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P75792

- SUPH_ECOLI

UniProt

P75792 - SUPH_ECOLI

Protein

Sugar phosphatase YbiV

Gene

ybiV

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 117 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      Previous versions | rss
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    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

    Magnesium. Can also use other divalent metal cations as manganese, cobalt and 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

    1. magnesium ion binding Source: UniProtKB
    2. sugar-phosphatase activity Source: EcoCyc

    GO - Biological processi

    1. dephosphorylation Source: GOC
    2. small molecule biosynthetic process Source: RefGenome

    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG13327. supH.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: RefGenome

    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

    Gene expression databases

    GenevestigatoriP75792.

    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 – 84
    Helixi10 – 145
    Helixi23 – 3614
    Beta strandi39 – 435
    Helixi48 – 514
    Helixi52 – 543
    Turni56 – 616
    Beta strandi62 – 665
    Helixi67 – 693
    Beta strandi71 – 744
    Beta strandi77 – 815
    Helixi86 – 9712
    Beta strandi103 – 1108
    Beta strandi112 – 1154
    Helixi120 – 1278
    Beta strandi131 – 1377
    Helixi139 – 1413
    Beta strandi146 – 1527
    Helixi155 – 1573
    Helixi158 – 16811
    Turni169 – 1713
    Beta strandi172 – 1776
    Beta strandi182 – 1865
    Helixi192 – 20312
    Helixi207 – 2093
    Beta strandi210 – 2145
    Helixi217 – 2193
    Helixi220 – 2256
    Beta strandi227 – 2315
    Helixi237 – 2426
    Beta strandi244 – 2463
    Helixi250 – 2523
    Helixi254 – 26411

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK07757.
    OMAiDHARFER.
    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

    MSVKVIVTDM DGTFLNDAKT YNQPRFMAQY QELKKRGIKF VVASGNQYYQ    50
    LISFFPELKD EISFVAENGA LVYEHGKQLF HGELTRHESR IVIGELLKDK 100
    QLNFVACGLQ SAYVSENAPE AFVALMAKHY HRLKPVKDYQ EIDDVLFKFS 150
    LNLPDEQIPL VIDKLHVALD GIMKPVTSGF GFIDLIIPGL HKANGISRLL 200
    KRWDLSPQNV VAIGDSGNDA EMLKMARYSF AMGNAAENIK QIARYATDDN 250
    NHEGALNVIQ AVLDNTSPFN S 271
    Length:271
    Mass (Da):30,413
    Last modified:February 1, 1997 - v1
    Checksum:iF8733636B422A9A9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC73909.1.
    AP009048 Genomic DNA. Translation: BAA35503.1.
    PIRiF64819.
    RefSeqiNP_415343.1. NC_000913.3.
    YP_489095.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73909; AAC73909; b0822.
    BAA35503; BAA35503; BAA35503.
    GeneIDi12934001.
    945432.
    KEGGiecj:Y75_p0795.
    eco:b0822.
    PATRICi32116847. VBIEscCol129921_0849.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC73909.1 .
    AP009048 Genomic DNA. Translation: BAA35503.1 .
    PIRi F64819.
    RefSeqi NP_415343.1. NC_000913.3.
    YP_489095.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1RLM X-ray 1.90 A/B/C/D 1-271 [» ]
    1RLO X-ray 2.00 A/B/C/D 1-271 [» ]
    1RLT X-ray 2.20 A/B/C/D 1-271 [» ]
    2HF2 X-ray 1.90 A/B 1-271 [» ]
    ProteinModelPortali P75792.
    SMRi P75792. Positions 1-270.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P75792. 10 interactions.
    STRINGi 511145.b0822.

    Proteomic databases

    PaxDbi P75792.
    PRIDEi P75792.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73909 ; AAC73909 ; b0822 .
    BAA35503 ; BAA35503 ; BAA35503 .
    GeneIDi 12934001.
    945432.
    KEGGi ecj:Y75_p0795.
    eco:b0822.
    PATRICi 32116847. VBIEscCol129921_0849.

    Organism-specific databases

    EchoBASEi EB3111.
    EcoGenei EG13327. supH.

    Phylogenomic databases

    eggNOGi COG0561.
    HOGENOMi HOG000184782.
    KOi K07757.
    OMAi DHARFER.
    OrthoDBi EOG6H7FNB.
    PhylomeDBi P75792.

    Enzyme and pathway databases

    BioCyci EcoCyc:G6425-MONOMER.
    ECOL316407:JW0806-MONOMER.
    MetaCyc:G6425-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P75792.
    PROi P75792.

    Gene expression databases

    Genevestigatori P75792.

    Family and domain databases

    Gene3Di 3.40.50.1000. 2 hits.
    InterProi IPR023214. HAD-like_dom.
    IPR006379. HAD-SF_hydro_IIB.
    IPR000150. Hypothet_cof.
    [Graphical view ]
    Pfami PF08282. Hydrolase_3. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56784. SSF56784. 1 hit.
    TIGRFAMsi TIGR00099. Cof-subfamily. 1 hit.
    TIGR01484. HAD-SF-IIB. 1 hit.
    PROSITEi PS01229. COF_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 117 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