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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)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei9 – 91Nucleophile1 Publication
    Metal bindingi9 – 91Magnesium
    Binding sitei10 – 101Phosphate; via amide nitrogenBy similarity
    Metal bindingi11 – 111Magnesium; via carbonyl oxygen
    Binding sitei197 – 1971PhosphateBy similarity
    Metal bindingi220 – 2201Magnesium
    Binding sitei223 – 2231PhosphateBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    • dephosphorylation Source: GOC
    • small molecule biosynthetic process Source: GO_Central
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11195. yidA.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi9 – 91D → A: Loss of the phosphatase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 270270Sugar phosphatase YidAPRO_0000054423Add
    BLAST

    Proteomic databases

    PaxDbiP0A8Y5.
    PRIDEiP0A8Y5.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A8Y5.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-36033N.
    IntActiP0A8Y5. 10 interactions.
    MINTiMINT-1238706.
    STRINGi511145.b3697.

    Structurei

    Secondary structure

    1
    270
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 84Combined sources
    Helixi10 – 145Combined sources
    Helixi23 – 3412Combined sources
    Beta strandi38 – 425Combined sources
    Helixi47 – 493Combined sources
    Helixi51 – 566Combined sources
    Beta strandi65 – 684Combined sources
    Helixi69 – 713Combined sources
    Beta strandi73 – 764Combined sources
    Turni77 – 793Combined sources
    Beta strandi82 – 854Combined sources
    Helixi90 – 10314Combined sources
    Beta strandi106 – 1105Combined sources
    Beta strandi115 – 1173Combined sources
    Helixi124 – 1329Combined sources
    Beta strandi137 – 1393Combined sources
    Helixi142 – 1443Combined sources
    Beta strandi153 – 1575Combined sources
    Helixi160 – 16910Combined sources
    Helixi172 – 1776Combined sources
    Beta strandi178 – 1847Combined sources
    Beta strandi187 – 1926Combined sources
    Helixi197 – 20812Combined sources
    Helixi212 – 2143Combined sources
    Beta strandi215 – 2195Combined sources
    Helixi222 – 2243Combined sources
    Helixi225 – 2306Combined sources
    Beta strandi231 – 2366Combined sources
    Helixi242 – 2476Combined sources
    Beta strandi249 – 2513Combined sources
    Turni255 – 2584Combined sources
    Helixi259 – 2679Combined sources

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP0A8Y5.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni43 – 442Phosphate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0561.
    HOGENOMiHOG000184780.
    InParanoidiP0A8Y5.
    KOiK07024.
    OMAiYCITNNG.
    OrthoDBiEOG6K13W0.
    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]
    PfamiPF00702. Hydrolase. 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.

    Genome annotation databases

    EnsemblBacteriaiAAC76720; AAC76720; b3697.
    BAE77597; BAE77597; BAE77597.
    GeneIDi948204.
    KEGGiecj:Y75_p3476.
    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.

    3D structure databases

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

    Protein-protein interaction databases

    DIPiDIP-36033N.
    IntActiP0A8Y5. 10 interactions.
    MINTiMINT-1238706.
    STRINGi511145.b3697.

    Proteomic databases

    PaxDbiP0A8Y5.
    PRIDEiP0A8Y5.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76720; AAC76720; b3697.
    BAE77597; BAE77597; BAE77597.
    GeneIDi948204.
    KEGGiecj:Y75_p3476.
    eco:b3697.
    PATRICi32122889. VBIEscCol129921_3820.

    Organism-specific databases

    EchoBASEiEB1181.
    EcoGeneiEG11195. yidA.

    Phylogenomic databases

    eggNOGiCOG0561.
    HOGENOMiHOG000184780.
    InParanoidiP0A8Y5.
    KOiK07024.
    OMAiYCITNNG.
    OrthoDBiEOG6K13W0.
    PhylomeDBiP0A8Y5.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP0A8Y5.
    PROiP0A8Y5.

    Gene expression databases

    GenevestigatoriP0A8Y5.

    Family and domain databases

    Gene3Di3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006379. HAD-SF_hydro_IIB.
    IPR000150. Hypothet_cof.
    [Graphical view]
    PfamiPF00702. Hydrolase. 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...

    Publicationsi

    « Hide 'large scale' publications
    1. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
      Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
      Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "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.
    4. "DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy."
      Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H., Gellert M., Mizuuchi K.
      Nucleic Acids Res. 15:771-784(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-195.
    5. "Enzyme genomics: application of general enzymatic screens to discover new enzymes."
      Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A., Arrowsmith C.H., Edwards A.M., Yakunin A.F.
      FEMS Microbiol. Rev. 29:263-279(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A PHOSPHATASE.
    6. "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family."
      Kuznetsova E., Proudfoot M., Gonzalez C.F., Brown G., Omelchenko M.V., Borozan I., Carmel L., Wolf Y.I., Mori H., Savchenko A.V., Arrowsmith C.H., Koonin E.V., Edwards A.M., Yakunin A.F.
      J. Biol. Chem. 281:36149-36161(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A PHOSPHATASE, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF ASP-9, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.
    7. "Crystal structure of NYSGRC target T1436: a hypothetical protein YidA."
      Ramagopal U.A., Almo S.C.
      Submitted (MAR-2004) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 2-270 IN COMPLEX WITH MAGNESIUM IONS, SUBUNIT.

    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: May 27, 2015
    This is version 85 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

    External Data

    Dasty 3

    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 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.