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Protein

GMP/IMP nucleotidase YrfG

Gene

yrfG

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 different purine nucleotides (GMP and IMP). Also hydrolyzes flavin mononucleotide (FMN).1 Publication

Catalytic activityi

A 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.

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=0.010 mM for IMP (with manganese ions as cofactor and at pH 9)1 Publication
  2. KM=0.012 mM for GMP (with manganese ions as cofactor and at pH 9)1 Publication
  3. KM=0.062 mM for GMP (with magnesium ions as cofactor and at pH 9)1 Publication
  4. KM=0.22 mM for IMP (with magnesium ions 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
    Metal bindingi11 – 111MagnesiumBy similarity
    Binding sitei149 – 1491SubstrateBy similarity
    Metal bindingi174 – 1741MagnesiumBy similarity

    GO - Molecular functioni

    • GMP 5'-nucleotidase activity Source: EcoCyc
    • IMP 5'-nucleotidase activity Source: EcoCyc
    • magnesium ion binding Source: UniProtKB
    • manganese ion binding Source: UniProtKB
    • purine nucleosidase activity Source: EcoliWiki

    GO - Biological processi

    • dephosphorylation Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Manganese, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7742-MONOMER.
    ECOL316407:JW5865-MONOMER.
    MetaCyc:G7742-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    GMP/IMP nucleotidase YrfG (EC:3.1.3.5)
    Gene namesi
    Name:yrfG
    Ordered Locus Names:b3399, JW5865
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12928. yrfG.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 222222GMP/IMP nucleotidase YrfGPRO_0000169542Add
    BLAST

    Proteomic databases

    PaxDbiP64636.

    Interactioni

    Protein-protein interaction databases

    BioGridi4260978. 19 interactions.
    STRINGi511145.b3399.

    Structurei

    3D structure databases

    ProteinModelPortaliP64636.
    SMRiP64636. Positions 70-190.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni9 – 113Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the HAD-like hydrolase superfamily.Curated

    Phylogenomic databases

    eggNOGiENOG4107Y3D. Bacteria.
    COG1011. LUCA.
    HOGENOMiHOG000271571.
    InParanoidiP64636.
    KOiK07025.
    OMAiNPDSQKP.
    OrthoDBiEOG6F81PG.
    PhylomeDBiP64636.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    PRINTSiPR00413. HADHALOGNASE.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01509. HAD-SF-IA-v3. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P64636-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MHINIAWQDV DTVLLDMDGT LLDLAFDNYF WQKLVPETWG AKNGVTPQEA
    60 70 80 90 100
    MEYMRQQYHD VQHTLNWYCL DYWSEQLGLD ICAMTTEMGP RAVLREDTIP
    110 120 130 140 150
    FLEALKASGK QRILLTNAHP HNLAVKLEHT GLDAHLDLLL STHTFGYPKE
    160 170 180 190 200
    DQRLWHAVAE ATGLKAERTL FIDDSEAILD AAAQFGIRYC LGVTNPDSGI
    210 220
    AEKQYQRHPS LNDYRRLIPS LM
    Length:222
    Mass (Da):25,399
    Last modified:October 11, 2004 - v1
    Checksum:iAC2AB3BCFE779491
    GO

    Sequence cautioni

    The sequence AAA58196.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA58196.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76424.2.
    AP009048 Genomic DNA. Translation: BAE77892.1.
    PIRiB65135.
    RefSeqiNP_417858.4. NC_000913.3.
    WP_001295168.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76424; AAC76424; b3399.
    BAE77892; BAE77892; BAE77892.
    GeneIDi947904.
    KEGGiecj:JW5865.
    eco:b3399.
    PATRICi32122232. VBIEscCol129921_3493.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18997 Genomic DNA. Translation: AAA58196.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76424.2.
    AP009048 Genomic DNA. Translation: BAE77892.1.
    PIRiB65135.
    RefSeqiNP_417858.4. NC_000913.3.
    WP_001295168.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP64636.
    SMRiP64636. Positions 70-190.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260978. 19 interactions.
    STRINGi511145.b3399.

    Proteomic databases

    PaxDbiP64636.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76424; AAC76424; b3399.
    BAE77892; BAE77892; BAE77892.
    GeneIDi947904.
    KEGGiecj:JW5865.
    eco:b3399.
    PATRICi32122232. VBIEscCol129921_3493.

    Organism-specific databases

    EchoBASEiEB2764.
    EcoGeneiEG12928. yrfG.

    Phylogenomic databases

    eggNOGiENOG4107Y3D. Bacteria.
    COG1011. LUCA.
    HOGENOMiHOG000271571.
    InParanoidiP64636.
    KOiK07025.
    OMAiNPDSQKP.
    OrthoDBiEOG6F81PG.
    PhylomeDBiP64636.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7742-MONOMER.
    ECOL316407:JW5865-MONOMER.
    MetaCyc:G7742-MONOMER.

    Miscellaneous databases

    PROiP64636.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006439. HAD-SF_hydro_IA.
    [Graphical view]
    PfamiPF13419. HAD_2. 1 hit.
    [Graphical view]
    PRINTSiPR00413. HADHALOGNASE.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01509. HAD-SF-IA-v3. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    2. "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.
    3. "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 PURINE NUCLEOTIDASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.

    Entry informationi

    Entry nameiYRFG_ECOLI
    AccessioniPrimary (citable) accession number: P64636
    Secondary accession number(s): P45801, Q2M764
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 11, 2004
    Last sequence update: October 11, 2004
    Last modified: January 20, 2016
    This is version 87 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

    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.