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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)DescriptionActionsGraphical viewLength
    Metal bindingi63Calcium1
    Metal bindingi65Calcium1
    Metal bindingi171Calcium1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10399. glpQ.

    Subcellular locationi

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Periplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 252 PublicationsAdd BLAST25
    ChainiPRO_000001259426 – 358Glycerophosphoryl diester phosphodiesteraseAdd BLAST333

    Proteomic databases

    EPDiP09394.
    PaxDbiP09394.
    PRIDEiP09394.

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Protein-protein interaction databases

    BioGridi4260486. 168 interactors.
    IntActiP09394. 11 interactors.
    STRINGi511145.b2239.

    Structurei

    Secondary structure

    1358
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi32 – 35Combined sources4
    Turni36 – 42Combined sources7
    Helixi48 – 56Combined sources9
    Beta strandi60 – 68Combined sources9
    Beta strandi74 – 76Combined sources3
    Beta strandi78 – 81Combined sources4
    Turni83 – 85Combined sources3
    Helixi88 – 91Combined sources4
    Helixi104 – 106Combined sources3
    Helixi109 – 114Combined sources6
    Beta strandi121 – 124Combined sources4
    Beta strandi127 – 132Combined sources6
    Helixi148 – 162Combined sources15
    Beta strandi167 – 172Combined sources6
    Helixi175 – 180Combined sources6
    Helixi185 – 195Combined sources11
    Beta strandi203 – 210Combined sources8
    Helixi212 – 220Combined sources9
    Helixi222 – 226Combined sources5
    Beta strandi231 – 236Combined sources6
    Helixi239 – 241Combined sources3
    Beta strandi245 – 247Combined sources3
    Beta strandi253 – 255Combined sources3
    Helixi259 – 262Combined sources4
    Helixi266 – 270Combined sources5
    Turni271 – 273Combined sources3
    Beta strandi275 – 280Combined sources6
    Helixi281 – 283Combined sources3
    Helixi299 – 305Combined sources7
    Helixi327 – 335Combined sources9
    Beta strandi341 – 346Combined sources6
    Helixi348 – 355Combined sources8

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP09394.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini31 – 355GP-PDEAdd BLAST325

    Sequence similaritiesi

    Contains 1 GP-PDE domain.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4106MZZ. Bacteria.
    COG0584. LUCA.
    HOGENOMiHOG000004696.
    InParanoidiP09394.
    KOiK01126.
    OMAiGRFYAID.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti27D → I AA sequence (PubMed:8899705).Curated1

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1T8QX-ray2.00A/B/C/D25-358[»]
    1YDYX-ray1.70A/B1-356[»]
    ProteinModelPortaliP09394.
    SMRiP09394.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260486. 168 interactors.
    IntActiP09394. 11 interactors.
    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.
    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...

    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: November 2, 2016
    This is version 146 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.