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Q03604

- RIR1_CAEEL

UniProt

Q03604 - RIR1_CAEEL

Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rnr-1

Organism
Caenorhabditis elegans
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 114 (01 Oct 2014)
      Sequence version 1 (01 Oct 1993)
      Previous versions | rss
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    Functioni

    Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.

    Catalytic activityi

    2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

    Enzyme regulationi

    Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the large subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site By similarity.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111Allosteric activatorBy similarity
    Binding sitei59 – 591Allosteric activatorBy similarity
    Binding sitei94 – 941Allosteric activatorBy similarity
    Binding sitei208 – 2081SubstrateBy similarity
    Sitei224 – 2241Important for hydrogen atom transferBy similarity
    Sitei232 – 2321Allosteric effector binding, determines substrate specificityBy similarity
    Binding sitei253 – 2531Substrate; via amide nitrogenBy similarity
    Sitei262 – 2621Allosteric effector binding, determines substrate specificityBy similarity
    Active sitei433 – 4331Proton acceptorBy similarity
    Active sitei435 – 4351Cysteine radical intermediateBy similarity
    Active sitei437 – 4371Proton acceptorBy similarity
    Sitei450 – 4501Important for hydrogen atom transferBy similarity
    Sitei743 – 7431Important for electron transferBy similarity
    Sitei744 – 7441Important for electron transferBy similarity
    Sitei783 – 7831Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei786 – 7861Interacts with thioredoxin/glutaredoxinBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB

    GO - Biological processi

    1. deoxyribonucleotide biosynthetic process Source: UniProtKB
    2. DNA replication Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase large subunit (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase large subunit
    Gene namesi
    Name:rnr-1
    ORF Names:T23G5.1
    OrganismiCaenorhabditis elegans
    Taxonomic identifieri6239 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
    ProteomesiUP000001940: Chromosome III

    Organism-specific databases

    WormBaseiT23G5.1; CE00331; WBGene00004391; rnr-1.

    Subcellular locationi

    GO - Cellular componenti

    1. ribonucleoside-diphosphate reductase complex Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 788788Ribonucleoside-diphosphate reductase large subunitPRO_0000187194Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi224 ↔ 450Redox-activeBy similarity

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiQ03604.
    PRIDEiQ03604.

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.

    Protein-protein interaction databases

    BioGridi41500. 3 interactions.
    DIPiDIP-26889N.
    IntActiQ03604. 3 interactions.
    MINTiMINT-1080458.
    STRINGi6239.T23G5.1.2.

    Structurei

    3D structure databases

    ProteinModelPortaliQ03604.
    SMRiQ03604. Positions 21-748.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini7 – 9892ATP-conePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni17 – 237Allosteric activator bindingBy similarity
    Regioni223 – 2242Substrate bindingBy similarity
    Regioni291 – 2944Allosteric effector binding, determines substrate specificityBy similarity
    Regioni433 – 4375Substrate bindingBy similarity
    Regioni609 – 6135Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0209.
    GeneTreeiENSGT00390000001372.
    HOGENOMiHOG000057035.
    InParanoidiQ03604.
    KOiK10807.
    OMAiEACLMCQ.
    PhylomeDBiQ03604.

    Family and domain databases

    InterProiIPR005144. ATP-cone.
    IPR013346. NrdE_NrdA.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR008926. RNR_R1-su_N.
    [Graphical view]
    PfamiPF03477. ATP-cone. 1 hit.
    PF02867. Ribonuc_red_lgC. 1 hit.
    PF00317. Ribonuc_red_lgN. 1 hit.
    [Graphical view]
    PRINTSiPR01183. RIBORDTASEM1.
    SUPFAMiSSF48168. SSF48168. 1 hit.
    TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
    PROSITEiPS51161. ATP_CONE. 1 hit.
    PS00089. RIBORED_LARGE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q03604-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQRYNSTYVV KRDGRKEDVH FDKITSRIQK LSYGLNMDFV DPVAVAIKVI    50
    SGLYKGVTTV ELDNLAAETA ASMTTQHPEY ALLAARIAVS NLHKKTNKVF 100
    SEVMKTLHEF HHPHTGKHAP MISDETWAII EKNADKLNSA IVYDRDYSYT 150
    YFGFKTLERS YLLKINKEIV ERPQQMLMRV SIGIHGDDIT SAIETYNLMS 200
    ERYMTHASPT LFNSGTCRPQ MSSCFLLTMS EDSILGIYDT LKQCALISKS 250
    AGGIGLNVHK IRATGSVIAG TNGTSNGLIP MLRVYNNTAR YVDQGGNKRP 300
    GAFAIYLEPW HADIFEFVSL RKNTGPEEER ARDLFLALWI PDLFMKRVEK 350
    DQEWSLMCPC ECPGLDDCWG EEFEALYAKY EAEGRVRKTV KARKLWEHIV 400
    SNQIETGLPY ITYKDAANRK SNQQNLGTIK CSNLCTEIIE YSAPDEIAVC 450
    NLASIALNRY VTPEKKFDFV KLAEVTKVIT RNLNKIIDVN YYPVEEARNS 500
    NMRHRPIGLG VQGLADCFML MRYPFTSAEA RDLNKRIFET IYYAALEASC 550
    ELAELNGPYS TYEGSPVSKG QLQFDMWGVT PTDQCDWATL RKKIAKHGIR 600
    NSLLMAPMPT ASTAQILGNN ESIEPYTSNI YSRRVLSGDF QIVNPHMLKD 650
    LVERGLWTDE MKNRLIANNG SIQNIDGIPS DIKELYRTVW EISQKDIIEM 700
    AADRGAYIDQ SQSLNIHMAK PSYAGITSMH FYGWKKGLKT GMYYLRTKPA 750
    VNAVQFTVDK NALKTNQQAE TPATVAESQD EGCLMCSG 788
    Length:788
    Mass (Da):88,970
    Last modified:October 1, 1993 - v1
    Checksum:iB1AF398B173407D4
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z19158 Genomic DNA. Translation: CAA79574.1.
    PIRiS28302.
    RefSeqiNP_499039.1. NM_066638.4.
    UniGeneiCel.7791.

    Genome annotation databases

    EnsemblMetazoaiT23G5.1.1; T23G5.1.1; WBGene00004391.
    T23G5.1.2; T23G5.1.2; WBGene00004391.
    GeneIDi176301.
    KEGGicel:CELE_T23G5.1.
    UCSCiT23G5.1.2. c. elegans.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z19158 Genomic DNA. Translation: CAA79574.1 .
    PIRi S28302.
    RefSeqi NP_499039.1. NM_066638.4.
    UniGenei Cel.7791.

    3D structure databases

    ProteinModelPortali Q03604.
    SMRi Q03604. Positions 21-748.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 41500. 3 interactions.
    DIPi DIP-26889N.
    IntActi Q03604. 3 interactions.
    MINTi MINT-1080458.
    STRINGi 6239.T23G5.1.2.

    Proteomic databases

    PaxDbi Q03604.
    PRIDEi Q03604.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblMetazoai T23G5.1.1 ; T23G5.1.1 ; WBGene00004391 .
    T23G5.1.2 ; T23G5.1.2 ; WBGene00004391 .
    GeneIDi 176301.
    KEGGi cel:CELE_T23G5.1.
    UCSCi T23G5.1.2. c. elegans.

    Organism-specific databases

    CTDi 176301.
    WormBasei T23G5.1 ; CE00331 ; WBGene00004391 ; rnr-1.

    Phylogenomic databases

    eggNOGi COG0209.
    GeneTreei ENSGT00390000001372.
    HOGENOMi HOG000057035.
    InParanoidi Q03604.
    KOi K10807.
    OMAi EACLMCQ.
    PhylomeDBi Q03604.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .

    Miscellaneous databases

    NextBioi 891992.
    PROi Q03604.

    Family and domain databases

    InterProi IPR005144. ATP-cone.
    IPR013346. NrdE_NrdA.
    IPR000788. RNR_lg_C.
    IPR013509. RNR_lsu_N.
    IPR008926. RNR_R1-su_N.
    [Graphical view ]
    Pfami PF03477. ATP-cone. 1 hit.
    PF02867. Ribonuc_red_lgC. 1 hit.
    PF00317. Ribonuc_red_lgN. 1 hit.
    [Graphical view ]
    PRINTSi PR01183. RIBORDTASEM1.
    SUPFAMi SSF48168. SSF48168. 1 hit.
    TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
    PROSITEi PS51161. ATP_CONE. 1 hit.
    PS00089. RIBORED_LARGE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Bristol N2.
    2. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
      The C. elegans sequencing consortium
      Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Bristol N2.

    Entry informationi

    Entry nameiRIR1_CAEEL
    AccessioniPrimary (citable) accession number: Q03604
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: October 1, 1993
    Last modified: October 1, 2014
    This is version 114 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programCaenorhabditis annotation project

    Miscellaneousi

    Keywords - Technical termi

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. Caenorhabditis elegans
      Caenorhabditis elegans: entries, gene names and cross-references to WormBase
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3