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Protein

Pyridoxal phosphate phosphatase YigL

Gene

yigL

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

Functioni

Catalyzes Strongly the dephosphorylation of pyridoxal-phosphate (PLP) and moderately the dephosphorylation of 2-deoxyglucose 6-phosphate (2bGLU6P) and beta-glucose 6-phosphate (bGlu6P). Also hydrolyzes both purines (GMP and IMP) and pyrimidines as secondary substrates.1 Publication

Catalytic activityi

Pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate.1 Publication
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=1.5 mM for PLP (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  2. KM=5.9 mM for bGlu6P (in the presence of magnesium ion as cofactor and at pH 9)1 Publication
  3. KM=7.5 mM for 2bGLU6P (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 sitei8 – 81NucleophileBy similarity
    Metal bindingi8 – 81MagnesiumBy similarity
    Binding sitei9 – 91Phosphate; via amide nitrogenBy similarity
    Metal bindingi10 – 101Magnesium; via carbonyl oxygenBy similarity
    Binding sitei191 – 1911PhosphateBy similarity
    Metal bindingi214 – 2141MagnesiumBy similarity
    Binding sitei217 – 2171PhosphateBy similarity

    GO - Molecular functioni

    • magnesium ion binding Source: UniProtKB
    • metal ion binding Source: EcoliWiki
    • phosphatase activity Source: EcoliWiki
    • pyridoxal 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:EG11470-MONOMER.
    ECOL316407:JW5854-MONOMER.
    MetaCyc:EG11470-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxal phosphate phosphatase YigL (EC:3.1.3.74)
    Alternative name(s):
    PLP phosphatase
    Sugar phosphatase (EC:3.1.3.23)
    Gene namesi
    Name:yigL
    Ordered Locus Names:b3826, JW5854
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11470. yigL.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 266266Pyridoxal phosphate phosphatase YigLPRO_0000054426Add
    BLAST

    Proteomic databases

    EPDiP27848.
    PaxDbiP27848.
    PRIDEiP27848.

    Interactioni

    Protein-protein interaction databases

    BioGridi4259609. 11 interactions.
    IntActiP27848. 2 interactions.
    STRINGi511145.b3826.

    Structurei

    3D structure databases

    ProteinModelPortaliP27848.
    SMRiP27848. Positions 2-265.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni42 – 432Phosphate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DQF. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184784.
    InParanoidiP27848.
    KOiK07024.
    OMAiAHYINDN.
    OrthoDBiEOG6K13W0.
    PhylomeDBiP27848.

    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.

    P27848-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MYQVVASDLD GTLLSPDHTL SPYAKETLKL LTARGINFVF ATGRHHVDVG
    60 70 80 90 100
    QIRDNLEIKS YMITSNGARV HDLDGNLIFA HNLDRDIASD LFGVVNDNPD
    110 120 130 140 150
    IITNVYRDDE WFMNRHRPEE MRFFKEAVFQ YALYEPGLLE PEGVSKVFFT
    160 170 180 190 200
    CDSHEQLLPL EQAINARWGD RVNVSFSTLT CLEVMAGGVS KGHALEAVAK
    210 220 230 240 250
    KLGYSLKDCI AFGDGMNDAE MLSMAGKGCI MGSAHQRLKD LHPELEVIGT
    260
    NADDAVPHYL RKLYLS
    Length:266
    Mass (Da):29,708
    Last modified:October 11, 2004 - v4
    Checksum:i7C9AFE9CF13D8B2B
    GO

    Sequence cautioni

    The sequence AAA67622.1 differs from that shown. Reason: Frameshift at several positions. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M87049 Genomic DNA. Translation: AAA67622.1. Frameshift.
    U00096 Genomic DNA. Translation: AAT48225.1.
    AP009048 Genomic DNA. Translation: BAE77475.1.
    X03155 Genomic DNA. No translation available.
    RefSeqiWP_000285362.1. NZ_LN832404.1.
    YP_026267.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAT48225; AAT48225; b3826.
    BAE77475; BAE77475; BAE77475.
    GeneIDi2847768.
    KEGGiecj:JW5854.
    eco:b3826.
    PATRICi32123153. VBIEscCol129921_3942.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M87049 Genomic DNA. Translation: AAA67622.1. Frameshift.
    U00096 Genomic DNA. Translation: AAT48225.1.
    AP009048 Genomic DNA. Translation: BAE77475.1.
    X03155 Genomic DNA. No translation available.
    RefSeqiWP_000285362.1. NZ_LN832404.1.
    YP_026267.1. NC_000913.3.

    3D structure databases

    ProteinModelPortaliP27848.
    SMRiP27848. Positions 2-265.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259609. 11 interactions.
    IntActiP27848. 2 interactions.
    STRINGi511145.b3826.

    Proteomic databases

    EPDiP27848.
    PaxDbiP27848.
    PRIDEiP27848.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAT48225; AAT48225; b3826.
    BAE77475; BAE77475; BAE77475.
    GeneIDi2847768.
    KEGGiecj:JW5854.
    eco:b3826.
    PATRICi32123153. VBIEscCol129921_3942.

    Organism-specific databases

    EchoBASEiEB1438.
    EcoGeneiEG11470. yigL.

    Phylogenomic databases

    eggNOGiENOG4105DQF. Bacteria.
    COG0561. LUCA.
    HOGENOMiHOG000184784.
    InParanoidiP27848.
    KOiK07024.
    OMAiAHYINDN.
    OrthoDBiEOG6K13W0.
    PhylomeDBiP27848.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11470-MONOMER.
    ECOL316407:JW5854-MONOMER.
    MetaCyc:EG11470-MONOMER.

    Miscellaneous databases

    PROiP27848.

    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
      Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
      Science 257:771-778(1992) [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. Cited for: SEQUENCE REVISION.
    4. "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.
    5. "Nucleotide sequence of the pldB gene and characteristics of deduced amino acid sequence of lysophospholipase L2 in Escherichia coli."
      Kobayashi T., Kudo I., Karasawa K., Mizushima H., Inoue K., Nojima S.
      J. Biochem. 98:1017-1025(1985) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-83.
      Strain: K12 / KL16-99.
    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, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.

    Entry informationi

    Entry nameiYIGL_ECOLI
    AccessioniPrimary (citable) accession number: P27848
    Secondary accession number(s): P76763, Q2M8D1, Q6BEY9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1992
    Last sequence update: October 11, 2004
    Last modified: March 16, 2016
    This is version 119 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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.