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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)DescriptionActionsGraphical viewLength
    Active sitei9NucleophileSequence analysis1
    Metal bindingi9Magnesium1
    Binding sitei10Phosphate; via amide nitrogen1
    Metal bindingi11Magnesium; via carbonyl oxygen1
    Binding sitei192Phosphate1
    Metal bindingi215Magnesium1
    Metal bindingi216Magnesium1
    Binding sitei218PhosphateBy similarity1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 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)DescriptionActionsGraphical viewLength
    ChainiPRO_00000544211 – 271Sugar phosphatase YbiVAdd BLAST271

    Proteomic databases

    PaxDbiP75792.
    PRIDEiP75792.

    Expressioni

    Inductioni

    Regulated by the cAMP receptor protein crp.Curated

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    BioGridi4262995. 213 interactors.
    IntActiP75792. 10 interactors.
    STRINGi511145.b0822.

    Structurei

    Secondary structure

    1271
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 8Combined sources4
    Helixi10 – 14Combined sources5
    Helixi23 – 36Combined sources14
    Beta strandi39 – 43Combined sources5
    Helixi48 – 51Combined sources4
    Helixi52 – 54Combined sources3
    Turni56 – 61Combined sources6
    Beta strandi62 – 66Combined sources5
    Helixi67 – 69Combined sources3
    Beta strandi71 – 74Combined sources4
    Beta strandi77 – 81Combined sources5
    Helixi86 – 97Combined sources12
    Beta strandi103 – 110Combined sources8
    Beta strandi112 – 115Combined sources4
    Helixi120 – 127Combined sources8
    Beta strandi131 – 137Combined sources7
    Helixi139 – 141Combined sources3
    Beta strandi146 – 152Combined sources7
    Helixi155 – 157Combined sources3
    Helixi158 – 168Combined sources11
    Turni169 – 171Combined sources3
    Beta strandi172 – 177Combined sources6
    Beta strandi182 – 186Combined sources5
    Helixi192 – 203Combined sources12
    Helixi207 – 209Combined sources3
    Beta strandi210 – 214Combined sources5
    Helixi217 – 219Combined sources3
    Helixi220 – 225Combined sources6
    Beta strandi227 – 231Combined sources5
    Helixi237 – 242Combined sources6
    Beta strandi244 – 246Combined sources3
    Helixi250 – 252Combined sources3
    Helixi254 – 264Combined sources11

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP75792.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni44 – 45Phosphate binding2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108HCJ. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184782.
    InParanoidiP75792.
    KOiK07757.
    OMAiQRVSDYH.
    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_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73909; AAC73909; b0822.
    BAA35503; BAA35503; BAA35503.
    GeneIDi945432.
    KEGGiecj:JW0806.
    eco: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_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262995. 213 interactors.
    IntActiP75792. 10 interactors.
    STRINGi511145.b0822.

    Proteomic databases

    PaxDbiP75792.
    PRIDEiP75792.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73909; AAC73909; b0822.
    BAA35503; BAA35503; BAA35503.
    GeneIDi945432.
    KEGGiecj:JW0806.
    eco:b0822.
    PATRICi32116847. VBIEscCol129921_0849.

    Organism-specific databases

    EchoBASEiEB3111.
    EcoGeneiEG13327. supH.

    Phylogenomic databases

    eggNOGiENOG4108HCJ. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184782.
    InParanoidiP75792.
    KOiK07757.
    OMAiQRVSDYH.
    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...

    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: November 2, 2016
    This is version 132 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.