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Protein

Pyridoxal phosphate phosphatase YbhA

Gene

ybhA

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 pyridoxal-phosphate (PLP). Can also hydrolyze erythrose-4-phosphate (Ery4P) and fructose-1,6-bis-phosphate (Fru1,6bisP).2 Publications

Catalytic activityi

Pyridoxal 5'-phosphate + H2O = pyridoxal + 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=0.37 mM for PLP (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  2. KM=1.3 mM for Fru1,6bisP (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 – 91NucleophileBy similarity
    Metal bindingi9 – 91MagnesiumBy similarity
    Binding sitei10 – 101Phosphate; via amide nitrogenBy similarity
    Metal bindingi11 – 111Magnesium; via carbonyl oxygenBy similarity
    Binding sitei200 – 2001PhosphateBy similarity
    Metal bindingi223 – 2231MagnesiumBy similarity
    Binding sitei226 – 2261PhosphateBy similarity

    GO - Molecular functioni

    • magnesium ion binding Source: EcoliWiki
    • phosphatase activity Source: EcoliWiki
    • phosphotransferase activity, alcohol group as acceptor Source: EcoliWiki
    • pyridoxal 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:EG11239-MONOMER.
    ECOL316407:JW0749-MONOMER.
    MetaCyc:EG11239-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxal phosphate phosphatase YbhA (EC:3.1.3.74)
    Short name:
    PLP phosphatase
    Gene namesi
    Name:ybhA
    Ordered Locus Names:b0766, JW0749
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11239. ybhA.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 272272Pyridoxal phosphate phosphatase YbhAPRO_0000054420Add
    BLAST

    Proteomic databases

    PaxDbiP21829.

    Interactioni

    Protein-protein interaction databases

    BioGridi4261146. 12 interactions.
    IntActiP21829. 3 interactions.
    STRINGi511145.b0766.

    Structurei

    3D structure databases

    ProteinModelPortaliP21829.
    SMRiP21829. Positions 2-267.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

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

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108K4B. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184780.
    InParanoidiP21829.
    KOiK07024.
    OMAiMTYRVIA.
    PhylomeDBiP21829.

    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.

    P21829-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTTRVIALDL DGTLLTPKKT LLPSSIEALA RAREAGYQLI IVTGRHHVAI
    60 70 80 90 100
    HPFYQALALD TPAICCNGTY LYDYHAKTVL EADPMPVIKA LQLIEMLNEH
    110 120 130 140 150
    HIHGLMYVDD AMVYEHPTGH VIRTSNWAQT LPPEQRPTFT QVASLAETAQ
    160 170 180 190 200
    QVNAVWKFAL THDDLPQLQH FGKHVEHELG LECEWSWHDQ VDIARGGNSK
    210 220 230 240 250
    GKRLTKWVEA QGWSMENVVA FGDNFNDISM LEAAGTGVAM GNADDAVKAR
    260 270
    ANIVIGDNTT DSIAQFIYSH LI
    Length:272
    Mass (Da):30,201
    Last modified:October 1, 1996 - v3
    Checksum:iBB4602AB4D26ACD2
    GO

    Sequence cautioni

    The sequence U07867 differs from that shown. Reason: Frameshift at position 217. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U27192 Genomic DNA. Translation: AAB60177.1.
    U07867 Genomic DNA. No translation available.
    U00096 Genomic DNA. Translation: AAC73853.1.
    AP009048 Genomic DNA. Translation: BAA35430.1.
    PIRiF64812.
    RefSeqiNP_415287.1. NC_000913.3.
    WP_001300666.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73853; AAC73853; b0766.
    BAA35430; BAA35430; BAA35430.
    GeneIDi945372.
    KEGGiecj:JW0749.
    eco:b0766.
    PATRICi32116733. VBIEscCol129921_0792.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U27192 Genomic DNA. Translation: AAB60177.1.
    U07867 Genomic DNA. No translation available.
    U00096 Genomic DNA. Translation: AAC73853.1.
    AP009048 Genomic DNA. Translation: BAA35430.1.
    PIRiF64812.
    RefSeqiNP_415287.1. NC_000913.3.
    WP_001300666.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP21829.
    SMRiP21829. Positions 2-267.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261146. 12 interactions.
    IntActiP21829. 3 interactions.
    STRINGi511145.b0766.

    Proteomic databases

    PaxDbiP21829.

    Protocols and materials databases

    DNASUi945372.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73853; AAC73853; b0766.
    BAA35430; BAA35430; BAA35430.
    GeneIDi945372.
    KEGGiecj:JW0749.
    eco:b0766.
    PATRICi32116733. VBIEscCol129921_0792.

    Organism-specific databases

    EchoBASEiEB1221.
    EcoGeneiEG11239. ybhA.

    Phylogenomic databases

    eggNOGiENOG4108K4B. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184780.
    InParanoidiP21829.
    KOiK07024.
    OMAiMTYRVIA.
    PhylomeDBiP21829.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11239-MONOMER.
    ECOL316407:JW0749-MONOMER.
    MetaCyc:EG11239-MONOMER.

    Miscellaneous databases

    PROiP21829.

    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 nameiYBHA_ECOLI
    AccessioniPrimary (citable) accession number: P21829
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: October 1, 1996
    Last modified: September 7, 2016
    This is version 137 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    This ORF is coded on the other strand of an ORF which has been called modD (by PubMed:7665460 and PubMed:8564363), but which seems to be wrong.Curated

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. 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.