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Protein

Sugar phosphatase YidA

Gene

yidA

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

Functioni

Catalyzes the dephosphorylation of different sugar phosphates including erythrose-4-phosphate (Ery4P), ribose-5-phosphate (Ribu5P), fructose-1-phosphate (Fru1P), fructose-6-phosphate (Fru6P), glucose-6-P (Glu6P), and also imidodiphosphate (Imido-di-P) and acetyl phosphate (Acetyl-P). Selectively hydrolyzes alpha-D-glucose-1-phosphate (Glu1P) and has no activity with the beta form.2 Publications

Catalytic activityi

Sugar phosphate + H2O = sugar + phosphate.1 Publication

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=0.019 mM for Ery4P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  2. KM=0.033 mM for Imido-di-P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  3. KM=0.21 mM for Glu1P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  4. KM=0.39 mM for Fru1P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  5. KM=0.44 mM for Fru6P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  6. KM=0.45 mM for Ribu5P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  7. KM=0.54 mM for Man1P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  8. KM=0.81 mM for Glu6P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  9. KM=3.8 mM for Acetyl-P (in the presence of magnesium ion 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 sitei9Nucleophile1 Publication1
    Metal bindingi9Magnesium1
    Binding sitei10Phosphate; via amide nitrogenBy similarity1
    Metal bindingi11Magnesium; via carbonyl oxygen1
    Binding sitei197PhosphateBy similarity1
    Metal bindingi220Magnesium1
    Binding sitei223PhosphateBy similarity1

    GO - Molecular functioni

    • magnesium ion binding Source: EcoliWiki
    • phosphatase activity Source: EcoliWiki
    • sugar-phosphatase activity Source: EcoliWiki

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11195-MONOMER.
    ECOL316407:JW3674-MONOMER.
    MetaCyc:EG11195-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sugar phosphatase YidA (EC:3.1.3.23)
    Gene namesi
    Name:yidA
    Ordered Locus Names:b3697, JW3674
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11195. yidA.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi9D → A: Loss of the phosphatase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000544231 – 270Sugar phosphatase YidAAdd BLAST270

    Proteomic databases

    EPDiP0A8Y5.
    PaxDbiP0A8Y5.
    PRIDEiP0A8Y5.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi4262577. 7 interactors.
    DIPiDIP-36033N.
    IntActiP0A8Y5. 10 interactors.
    MINTiMINT-1238706.
    STRINGi511145.b3697.

    Structurei

    Secondary structure

    1270
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 8Combined sources4
    Helixi10 – 14Combined sources5
    Helixi23 – 34Combined sources12
    Beta strandi38 – 42Combined sources5
    Helixi47 – 49Combined sources3
    Helixi51 – 56Combined sources6
    Beta strandi65 – 68Combined sources4
    Helixi69 – 71Combined sources3
    Beta strandi73 – 76Combined sources4
    Turni77 – 79Combined sources3
    Beta strandi82 – 85Combined sources4
    Helixi90 – 103Combined sources14
    Beta strandi106 – 110Combined sources5
    Beta strandi115 – 117Combined sources3
    Helixi124 – 132Combined sources9
    Beta strandi137 – 139Combined sources3
    Helixi142 – 144Combined sources3
    Beta strandi153 – 157Combined sources5
    Helixi160 – 169Combined sources10
    Helixi172 – 177Combined sources6
    Beta strandi178 – 184Combined sources7
    Beta strandi187 – 192Combined sources6
    Helixi197 – 208Combined sources12
    Helixi212 – 214Combined sources3
    Beta strandi215 – 219Combined sources5
    Helixi222 – 224Combined sources3
    Helixi225 – 230Combined sources6
    Beta strandi231 – 236Combined sources6
    Helixi242 – 247Combined sources6
    Beta strandi249 – 251Combined sources3
    Turni255 – 258Combined sources4
    Helixi259 – 267Combined sources9

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1RKQX-ray1.40A/B2-270[»]
    ProteinModelPortaliP0A8Y5.
    SMRiP0A8Y5.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A8Y5.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni43 – 44Phosphate bindingBy similarity2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG410667J. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184780.
    InParanoidiP0A8Y5.
    OMAiLFYNGSM.
    PhylomeDBiP0A8Y5.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006379. HAD-SF_hydro_IIB.
    IPR000150. Hypothet_cof.
    [Graphical view]
    PfamiPF08282. Hydrolase_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR00099. Cof-subfamily. 1 hit.
    TIGR01484. HAD-SF-IIB. 1 hit.
    PROSITEiPS01228. COF_1. 1 hit.
    PS01229. COF_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A8Y5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAIKLIAIDM DGTLLLPDHT ISPAVKNAIA AARARGVNVV LTTGRPYAGV
    60 70 80 90 100
    HNYLKELHME QPGDYCITYN GALVQKAADG STVAQTALSY DDYRFLEKLS
    110 120 130 140 150
    REVGSHFHAL DRTTLYTANR DISYYTVHES FVATIPLVFC EAEKMDPNTQ
    160 170 180 190 200
    FLKVMMIDEP AILDQAIARI PQEVKEKYTV LKSAPYFLEI LDKRVNKGTG
    210 220 230 240 250
    VKSLADVLGI KPEEIMAIGD QENDIAMIEY AGVGVAMDNA IPSVKEVANF
    260 270
    VTKSNLEDGV AFAIEKYVLN
    Length:270
    Mass (Da):29,721
    Last modified:June 21, 2005 - v1
    Checksum:i04E749788D8A9446
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10328 Genomic DNA. Translation: AAA62048.1.
    U00096 Genomic DNA. Translation: AAC76720.1.
    AP009048 Genomic DNA. Translation: BAE77597.1.
    X04341 Genomic DNA. Translation: CAA27873.1.
    PIRiB65172. QQECGB.
    RefSeqiNP_418152.1. NC_000913.3.
    WP_000985549.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76720; AAC76720; b3697.
    BAE77597; BAE77597; BAE77597.
    GeneIDi948204.
    KEGGiecj:JW3674.
    eco:b3697.
    PATRICi32122889. VBIEscCol129921_3820.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10328 Genomic DNA. Translation: AAA62048.1.
    U00096 Genomic DNA. Translation: AAC76720.1.
    AP009048 Genomic DNA. Translation: BAE77597.1.
    X04341 Genomic DNA. Translation: CAA27873.1.
    PIRiB65172. QQECGB.
    RefSeqiNP_418152.1. NC_000913.3.
    WP_000985549.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1RKQX-ray1.40A/B2-270[»]
    ProteinModelPortaliP0A8Y5.
    SMRiP0A8Y5.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262577. 7 interactors.
    DIPiDIP-36033N.
    IntActiP0A8Y5. 10 interactors.
    MINTiMINT-1238706.
    STRINGi511145.b3697.

    Proteomic databases

    EPDiP0A8Y5.
    PaxDbiP0A8Y5.
    PRIDEiP0A8Y5.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76720; AAC76720; b3697.
    BAE77597; BAE77597; BAE77597.
    GeneIDi948204.
    KEGGiecj:JW3674.
    eco:b3697.
    PATRICi32122889. VBIEscCol129921_3820.

    Organism-specific databases

    EchoBASEiEB1181.
    EcoGeneiEG11195. yidA.

    Phylogenomic databases

    eggNOGiENOG410667J. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184780.
    InParanoidiP0A8Y5.
    OMAiLFYNGSM.
    PhylomeDBiP0A8Y5.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11195-MONOMER.
    ECOL316407:JW3674-MONOMER.
    MetaCyc:EG11195-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP0A8Y5.
    PROiP0A8Y5.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006379. HAD-SF_hydro_IIB.
    IPR000150. Hypothet_cof.
    [Graphical view]
    PfamiPF08282. Hydrolase_3. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR00099. Cof-subfamily. 1 hit.
    TIGR01484. HAD-SF-IIB. 1 hit.
    PROSITEiPS01228. COF_1. 1 hit.
    PS01229. COF_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYIDA_ECOLI
    AccessioniPrimary (citable) accession number: P0A8Y5
    Secondary accession number(s): P09997, P76737, Q2M809
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 21, 2005
    Last sequence update: June 21, 2005
    Last modified: November 2, 2016
    This is version 97 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.