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Protein

2-deoxyglucose-6-phosphate phosphatase

Gene

yniC

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

Functioni

Catalyzes strongly the dephosphorylation of 2-deoxyglucose 6-phosphate (2dGlu6P) and slightly the dephosphorylation of mannose 6-phosphate (Man6P), 2-deoxyribose-5-phosphate (2dRib5P), ribose-5-phosphate (Rib5P) and glucose-6-phosphate (Glu6P).2 Publications

Catalytic activityi

2-deoxy-D-glucose 6-phosphate + H2O = 2-deoxy-D-glucose + phosphate.
Sugar phosphate + H2O = sugar + phosphate.

Cofactori

Mg2+1 Publication, Mn2+1 Publication, Co2+1 Publication, Zn2+1 PublicationNote: Magnesium. Can also use other divalent metal cations as manganese, cobalt or zinc.1 Publication

Kineticsi

  1. KM=0.61 mM for 2dGlu6P (with manganese ions as cofactor and at pH 9)1 Publication
  2. KM=2.5 mM for 2dRib5P (with zinc ions as cofactor and at pH 9)1 Publication
  3. KM=2.6 mM for Rib5P (with zinc ions as cofactor and at pH 9)1 Publication
  4. KM=3.6 mM for Glu6P (with zinc ions as cofactor and at pH 9)1 Publication
  5. KM=4.7 mM for Man6P (with zinc ions as cofactor and at pH 9)1 Publication

    pH dependencei

    Optimum pH is between 6 and 7.5.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei13Nucleophile1
    Metal bindingi13Magnesium1
    Metal bindingi15Magnesium1
    Binding sitei148Substrate1
    Metal bindingi173Magnesium1

    GO - Molecular functioni

    • 2-deoxyglucose-6-phosphatase activity Source: EcoliWiki
    • glucose-6-phosphatase activity Source: EcoliWiki
    • magnesium ion binding Source: UniProtKB
    • metal ion binding Source: EcoliWiki
    • phosphatase activity Source: EcoliWiki
    • sugar-phosphatase activity Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G6932-MONOMER.
    ECOL316407:JW1716-MONOMER.
    MetaCyc:G6932-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-deoxyglucose-6-phosphate phosphatase (EC:3.1.3.68)
    Alternative name(s):
    Sugar phosphatase (EC:3.1.3.23)
    Gene namesi
    Name:yniC
    Ordered Locus Names:b1727, JW1716
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13988. yniC.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene are hypersensitive to 2-deoxyglucose.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi13D → A: Loss of the phosphatase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001080611 – 2222-deoxyglucose-6-phosphate phosphataseAdd BLAST222

    Proteomic databases

    EPDiP77247.
    PaxDbiP77247.
    PRIDEiP77247.

    2D gel databases

    SWISS-2DPAGEP77247.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi4263414. 9 interactors.
    DIPiDIP-12777N.
    IntActiP77247. 8 interactors.
    MINTiMINT-1257246.
    STRINGi511145.b1727.

    Structurei

    Secondary structure

    1222
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi9 – 12Combined sources4
    Turni15 – 17Combined sources3
    Helixi22 – 35Combined sources14
    Helixi40 – 45Combined sources6
    Helixi54 – 64Combined sources11
    Beta strandi68 – 70Combined sources3
    Helixi72 – 90Combined sources19
    Helixi97 – 106Combined sources10
    Beta strandi110 – 117Combined sources8
    Helixi119 – 128Combined sources10
    Helixi132 – 134Combined sources3
    Beta strandi136 – 140Combined sources5
    Helixi152 – 161Combined sources10
    Helixi165 – 167Combined sources3
    Beta strandi168 – 174Combined sources7
    Helixi175 – 183Combined sources9
    Beta strandi187 – 190Combined sources4
    Turni194 – 198Combined sources5
    Helixi200 – 204Combined sources5
    Beta strandi205 – 208Combined sources4
    Helixi212 – 214Combined sources3
    Helixi217 – 221Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1TE2X-ray1.76A/B1-222[»]
    ProteinModelPortaliP77247.
    SMRiP77247.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77247.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni13 – 15Substrate binding3
    Regioni115 – 116Substrate binding2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107UW8. Bacteria.
    COG0637. LUCA.
    HOGENOMiHOG000248341.
    InParanoidiP77247.
    KOiK19270.
    OMAiWYAQQPW.
    PhylomeDBiP77247.

    Family and domain databases

    Gene3Di1.10.150.240. 1 hit.
    3.40.50.1000. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    IPR023198. PGP_dom2.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    PRINTSiPR00413. HADHALOGNASE.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01509. HAD-SF-IA-v3. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P77247-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSTPRQILAA IFDMDGLLID SEPLWDRAEL DVMASLGVDI SRRNELPDTL
    60 70 80 90 100
    GLRIDMVVDL WYARQPWNGP SRQEVVERVI ARAISLVEET RPLLPGVREA
    110 120 130 140 150
    VALCKEQGLL VGLASASPLH MLEKVLTMFD LRDSFDALAS AEKLPYSKPH
    160 170 180 190 200
    PQVYLDCAAK LGVDPLTCVA LEDSVNGMIA SKAARMRSIV VPAPEAQNDP
    210 220
    RFVLADVKLS SLTELTAKDL LG
    Length:222
    Mass (Da):24,330
    Last modified:February 1, 1997 - v1
    Checksum:i76FE1F2A331476A7
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74797.1.
    AP009048 Genomic DNA. Translation: BAA15508.1.
    PIRiG64931.
    RefSeqiNP_416241.1. NC_000913.3.
    WP_000106833.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74797; AAC74797; b1727.
    BAA15508; BAA15508; BAA15508.
    GeneIDi945632.
    KEGGiecj:JW1716.
    eco:b1727.
    PATRICi32118761. VBIEscCol129921_1798.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74797.1.
    AP009048 Genomic DNA. Translation: BAA15508.1.
    PIRiG64931.
    RefSeqiNP_416241.1. NC_000913.3.
    WP_000106833.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1TE2X-ray1.76A/B1-222[»]
    ProteinModelPortaliP77247.
    SMRiP77247.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263414. 9 interactors.
    DIPiDIP-12777N.
    IntActiP77247. 8 interactors.
    MINTiMINT-1257246.
    STRINGi511145.b1727.

    2D gel databases

    SWISS-2DPAGEP77247.

    Proteomic databases

    EPDiP77247.
    PaxDbiP77247.
    PRIDEiP77247.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74797; AAC74797; b1727.
    BAA15508; BAA15508; BAA15508.
    GeneIDi945632.
    KEGGiecj:JW1716.
    eco:b1727.
    PATRICi32118761. VBIEscCol129921_1798.

    Organism-specific databases

    EchoBASEiEB3744.
    EcoGeneiEG13988. yniC.

    Phylogenomic databases

    eggNOGiENOG4107UW8. Bacteria.
    COG0637. LUCA.
    HOGENOMiHOG000248341.
    InParanoidiP77247.
    KOiK19270.
    OMAiWYAQQPW.
    PhylomeDBiP77247.

    Enzyme and pathway databases

    BioCyciEcoCyc:G6932-MONOMER.
    ECOL316407:JW1716-MONOMER.
    MetaCyc:G6932-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP77247.
    PROiP77247.

    Family and domain databases

    Gene3Di1.10.150.240. 1 hit.
    3.40.50.1000. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    IPR023198. PGP_dom2.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    PRINTSiPR00413. HADHALOGNASE.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01509. HAD-SF-IA-v3. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYNIC_ECOLI
    AccessioniPrimary (citable) accession number: P77247
    Secondary accession number(s): P78167
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: February 1, 1997
    Last modified: November 2, 2016
    This is version 129 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, 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.