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Protein

Glycerophosphoryl diester phosphodiesterase

Gene

glpQ

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

Functioni

Glycerophosphoryl diester phosphodiesterase hydrolyzes deacylated phospholipids to G3P and the corresponding alcohols.

Catalytic activityi

A glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate.1 Publication

Cofactori

Ca2+1 PublicationNote: Binds 1 Ca2+ ion per subunit.1 Publication

Kineticsi

  1. KM=0.28 mM for glycerophosphocholine1 Publication
  2. KM=0.24 mM for glycerophosphoethanolamine1 Publication
  3. KM=0.35 mM for glycerophosphoglycerol1 Publication
  4. KM=0.59 mM for glycerophosphoserine1 Publication
  5. KM=1.0 mM for glycerophosphoinositol1 Publication

    pH dependencei

    Optimum pH is 7.8.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi63 – 631Calcium
    Metal bindingi65 – 651Calcium
    Metal bindingi171 – 1711Calcium

    GO - Molecular functioni

    • calcium ion binding Source: EcoCyc
    • glycerophosphodiester phosphodiesterase activity Source: EcoCyc
    • metal ion binding Source: EcoCyc

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Glycerol metabolism

    Keywords - Ligandi

    Calcium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:GLYCPDIESTER-PERI-MONOMER.
    ECOL316407:JW2233-MONOMER.
    MetaCyc:GLYCPDIESTER-PERI-MONOMER.
    BRENDAi3.1.4.46. 2026.
    SABIO-RKP09394.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycerophosphoryl diester phosphodiesterase (EC:3.1.4.46)
    Short name:
    Glycerophosphodiester phosphodiesterase
    Gene namesi
    Name:glpQ
    Ordered Locus Names:b2239, JW2233
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10399. glpQ.

    Subcellular locationi

    • Periplasm 1 Publication

    GO - Cellular componenti

    • periplasmic space Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 25252 PublicationsAdd
    BLAST
    Chaini26 – 358333Glycerophosphoryl diester phosphodiesterasePRO_0000012594Add
    BLAST

    Proteomic databases

    EPDiP09394.
    PaxDbiP09394.
    PRIDEiP09394.

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Protein-protein interaction databases

    BioGridi4260486. 168 interactions.
    IntActiP09394. 11 interactions.
    STRINGi511145.b2239.

    Structurei

    Secondary structure

    1
    358
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi32 – 354Combined sources
    Turni36 – 427Combined sources
    Helixi48 – 569Combined sources
    Beta strandi60 – 689Combined sources
    Beta strandi74 – 763Combined sources
    Beta strandi78 – 814Combined sources
    Turni83 – 853Combined sources
    Helixi88 – 914Combined sources
    Helixi104 – 1063Combined sources
    Helixi109 – 1146Combined sources
    Beta strandi121 – 1244Combined sources
    Beta strandi127 – 1326Combined sources
    Helixi148 – 16215Combined sources
    Beta strandi167 – 1726Combined sources
    Helixi175 – 1806Combined sources
    Helixi185 – 19511Combined sources
    Beta strandi203 – 2108Combined sources
    Helixi212 – 2209Combined sources
    Helixi222 – 2265Combined sources
    Beta strandi231 – 2366Combined sources
    Helixi239 – 2413Combined sources
    Beta strandi245 – 2473Combined sources
    Beta strandi253 – 2553Combined sources
    Helixi259 – 2624Combined sources
    Helixi266 – 2705Combined sources
    Turni271 – 2733Combined sources
    Beta strandi275 – 2806Combined sources
    Helixi281 – 2833Combined sources
    Helixi299 – 3057Combined sources
    Helixi327 – 3359Combined sources
    Beta strandi341 – 3466Combined sources
    Helixi348 – 3558Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1T8QX-ray2.00A/B/C/D25-358[»]
    1YDYX-ray1.70A/B1-356[»]
    ProteinModelPortaliP09394.
    SMRiP09394. Positions 29-357.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP09394.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini31 – 355325GP-PDEAdd
    BLAST

    Sequence similaritiesi

    Contains 1 GP-PDE domain.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4106MZZ. Bacteria.
    COG0584. LUCA.
    HOGENOMiHOG000004696.
    InParanoidiP09394.
    KOiK01126.
    OMAiGRFYAID.
    OrthoDBiEOG65N189.
    PhylomeDBiP09394.

    Family and domain databases

    Gene3Di3.20.20.190. 1 hit.
    InterProiIPR004129. GlyceroP-diester-Pdiesterase.
    IPR030395. GP_PDE_dom.
    IPR017946. PLC-like_Pdiesterase_TIM-brl.
    [Graphical view]
    PANTHERiPTHR23344. PTHR23344. 1 hit.
    PfamiPF03009. GDPD. 1 hit.
    [Graphical view]
    SUPFAMiSSF51695. SSF51695. 1 hit.
    PROSITEiPS51704. GP_PDE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    P09394-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKLTLKNLSM AIMMSTIVMG SSAMAADSNE KIVIAHRGAS GYLPEHTLPA
    60 70 80 90 100
    KAMAYAQGAD YLEQDLVMTK DDNLVVLHDH YLDRVTDVAD RFPDRARKDG
    110 120 130 140 150
    RYYAIDFTLD EIKSLKFTEG FDIENGKKVQ TYPGRFPMGK SDFRVHTFEE
    160 170 180 190 200
    EIEFVQGLNH STGKNIGIYP EIKAPWFHHQ EGKDIAAKTL EVLKKYGYTG
    210 220 230 240 250
    KDDKVYLQCF DADELKRIKN ELEPKMGMEL NLVQLIAYTD WNETQQKQPD
    260 270 280 290 300
    GSWVNYNYDW MFKPGAMKQV AEYADGIGPD YHMLIEETSQ PGNIKLTGMV
    310 320 330 340 350
    QDAQQNKLVV HPYTVRSDKL PEYTPDVNQL YDALYNKAGV NGLFTDFPDK

    AVKFLNKE
    Length:358
    Mass (Da):40,843
    Last modified:November 1, 1991 - v2
    Checksum:iB08FD27399641616
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti27 – 271D → I AA sequence (PubMed:8899705).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X56907 Genomic DNA. Translation: CAA40223.1.
    U00096 Genomic DNA. Translation: AAC75299.1.
    AP009048 Genomic DNA. Translation: BAA16058.1.
    Y00536 Genomic DNA. Translation: CAA68599.1.
    PIRiS15945.
    RefSeqiNP_416742.1. NC_000913.3.
    WP_000779105.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75299; AAC75299; b2239.
    BAA16058; BAA16058; BAA16058.
    GeneIDi946725.
    KEGGiecj:JW2233.
    eco:b2239.
    PATRICi32119837. VBIEscCol129921_2328.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X56907 Genomic DNA. Translation: CAA40223.1.
    U00096 Genomic DNA. Translation: AAC75299.1.
    AP009048 Genomic DNA. Translation: BAA16058.1.
    Y00536 Genomic DNA. Translation: CAA68599.1.
    PIRiS15945.
    RefSeqiNP_416742.1. NC_000913.3.
    WP_000779105.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1T8QX-ray2.00A/B/C/D25-358[»]
    1YDYX-ray1.70A/B1-356[»]
    ProteinModelPortaliP09394.
    SMRiP09394. Positions 29-357.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260486. 168 interactions.
    IntActiP09394. 11 interactions.
    STRINGi511145.b2239.

    Proteomic databases

    EPDiP09394.
    PaxDbiP09394.
    PRIDEiP09394.

    Protocols and materials databases

    DNASUi946725.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75299; AAC75299; b2239.
    BAA16058; BAA16058; BAA16058.
    GeneIDi946725.
    KEGGiecj:JW2233.
    eco:b2239.
    PATRICi32119837. VBIEscCol129921_2328.

    Organism-specific databases

    EchoBASEiEB0394.
    EcoGeneiEG10399. glpQ.

    Phylogenomic databases

    eggNOGiENOG4106MZZ. Bacteria.
    COG0584. LUCA.
    HOGENOMiHOG000004696.
    InParanoidiP09394.
    KOiK01126.
    OMAiGRFYAID.
    OrthoDBiEOG65N189.
    PhylomeDBiP09394.

    Enzyme and pathway databases

    BioCyciEcoCyc:GLYCPDIESTER-PERI-MONOMER.
    ECOL316407:JW2233-MONOMER.
    MetaCyc:GLYCPDIESTER-PERI-MONOMER.
    BRENDAi3.1.4.46. 2026.
    SABIO-RKP09394.

    Miscellaneous databases

    EvolutionaryTraceiP09394.
    PROiP09394.

    Family and domain databases

    Gene3Di3.20.20.190. 1 hit.
    InterProiIPR004129. GlyceroP-diester-Pdiesterase.
    IPR030395. GP_PDE_dom.
    IPR017946. PLC-like_Pdiesterase_TIM-brl.
    [Graphical view]
    PANTHERiPTHR23344. PTHR23344. 1 hit.
    PfamiPF03009. GDPD. 1 hit.
    [Graphical view]
    SUPFAMiSSF51695. SSF51695. 1 hit.
    PROSITEiPS51704. GP_PDE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Characterization of two genes, glpQ and ugpQ, encoding glycerophosphoryl diester phosphodiesterases of Escherichia coli."
      Tommassen J., Eiglmeier K., Cole S.T., Overduin P., Larson T.J., Boos W.
      Mol. Gen. Genet. 226:321-327(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 26-31.
    2. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Nucleotide sequence and transcriptional startpoint of the glpT gene of Escherichia coli: extensive sequence homology of the glycerol-3-phosphate transport protein with components of the hexose-6-phosphate transport system."
      Eiglmeier K., Boos W., Cole S.
      Mol. Microbiol. 1:251-258(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-9.
      Strain: K12.
    6. "FIS is a regulator of metabolism in Escherichia coli."
      Gonzalez-Gil G., Bringmann P., Kahmann R.
      Mol. Microbiol. 22:21-29(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 26-44.
      Strain: K12.
    7. "Purification and characterization of glpQ-encoded glycerophosphodiester phosphodiesterase from Escherichia coli K-12."
      Larson T.J., van Loo-Bhattacharya A.T.
      Arch. Biochem. Biophys. 260:577-584(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, SUBCELLULAR LOCATION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR.
      Strain: K12.
    8. "Escherichia coli proteome analysis using the gene-protein database."
      VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
      Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY 2D-GEL.
    9. "Crystal structure of periplasmic glycerophosphodiester phosphodiesterase from Escherichia coli."
      New York structural genomix research consortium (NYSGXRC)
      Submitted (JAN-2005) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 1-356 IN COMPLEX WITH CALCIUM IONS, SUBUNIT.
    10. "The crystal structure of glycerophosphoryl diester phosphodiesterase from E. coli."
      Midwest center for structural genomics (MCSG)
      Submitted (MAY-2007) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-358 IN COMPLEX WITH MAGNESIUM IONS, SUBUNIT.

    Entry informationi

    Entry nameiGLPQ_ECOLI
    AccessioniPrimary (citable) accession number: P09394
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1989
    Last sequence update: November 1, 1991
    Last modified: March 16, 2016
    This is version 143 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    There are 2 isozymes of glycerophosphoryl diester phosphodiesterase in E.coli: a periplasmic isozyme (GlpQ) and a cytosolic isozyme (UgpQ).

    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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.