosphatidate as substrate
CC {ECO:0000269|PubMed:18411271, ECO:0000269|PubMed:8940025};
CC pH dependence:
CC Optimum pH is 6.5 for DGPP phosphatase activity and 6.5-7.5 for
CC undecaprenyl pyrophosphate phosphatase activity.
CC {ECO:0000269|PubMed:18411271, ECO:0000269|PubMed:8940025};
CC -!- PATHWAY: Phospholipid metabolism; phosphatidylglycerol biosynthesis;
CC phosphatidylglycerol from CDP-diacylglycerol: step 2/2.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane
CC {ECO:0000269|PubMed:15919996}; Multi-pass membrane protein
CC {ECO:0000269|PubMed:15919996}. Cell outer membrane
CC {ECO:0000269|PubMed:15919996}; Multi-pass membrane protein
CC {ECO:0000269|PubMed:15919996}.
CC -!- PTM: The N-terminus is blocked.
CC -!- MASS SPECTROMETRY: Mass=30151; Method=MALDI; Note=Reported mass
CC includes mass of a C-terminal His6 tag.;
CC Evidence={ECO:0000269|PubMed:18411271};
CC -!- MISCELLANEOUS: The enzyme active site contains a catalytic triad that
CC establishes a charge relay system. This catalytic triad is essential
CC for the dephosphorylation of LPA, PA, and sphingosine-1-phosphate, but
CC is not essential in its entirety for the dephosphorylation of PGP, the
CC nucleophilic histidine alone is sufficient to hydrolyze PGP.
CC {ECO:0000269|PubMed:27405756}.
CC -!- SIMILARITY: Belongs to the PA-phosphatase related phosphoesterase
CC family. {ECO:0000305}.
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DR EMBL; M23628; AAB36618.1; -; Unassigned_DNA.
DR EMBL; U00096; AAC74360.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14832.1; -; Genomic_DNA.
DR PIR; A30193; PAECGB.
DR RefSeq; NP_415794.1; NC_000913.3.
DR RefSeq; WP_001256538.1; NZ_STEB01000005.1.
DR PDB; 4PX7; X-ray; 3.20 A; A=2-254.
DR PDB; 5JWY; X-ray; 3.20 A; A=1-254.
DR PDBsum; 4PX7; -.
DR PDBsum; 5JWY; -.
DR AlphaFoldDB; P0A924; -.
DR SMR; P0A924; -.
DR BioGRID; 4262195; 215.
DR IntAct; P0A924; 1.
DR STRING; 511145.b1278; -.
DR PaxDb; P0A924; -.
DR PRIDE; P0A924; -.
DR EnsemblBacteria; AAC74360; AAC74360; b1278.
DR EnsemblBacteria; BAA14832; BAA14832; BAA14832.
DR GeneID; 66674897; -.
DR GeneID; 945863; -.
DR KEGG; ecj:JW1270; -.
DR KEGG; eco:b1278; -.
DR PATRIC; fig|1411691.4.peg.1003; -.
DR EchoBASE; EB0699; -.
DR eggNOG; COG0671; Bacteria.
DR HOGENOM; CLU_083863_0_0_6; -.
DR InParanoid; P0A924; -.
DR OMA; AWFLWCL; -.
DR PhylomeDB; P0A924; -.
DR BioCyc; EcoCyc:PGPPHOSPHAB-MON; -.
DR BioCyc; MetaCyc:PGPPHOSPHAB-MON; -.
DR BRENDA; 3.1.3.27; 2026.
DR UniPathway; UPA00084; UER00504.
DR PRO; PR:P0A924; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0009279; C:cell outer membrane; IMP:EcoCyc.
DR GO; GO:0005887; C:integral component of plasma membrane; IDA:EcoCyc.
DR GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR GO; GO:0000810; F:diacylglycerol diphosphate phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0008195; F:phosphatidate phosphatase activity; IEA:UniProtKB-EC.
DR GO; GO:0008962; F:phosphatidylglycerophosphatase activity; IMP:EcoCyc.
DR GO; GO:0050380; F:undecaprenyl-diphosphatase activity; IDA:EcoCyc.
DR GO; GO:0046474; P:glycerophospholipid biosynthetic process; IMP:EcoCyc.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IMP:EcoCyc.
DR GO; GO:0006655; P:phosphatidylglycerol biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0009395; P:phospholipid catabolic process; IEA:UniProtKB-KW.
DR InterPro; IPR036938; P_Acid_Pase_2/haloperoxi_sf.
DR InterPro; IPR000326; P_Acid_Pase_2/haloperoxidase.
DR Pfam; PF01569; PAP2; 1.
DR SMART; SM00014; acidPPc; 1.
DR SUPFAM; SSF48317; SSF48317; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Cell outer membrane;
KW Direct protein sequencing; Hydrolase; Lipid degradation; Lipid metabolism;
KW Membrane; Phospholipid degradation; Phospholipid metabolism;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT INIT_MET 1
FT /note="Removed"
FT CHAIN 2..254
FT /note="Phosphatidylglycerophosphatase B"
FT /id="PRO_0000058362"
FT TRANSMEM 2..24
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:24821770"
FT TOPO_DOM 25..54
FT /note="Periplasmic"
FT /evidence="ECO:0000305|PubMed:24821770"
FT TRANSMEM 55..66
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:24821770"
FT TOPO_DOM 67..71
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305|PubMed:24821770"
FT TRANSMEM 72..94
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:24821770"
FT TOPO_DOM 95..161
FT /note="Periplasmic"
FT /evidence="ECO:0000305|PubMed:24821770"
FT TRANSMEM 162..176
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:24821770"
FT TOPO_DOM 177..182
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305|PubMed:24821770"
FT TRANSMEM 183..202
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:24821770"
FT TOPO_DOM 203..208
FT /note="Periplasmic"
FT /evidence="ECO:0000305|PubMed:24821770"
FT TRANSMEM 209..232
FT /note="Helical"
FT /evidence="ECO:0000269|PubMed:24821770"
FT TOPO_DOM 233..254
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305|PubMed:24821770"
FT REGION 97..105
FT /note="Phosphatase sequence motif I"
FT /evidence="ECO:0000305"
FT REGION 160..163
FT /note="Phosphatase sequence motif II"
FT /evidence="ECO:0000305"
FT REGION 200..211
FT /note="Phosphatase sequence motif III"
FT /evidence="ECO:0000305"
FT ACT_SITE 163
FT /note="Proton donor; for a subset of substrates"
FT /evidence="ECO:0000269|PubMed:27405756"
FT ACT_SITE 207
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:27405756"
FT SITE 211
FT /note="Stabilizes the active site histidine for
FT nucleophilic attack"
FT /evidence="ECO:0000305|PubMed:27405756"
FT HELIX 3..25
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 35..46
FT /evidence="ECO:0007829|PDB:5JWY"
FT TURN 50..52
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 53..67
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 69..71
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 72..96
FT /evidence="ECO:0007829|PDB:5JWY"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 105..113
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 118..122
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 126..139
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 145..154
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 162..178
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 184..203
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 209..234
FT /evidence="ECO:0007829|PDB:5JWY"
FT HELIX 241..254
FT /evidence="ECO:0007829|PDB:5JWY"
SQ SEQUENCE 254 AA; 29021 MW; 9F4E6E88C34D458C CRC64;
MRSIARRTAV GAALLLVMPV AVWISGWRWQ PGEQSWLLKA AFWVTETVTQ PWGVITHLIL
FGWFLWCLRF RIKAAFVLFA ILAAAILVGQ GVKSWIKDKV QEPRPFVIWL EKTHHIPVDE
FYTLKRAERG NLVKEQLAEE KNIPQYLRSH WQKETGFAFP SGHTMFAASW ALLAVGLLWP
RRRTLTIAIL LVWATGVMGS RLLLGMHWPR DLVVATLISW ALVAVATWLA QRICGPLTPP
AEENREIAQR EQES
