GLPQ_ECOLI
ID GLPQ_ECOLI Reviewed; 358 AA.
AC P09394;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1991, sequence version 2.
DT 03-AUG-2022, entry version 173.
DE RecName: Full=Glycerophosphodiester phosphodiesterase, periplasmic;
DE Short=Glycerophosphoryl diester phosphodiesterase, periplasmic;
DE EC=3.1.4.46;
DE Flags: Precursor;
GN Name=glpQ; OrderedLocusNames=b2239, JW2233;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 26-31.
RX PubMed=1851953; DOI=10.1007/bf00273621;
RA Tommassen J., Eiglmeier K., Cole S.T., Overduin P., Larson T.J., Boos W.;
RT "Characterization of two genes, glpQ and ugpQ, encoding glycerophosphoryl
RT diester phosphodiesterases of Escherichia coli.";
RL Mol. Gen. Genet. 226:321-327(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-9.
RC STRAIN=K12;
RX PubMed=3329281; DOI=10.1111/j.1365-2958.1987.tb01931.x;
RA Eiglmeier K., Boos W., Cole S.;
RT "Nucleotide sequence and transcriptional startpoint of the glpT gene of
RT Escherichia coli: extensive sequence homology of the glycerol-3-phosphate
RT transport protein with components of the hexose-6-phosphate transport
RT system.";
RL Mol. Microbiol. 1:251-258(1987).
RN [6]
RP PROTEIN SEQUENCE OF 26-44.
RC STRAIN=K12;
RX PubMed=8899705; DOI=10.1111/j.1365-2958.1996.tb02652.x;
RA Gonzalez-Gil G., Bringmann P., Kahmann R.;
RT "FIS is a regulator of metabolism in Escherichia coli.";
RL Mol. Microbiol. 22:21-29(1996).
RN [7]
RP SUBUNIT, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND COFACTOR.
RC STRAIN=K12;
RX PubMed=2829735; DOI=10.1016/0003-9861(88)90484-5;
RA Larson T.J., van Loo-Bhattacharya A.T.;
RT "Purification and characterization of glpQ-encoded glycerophosphodiester
RT phosphodiesterase from Escherichia coli K-12.";
RL Arch. Biochem. Biophys. 260:577-584(1988).
RN [8]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1-356 IN COMPLEX WITH CALCIUM
RP IONS, AND SUBUNIT.
RG New York structural genomix research consortium (NYSGXRC);
RT "Crystal structure of periplasmic glycerophosphodiester phosphodiesterase
RT from Escherichia coli.";
RL Submitted (JAN-2005) to the PDB data bank.
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-358 IN COMPLEX WITH MAGNESIUM
RP IONS, AND SUBUNIT.
RG Midwest center for structural genomics (MCSG);
RT "The crystal structure of glycerophosphoryl diester phosphodiesterase from
RT E. coli.";
RL Submitted (MAY-2007) to the PDB data bank.
CC -!- FUNCTION: Glycerophosphoryl diester phosphodiesterase hydrolyzes
CC deacylated phospholipids to G3P and the corresponding alcohols.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a sn-glycero-3-phosphodiester + H2O = an alcohol + H(+) + sn-
CC glycerol 3-phosphate; Xref=Rhea:RHEA:12969, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30879, ChEBI:CHEBI:57597,
CC ChEBI:CHEBI:83408; EC=3.1.4.46;
CC Evidence={ECO:0000269|PubMed:2829735};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000269|PubMed:2829735};
CC Note=Binds 1 Ca(2+) ion per subunit. {ECO:0000269|PubMed:2829735};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.28 mM for glycerophosphocholine {ECO:0000269|PubMed:2829735};
CC KM=0.24 mM for glycerophosphoethanolamine
CC {ECO:0000269|PubMed:2829735};
CC KM=0.35 mM for glycerophosphoglycerol {ECO:0000269|PubMed:2829735};
CC KM=0.59 mM for glycerophosphoserine {ECO:0000269|PubMed:2829735};
CC KM=1.0 mM for glycerophosphoinositol {ECO:0000269|PubMed:2829735};
CC pH dependence:
CC Optimum pH is 7.8. {ECO:0000269|PubMed:2829735};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:2829735, ECO:0000269|Ref.10,
CC ECO:0000269|Ref.9}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:2829735}.
CC -!- MISCELLANEOUS: There are 2 isozymes of glycerophosphoryl diester
CC phosphodiesterase in E.coli: a periplasmic isozyme (GlpQ) and a
CC cytosolic isozyme (UgpQ).
CC -!- SIMILARITY: Belongs to the glycerophosphoryl diester phosphodiesterase
CC family. {ECO:0000305}.
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DR EMBL; X56907; CAA40223.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75299.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16058.1; -; Genomic_DNA.
DR EMBL; Y00536; CAA68599.1; -; Genomic_DNA.
DR PIR; S15945; S15945.
DR RefSeq; NP_416742.1; NC_000913.3.
DR RefSeq; WP_000779105.1; NZ_LN832404.1.
DR PDB; 1T8Q; X-ray; 2.00 A; A/B/C/D=25-358.
DR PDB; 1YDY; X-ray; 1.70 A; A/B=1-356.
DR PDBsum; 1T8Q; -.
DR PDBsum; 1YDY; -.
DR AlphaFoldDB; P09394; -.
DR SMR; P09394; -.
DR BioGRID; 4260486; 185.
DR IntAct; P09394; 11.
DR STRING; 511145.b2239; -.
DR jPOST; P09394; -.
DR PaxDb; P09394; -.
DR PRIDE; P09394; -.
DR DNASU; 946725; -.
DR EnsemblBacteria; AAC75299; AAC75299; b2239.
DR EnsemblBacteria; BAA16058; BAA16058; BAA16058.
DR GeneID; 946725; -.
DR KEGG; ecj:JW2233; -.
DR KEGG; eco:b2239; -.
DR PATRIC; fig|511145.12.peg.2328; -.
DR EchoBASE; EB0394; -.
DR eggNOG; COG0584; Bacteria.
DR HOGENOM; CLU_030226_1_0_6; -.
DR InParanoid; P09394; -.
DR OMA; CRHENDI; -.
DR PhylomeDB; P09394; -.
DR BioCyc; EcoCyc:GLYCPDIESTER-PERI-MON; -.
DR BioCyc; MetaCyc:GLYCPDIESTER-PERI-MON; -.
DR BRENDA; 3.1.4.46; 2026.
DR SABIO-RK; P09394; -.
DR EvolutionaryTrace; P09394; -.
DR PRO; PR:P09394; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0042597; C:periplasmic space; IDA:EcoCyc.
DR GO; GO:0005509; F:calcium ion binding; IDA:EcoCyc.
DR GO; GO:0008889; F:glycerophosphodiester phosphodiesterase activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IDA:EcoCyc.
DR GO; GO:0006071; P:glycerol metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006629; P:lipid metabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.190; -; 1.
DR InterPro; IPR030395; GP_PDE_dom.
DR InterPro; IPR017946; PLC-like_Pdiesterase_TIM-brl.
DR Pfam; PF03009; GDPD; 1.
DR SUPFAM; SSF51695; SSF51695; 1.
DR PROSITE; PS51704; GP_PDE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Direct protein sequencing; Glycerol metabolism;
KW Hydrolase; Metal-binding; Periplasm; Reference proteome; Signal.
FT SIGNAL 1..25
FT /evidence="ECO:0000269|PubMed:1851953,
FT ECO:0000269|PubMed:8899705"
FT CHAIN 26..358
FT /note="Glycerophosphodiester phosphodiesterase,
FT periplasmic"
FT /id="PRO_0000012594"
FT DOMAIN 31..355
FT /note="GP-PDE"
FT BINDING 63
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 65
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 171
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT CONFLICT 27
FT /note="D -> I (in Ref. 6; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:1YDY"
FT TURN 36..42
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 48..56
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 60..68
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:1YDY"
FT TURN 83..85
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 88..91
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 109..114
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 121..124
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 127..132
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 148..162
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 167..172
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 175..180
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 185..195
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 203..210
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 212..220
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 222..226
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 253..255
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 259..262
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 266..270
FT /evidence="ECO:0007829|PDB:1YDY"
FT TURN 271..273
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 275..280
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 281..283
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 299..305
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 327..335
FT /evidence="ECO:0007829|PDB:1YDY"
FT STRAND 341..346
FT /evidence="ECO:0007829|PDB:1YDY"
FT HELIX 348..355
FT /evidence="ECO:0007829|PDB:1YDY"
SQ SEQUENCE 358 AA; 40843 MW; B08FD27399641616 CRC64;
MKLTLKNLSM AIMMSTIVMG SSAMAADSNE KIVIAHRGAS GYLPEHTLPA KAMAYAQGAD
YLEQDLVMTK DDNLVVLHDH YLDRVTDVAD RFPDRARKDG RYYAIDFTLD EIKSLKFTEG
FDIENGKKVQ TYPGRFPMGK SDFRVHTFEE EIEFVQGLNH STGKNIGIYP EIKAPWFHHQ
EGKDIAAKTL EVLKKYGYTG KDDKVYLQCF DADELKRIKN ELEPKMGMEL NLVQLIAYTD
WNETQQKQPD GSWVNYNYDW MFKPGAMKQV AEYADGIGPD YHMLIEETSQ PGNIKLTGMV
QDAQQNKLVV HPYTVRSDKL PEYTPDVNQL YDALYNKAGV NGLFTDFPDK AVKFLNKE
