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Protein

Nudix hydrolase DR_0079

Gene

DR_0079

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolase that converts various nucleotide triphosphates (NTPs) to the corresponding nucleotide monophosphates and diphosphate, and nucleotide diphosphates to nucleotide monophosphates and inorganic phosphate. Has a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). Has lower activity towards the deoxyribose nucleotides dCDP and dCTP, and towards dGDP, TDP and UDP.2 Publications

Cofactori

Mg2+2 Publications

Enzyme regulationi

Inhibited by zinc, calcium or copper ions.1 Publication

Kineticsi

  1. KM=0.082 mM for CDP1 Publication
  2. KM=0.034 mM for CTP1 Publication
  3. KM=0.092 mM for dCDP1 Publication
  4. KM=0.105 mM for TDP1 Publication
  5. KM=0.137 mM for UDP1 Publication
  6. KM=0.092 mM for GDP1 Publication
  7. KM=0.051 mM for dGDP1 Publication
  8. KM=0.046 mM for IDP1 Publication

    pH dependencei

    Optimum pH is 9.0-9.5.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi85 – 851MagnesiumCurated
    Metal bindingi89 – 891MagnesiumCurated

    GO - Molecular functioni

    • hydrolase activity Source: CACAO
    • metal ion binding Source: UniProtKB-KW
    • nucleotide binding Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciDRAD243230:GH46-84-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Nudix hydrolase DR_0079 (EC:3.6.1.-)
    Gene namesi
    Ordered Locus Names:DR_0079
    OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
    Taxonomic identifieri243230 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
    Proteomesi
    • UP000002524 Componenti: Chromosome I

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 171171Nudix hydrolase DR_0079PRO_0000057076Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    STRINGi243230.DR_0079.

    Structurei

    Secondary structure

    1
    171
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 125Combined sources
    Beta strandi18 – 236Combined sources
    Helixi31 – 333Combined sources
    Beta strandi34 – 429Combined sources
    Turni44 – 463Combined sources
    Beta strandi48 – 525Combined sources
    Beta strandi58 – 603Combined sources
    Beta strandi67 – 715Combined sources
    Beta strandi73 – 764Combined sources
    Helixi78 – 9013Combined sources
    Helixi94 – 963Combined sources
    Beta strandi97 – 1059Combined sources
    Turni107 – 1093Combined sources
    Beta strandi113 – 12210Combined sources
    Turni131 – 1333Combined sources
    Beta strandi135 – 1406Combined sources
    Helixi142 – 15110Combined sources
    Helixi159 – 1668Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Q27NMR-A1-171[»]
    2O5FX-ray1.90A/B1-171[»]
    ProteinModelPortaliQ9RY71.
    SMRiQ9RY71. Positions 1-171.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9RY71.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini32 – 162131Nudix hydrolasePROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi69 – 9123Nudix boxAdd
    BLAST

    Sequence similaritiesi

    Belongs to the Nudix hydrolase family.Curated
    Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0494. LUCA.
    HOGENOMiHOG000099699.
    InParanoidiQ9RY71.
    OMAiDFIESFW.
    OrthoDBiPOG091H0F74.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9RY71-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MGGVSDERLD LVNERDEVVG QILRTDPALR WERVRVVNAF LRNSQGQLWI
    60 70 80 90 100
    PRRSPSKSLF PNALDVSVGG AVQSGETYEE AFRREAREEL NVEIDALSWR
    110 120 130 140 150
    PLASFSPFQT TLSSFMCVYE LRSDATPIFN PNDISGGEWL TPEHLLARIA
    160 170
    AGEAAKGDLA ELVRRCYREE E
    Length:171
    Mass (Da):19,283
    Last modified:May 1, 2000 - v1
    Checksum:i254C737BB2A0276E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000513 Genomic DNA. Translation: AAF09672.1.
    PIRiE75562.
    RefSeqiNP_293805.1. NC_001263.1.
    WP_010886727.1. NC_001263.1.

    Genome annotation databases

    EnsemblBacteriaiAAF09672; AAF09672; DR_0079.
    GeneIDi1797409.
    KEGGidra:DR_0079.
    PATRICi21627631. VBIDeiRad64572_0242.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000513 Genomic DNA. Translation: AAF09672.1.
    PIRiE75562.
    RefSeqiNP_293805.1. NC_001263.1.
    WP_010886727.1. NC_001263.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Q27NMR-A1-171[»]
    2O5FX-ray1.90A/B1-171[»]
    ProteinModelPortaliQ9RY71.
    SMRiQ9RY71. Positions 1-171.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243230.DR_0079.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAF09672; AAF09672; DR_0079.
    GeneIDi1797409.
    KEGGidra:DR_0079.
    PATRICi21627631. VBIDeiRad64572_0242.

    Phylogenomic databases

    eggNOGiCOG0494. LUCA.
    HOGENOMiHOG000099699.
    InParanoidiQ9RY71.
    OMAiDFIESFW.
    OrthoDBiPOG091H0F74.

    Enzyme and pathway databases

    BioCyciDRAD243230:GH46-84-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ9RY71.

    Family and domain databases

    Gene3Di3.90.79.10. 1 hit.
    InterProiIPR020084. NUDIX_hydrolase_CS.
    IPR000086. NUDIX_hydrolase_dom.
    IPR015797. NUDIX_hydrolase_dom-like.
    [Graphical view]
    PfamiPF00293. NUDIX. 1 hit.
    [Graphical view]
    SUPFAMiSSF55811. SSF55811. 1 hit.
    PROSITEiPS51462. NUDIX. 1 hit.
    PS00893. NUDIX_BOX. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiY079_DEIRA
    AccessioniPrimary (citable) accession number: Q9RY71
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 10, 2003
    Last sequence update: May 1, 2000
    Last modified: September 7, 2016
    This is version 97 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.