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Protein

Cyclic di-GMP phosphodiesterase YahA

Gene

yahA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes c-di-GMP (cyclic bis(3'-5') dimeric GMP) to 5'-pGpG, known as PDE-A activity. PDE-B activity, that is hydrolysis of 5'-pGpG to GMP, proceeds only very slowly.

Cofactori

Mg2+1 Publication, Mn2+1 Publication

Kineticsi

  1. KM=25 µM for c-di-GMP

    pH dependencei

    Optimum pH is 9.35.

    GO - Molecular functioni

    • cyclic-guanylate-specific phosphodiesterase activity Source: EcoCyc
    • DNA binding Source: UniProtKB-KW

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    c-di-GMP, DNA-binding, Magnesium, Manganese

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11236-MONOMER.
    ECOL316407:JW0307-MONOMER.
    MetaCyc:EG11236-MONOMER.
    SABIO-RKP21514.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cyclic di-GMP phosphodiesterase YahA (EC:3.1.4.-)
    Gene namesi
    Name:yahA
    Ordered Locus Names:b0315, JW0307
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11236. yahA.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 362362Cyclic di-GMP phosphodiesterase YahAPRO_0000168573Add
    BLAST

    Proteomic databases

    PaxDbiP21514.
    PRIDEiP21514.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4262803. 8 interactions.
    IntActiP21514. 3 interactions.
    STRINGi511145.b0315.

    Structurei

    Secondary structure

    1
    362
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi105 – 1084Combined sources
    Helixi110 – 1189Combined sources
    Beta strandi122 – 13110Combined sources
    Turni132 – 1343Combined sources
    Beta strandi137 – 14812Combined sources
    Turni149 – 1513Combined sources
    Beta strandi152 – 1543Combined sources
    Helixi156 – 1583Combined sources
    Helixi160 – 1667Combined sources
    Helixi169 – 18416Combined sources
    Helixi185 – 1906Combined sources
    Beta strandi195 – 2006Combined sources
    Helixi203 – 2075Combined sources
    Helixi211 – 22212Combined sources
    Turni224 – 2263Combined sources
    Beta strandi227 – 23711Combined sources
    Helixi243 – 25412Combined sources
    Beta strandi258 – 2636Combined sources
    Helixi268 – 2769Combined sources
    Beta strandi280 – 2845Combined sources
    Helixi286 – 2927Combined sources
    Helixi296 – 30813Combined sources
    Turni311 – 3133Combined sources
    Beta strandi315 – 3184Combined sources
    Helixi324 – 3329Combined sources
    Beta strandi337 – 3404Combined sources
    Turni341 – 3433Combined sources
    Helixi349 – 3568Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4KIEX-ray1.70A96-362[»]
    4LJ3X-ray1.70A/B101-362[»]
    4LYKX-ray2.40A/B/C/D101-362[»]
    ProteinModelPortaliP21514.
    SMRiP21514. Positions 25-75, 98-358.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini18 – 8366HTH luxR-typePROSITE-ProRule annotationAdd
    BLAST
    Domaini106 – 360255EALPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 EAL domain.PROSITE-ProRule annotation
    Contains 1 HTH luxR-type DNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG4105BZU. Bacteria.
    COG2200. LUCA.
    COG2771. LUCA.
    HOGENOMiHOG000117345.
    InParanoidiP21514.
    KOiK13244.
    OMAiTTELMNC.
    PhylomeDBiP21514.

    Family and domain databases

    CDDicd01948. EAL. 1 hit.
    cd06170. LuxR_C_like. 1 hit.
    Gene3Di1.10.10.10. 1 hit.
    3.20.20.450. 1 hit.
    InterProiIPR001633. EAL_dom.
    IPR016032. Sig_transdc_resp-reg_C-effctor.
    IPR000792. Tscrpt_reg_LuxR_C.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF00563. EAL. 1 hit.
    PF00196. GerE. 1 hit.
    [Graphical view]
    SMARTiSM00052. EAL. 1 hit.
    SM00421. HTH_LUXR. 1 hit.
    [Graphical view]
    SUPFAMiSSF141868. SSF141868. 1 hit.
    SSF46894. SSF46894. 1 hit.
    PROSITEiPS50883. EAL. 1 hit.
    PS50043. HTH_LUXR_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P21514-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNSCDFRVFL QEFGTTVHLS LPGSVSEKER LLLKLLMQGM SVTEISQYRN
    60 70 80 90 100
    RSAKTISHQK KQLFEKLGIQ SDITFWRDIF FQYNPEIISA TGSNSHRYIN
    110 120 130 140 150
    DNHYHHIVTP EAISLALENH EFKPWIQPVF CAQTGVLTGC EVLVRWEHPQ
    160 170 180 190 200
    TGIIPPDQFI PLAESSGLIV IMTRQLMKQT ADILMPVKHL LPDNFHIGIN
    210 220 230 240 250
    VSAGCFLAAG FEKECLNLVN KLGNDKIKLV LELTERNPIP VTPEARAIFD
    260 270 280 290 300
    SLHQHNITFA LDDFGTGYAT YRYLQAFPVD FIKIDKSFVQ MASVDEISGH
    310 320 330 340 350
    IVDNIVELAR KPGLSIVAEG VETQEQADLM IGKGVHFLQG YLYSPPVPGN
    360
    KFISEWVMKA GG
    Length:362
    Mass (Da):40,725
    Last modified:November 1, 1997 - v2
    Checksum:i4BCA091840F27A0D
    GO

    Sequence cautioni

    The sequence AAB18041 differs from that shown. Reason: Erroneous initiation. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U73857 Genomic DNA. Translation: AAB18041.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73418.1.
    AP009048 Genomic DNA. Translation: BAE76098.1.
    X52905 Genomic DNA. Translation: CAA37089.1.
    PIRiC64758.
    RefSeqiNP_414849.1. NC_000913.3.
    WP_001301264.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73418; AAC73418; b0315.
    BAE76098; BAE76098; BAE76098.
    GeneIDi947459.
    KEGGiecj:JW0307.
    eco:b0315.
    PATRICi32115759. VBIEscCol129921_0322.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U73857 Genomic DNA. Translation: AAB18041.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73418.1.
    AP009048 Genomic DNA. Translation: BAE76098.1.
    X52905 Genomic DNA. Translation: CAA37089.1.
    PIRiC64758.
    RefSeqiNP_414849.1. NC_000913.3.
    WP_001301264.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4KIEX-ray1.70A96-362[»]
    4LJ3X-ray1.70A/B101-362[»]
    4LYKX-ray2.40A/B/C/D101-362[»]
    ProteinModelPortaliP21514.
    SMRiP21514. Positions 25-75, 98-358.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4262803. 8 interactions.
    IntActiP21514. 3 interactions.
    STRINGi511145.b0315.

    Proteomic databases

    PaxDbiP21514.
    PRIDEiP21514.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73418; AAC73418; b0315.
    BAE76098; BAE76098; BAE76098.
    GeneIDi947459.
    KEGGiecj:JW0307.
    eco:b0315.
    PATRICi32115759. VBIEscCol129921_0322.

    Organism-specific databases

    EchoBASEiEB1218.
    EcoGeneiEG11236. yahA.

    Phylogenomic databases

    eggNOGiENOG4105BZU. Bacteria.
    COG2200. LUCA.
    COG2771. LUCA.
    HOGENOMiHOG000117345.
    InParanoidiP21514.
    KOiK13244.
    OMAiTTELMNC.
    PhylomeDBiP21514.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11236-MONOMER.
    ECOL316407:JW0307-MONOMER.
    MetaCyc:EG11236-MONOMER.
    SABIO-RKP21514.

    Miscellaneous databases

    PROiP21514.

    Family and domain databases

    CDDicd01948. EAL. 1 hit.
    cd06170. LuxR_C_like. 1 hit.
    Gene3Di1.10.10.10. 1 hit.
    3.20.20.450. 1 hit.
    InterProiIPR001633. EAL_dom.
    IPR016032. Sig_transdc_resp-reg_C-effctor.
    IPR000792. Tscrpt_reg_LuxR_C.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF00563. EAL. 1 hit.
    PF00196. GerE. 1 hit.
    [Graphical view]
    SMARTiSM00052. EAL. 1 hit.
    SM00421. HTH_LUXR. 1 hit.
    [Graphical view]
    SUPFAMiSSF141868. SSF141868. 1 hit.
    SSF46894. SSF46894. 1 hit.
    PROSITEiPS50883. EAL. 1 hit.
    PS50043. HTH_LUXR_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYAHA_ECOLI
    AccessioniPrimary (citable) accession number: P21514
    Secondary accession number(s): P75689, Q2MCA8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: November 1, 1997
    Last modified: September 7, 2016
    This is version 128 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    An overexpressed EAL domain (residues 77-362) has similar KM, Vmax, pH and metal dependence and subunit composition as the full-length protein.

    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.