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Protein

Sugar phosphatase YbiV

Gene

ybiV

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

Functioni

Catalyzes the hydrolysis of sugar phosphate to sugar and inorganic phosphate. Has a wide substrate specificity catalyzing the hydrolysis of ribose-5-phosphate, glucose-6-phosphate, fructose-1-phosphate, acetyl-phosphate, glycerol-1-phosphate, glycerol-2-phosphate, 2-deoxy-glucose-6-phosphate, mannose-6-phosphate and fructose-6-phosphate. Appears to have a low level of phosphotransferase activity using monophosphates as the phosphate donor.3 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

Glucose-6-phosphate is also a good substrate with a relative activity of 62.5% versus the activity with ribose-5-phosphate.

  1. KM=0.12 mM for imido-di-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  2. KM=1.4 mM for fructose-1-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  3. KM=2.4 mM for ribose-5-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  4. KM=3.1 mM for glucose-6-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  5. KM=4.9 mM for acetyl-phosphate (in the presence of magnesium ion as cofactor and at pH 9)2 Publications
  6. KM=6 mM for ribose-5-phosphate (at pH 5.4)2 Publications
  7. KM=6 mM for glycerol-1-phosphate (at pH 5.4)2 Publications
  8. KM=4.5 mM for glycerol-2-phosphate (at pH 5.4)2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei9 – 91NucleophileSequence Analysis
    Metal bindingi9 – 91Magnesium
    Binding sitei10 – 101Phosphate; via amide nitrogen
    Metal bindingi11 – 111Magnesium; via carbonyl oxygen
    Binding sitei192 – 1921Phosphate
    Metal bindingi215 – 2151Magnesium
    Metal bindingi216 – 2161Magnesium
    Binding sitei218 – 2181PhosphateBy similarity

    GO - Molecular functioni

    • magnesium ion binding Source: UniProtKB
    • sugar-phosphatase activity Source: EcoCyc

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G6425-MONOMER.
    ECOL316407:JW0806-MONOMER.
    MetaCyc:G6425-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sugar phosphatase YbiV (EC:3.1.3.23)
    Gene namesi
    Name:ybiV
    Synonyms:supH
    Ordered Locus Names:b0822, JW0806
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13327. supH.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 271271Sugar phosphatase YbiVPRO_0000054421Add
    BLAST

    Proteomic databases

    PaxDbiP75792.
    PRIDEiP75792.

    Expressioni

    Inductioni

    Regulated by the cAMP receptor protein crp.Curated

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    IntActiP75792. 10 interactions.
    STRINGi511145.b0822.

    Structurei

    Secondary structure

    1
    271
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 84Combined sources
    Helixi10 – 145Combined sources
    Helixi23 – 3614Combined sources
    Beta strandi39 – 435Combined sources
    Helixi48 – 514Combined sources
    Helixi52 – 543Combined sources
    Turni56 – 616Combined sources
    Beta strandi62 – 665Combined sources
    Helixi67 – 693Combined sources
    Beta strandi71 – 744Combined sources
    Beta strandi77 – 815Combined sources
    Helixi86 – 9712Combined sources
    Beta strandi103 – 1108Combined sources
    Beta strandi112 – 1154Combined sources
    Helixi120 – 1278Combined sources
    Beta strandi131 – 1377Combined sources
    Helixi139 – 1413Combined sources
    Beta strandi146 – 1527Combined sources
    Helixi155 – 1573Combined sources
    Helixi158 – 16811Combined sources
    Turni169 – 1713Combined sources
    Beta strandi172 – 1776Combined sources
    Beta strandi182 – 1865Combined sources
    Helixi192 – 20312Combined sources
    Helixi207 – 2093Combined sources
    Beta strandi210 – 2145Combined sources
    Helixi217 – 2193Combined sources
    Helixi220 – 2256Combined sources
    Beta strandi227 – 2315Combined sources
    Helixi237 – 2426Combined sources
    Beta strandi244 – 2463Combined sources
    Helixi250 – 2523Combined sources
    Helixi254 – 26411Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1RLMX-ray1.90A/B/C/D1-271[»]
    1RLOX-ray2.00A/B/C/D1-271[»]
    1RLTX-ray2.20A/B/C/D1-271[»]
    2HF2X-ray1.90A/B1-271[»]
    ProteinModelPortaliP75792.
    SMRiP75792. Positions 1-270.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP75792.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni44 – 452Phosphate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0561.
    HOGENOMiHOG000184782.
    InParanoidiP75792.
    KOiK07757.
    OMAiQRVSDYH.
    OrthoDBiEOG6H7FNB.
    PhylomeDBiP75792.

    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.
    PROSITEiPS01229. COF_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P75792-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSVKVIVTDM DGTFLNDAKT YNQPRFMAQY QELKKRGIKF VVASGNQYYQ
    60 70 80 90 100
    LISFFPELKD EISFVAENGA LVYEHGKQLF HGELTRHESR IVIGELLKDK
    110 120 130 140 150
    QLNFVACGLQ SAYVSENAPE AFVALMAKHY HRLKPVKDYQ EIDDVLFKFS
    160 170 180 190 200
    LNLPDEQIPL VIDKLHVALD GIMKPVTSGF GFIDLIIPGL HKANGISRLL
    210 220 230 240 250
    KRWDLSPQNV VAIGDSGNDA EMLKMARYSF AMGNAAENIK QIARYATDDN
    260 270
    NHEGALNVIQ AVLDNTSPFN S
    Length:271
    Mass (Da):30,413
    Last modified:February 1, 1997 - v1
    Checksum:iF8733636B422A9A9
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC73909.1.
    AP009048 Genomic DNA. Translation: BAA35503.1.
    PIRiF64819.
    RefSeqiNP_415343.1. NC_000913.3.
    WP_000114272.1. NZ_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73909; AAC73909; b0822.
    BAA35503; BAA35503; BAA35503.
    GeneIDi945432.
    KEGGieco:b0822.
    PATRICi32116847. VBIEscCol129921_0849.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC73909.1.
    AP009048 Genomic DNA. Translation: BAA35503.1.
    PIRiF64819.
    RefSeqiNP_415343.1. NC_000913.3.
    WP_000114272.1. NZ_CP010445.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1RLMX-ray1.90A/B/C/D1-271[»]
    1RLOX-ray2.00A/B/C/D1-271[»]
    1RLTX-ray2.20A/B/C/D1-271[»]
    2HF2X-ray1.90A/B1-271[»]
    ProteinModelPortaliP75792.
    SMRiP75792. Positions 1-270.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP75792. 10 interactions.
    STRINGi511145.b0822.

    Proteomic databases

    PaxDbiP75792.
    PRIDEiP75792.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73909; AAC73909; b0822.
    BAA35503; BAA35503; BAA35503.
    GeneIDi945432.
    KEGGieco:b0822.
    PATRICi32116847. VBIEscCol129921_0849.

    Organism-specific databases

    EchoBASEiEB3111.
    EcoGeneiEG13327. supH.

    Phylogenomic databases

    eggNOGiCOG0561.
    HOGENOMiHOG000184782.
    InParanoidiP75792.
    KOiK07757.
    OMAiQRVSDYH.
    OrthoDBiEOG6H7FNB.
    PhylomeDBiP75792.

    Enzyme and pathway databases

    BioCyciEcoCyc:G6425-MONOMER.
    ECOL316407:JW0806-MONOMER.
    MetaCyc:G6425-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP75792.
    PROiP75792.

    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.
    PROSITEiPS01229. COF_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    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. "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.
    5. "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, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.
    6. Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PHOSPHATE ANALOGS AND MAGNESIUM ION, FUNCTION AS A PHOSPHATASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.
    7. "Domain shifting confirms monomeric structure of Escherichia coli sugar phosphatase suph."
      New York structural genomix research consortium (NYSGXRC)
      Submitted (JUL-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-271, SUBUNIT.

    Entry informationi

    Entry nameiSUPH_ECOLI
    AccessioniPrimary (citable) accession number: P75792
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: February 1, 1997
    Last modified: July 22, 2015
    This is version 124 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.