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P79732

- RIR1_DANRE

UniProt

P79732 - RIR1_DANRE

Protein

Ribonucleoside-diphosphate reductase large subunit

Gene

rrm1

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 1 (01 May 1997)
      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 M1 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 sitei5 – 51Allosteric activatorBy similarity
    Binding sitei53 – 531Allosteric activatorBy similarity
    Binding sitei88 – 881Allosteric activatorBy similarity
    Binding sitei202 – 2021SubstrateBy similarity
    Sitei218 – 2181Important for hydrogen atom transferBy similarity
    Sitei226 – 2261Allosteric effector binding, determines substrate specificityBy similarity
    Binding sitei247 – 2471Substrate; via amide nitrogenBy similarity
    Sitei256 – 2561Allosteric effector binding, determines substrate specificityBy similarity
    Active sitei427 – 4271Proton acceptorBy similarity
    Active sitei429 – 4291Cysteine radical intermediateBy similarity
    Active sitei431 – 4311Proton acceptorBy similarity
    Sitei444 – 4441Important for hydrogen atom transferBy similarity
    Sitei737 – 7371Important for electron transferBy similarity
    Sitei738 – 7381Important for electron transferBy similarity
    Sitei789 – 7891Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei792 – 7921Interacts 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):
    Ribonucleoside-diphosphate reductase subunit M1
    Ribonucleotide reductase large subunit
    Ribonucleotide reductase protein R1 class I
    Gene namesi
    Name:rrm1
    OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
    Taxonomic identifieri7955 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
    ProteomesiUP000000437: Unplaced

    Organism-specific databases

    ZFINiZDB-GENE-990415-247. rrm1.

    Subcellular locationi

    GO - Cellular componenti

    1. ribonucleoside-diphosphate reductase complex Source: InterPro

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 794794Ribonucleoside-diphosphate reductase large subunitPRO_0000187192Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi218 ↔ 444Redox-activeBy similarity

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PRIDEiP79732.

    Interactioni

    Subunit structurei

    Heterodimer of a large and a small subunit.

    Protein-protein interaction databases

    STRINGi7955.ENSDARP00000010800.

    Structurei

    3D structure databases

    ProteinModelPortaliP79732.
    SMRiP79732. Positions 15-755.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 9292ATP-conePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni11 – 177Allosteric activator bindingBy similarity
    Regioni217 – 2182Substrate bindingBy similarity
    Regioni285 – 2884Allosteric effector binding, determines substrate specificityBy similarity
    Regioni427 – 4315Substrate bindingBy similarity
    Regioni603 – 6075Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0209.
    HOGENOMiHOG000057035.
    HOVERGENiHBG003447.
    InParanoidiP79732.
    PhylomeDBiP79732.

    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.

    P79732-1 [UniParc]FASTAAdd to Basket

    « Hide

    MHVIKRDGGQ EGVMFDKITS RIQKLCYGLN SDFVDPTQIT MKVIQGLYSG    50
    VTTVELDTLA AETAATSTTK HPDYAILAAR IAVSNLHKET KKVFSEVMED 100
    LYNYVNPLNS RHSPMISKET LDIVLANKDR LNSAIIYDRD FSYNFFGFKT 150
    LERSYLLKIN GKVAERPQHM LMRVSVGIHK EDIAAAIETY NLLSEKWFTH 200
    ASPTLFNAGT NRPQLSSCFL LAMKDDSIEG IYDTLKQCAL ISKSAGGIGV 250
    AVSCIRATGR YIAGTNGNSN GLVPMLRVNN NTARYVDQGG NKRPGAFAMY 300
    LEPWHFDIFD FLELKKNTGK EEQRARDLFY ALWIPDLFMK RVETNGDWSL 350
    MCPNDCPGLD ECWGEEFEKL YAKYEQEGRA KRVVKAQQLW YAIIESQTET 400
    GTPYMLYKDA CNRKSNRQNL GTIKCSNLCT EIVEYTSADE VAVCNLASIA 450
    LNMYVTSERT FDFQKLASVT KVIVKNLNKI IDINYYPVKE AENSNKRHRP 500
    IGIGVQGLAD AFILMRFPFE STEAQLLNTQ IFETIYYAAL ESSCELAAEY 550
    GPYQTYAGCP VSKGILQYDM WEKTPTDLWD WAALKEKIAN DGVRNSLLLA 600
    PMPTASTAQI LGNNESIEPY TSNIYHRRVL SGEFQIVNPH LLKDLTERGL 650
    WNEEMKNQII AQNGSIQTIP AIPDDLKELY KTVWEISQKT ILKMAADRGA 700
    YIDQSQSLNI HIAEPNYGKL TSMHFYGWKQ GLKTGMYYLR TKPGANPIQF 750
    TLNKEKLKET QKTTSSEDEE TKERNKAAMV CSLENRHECL MCGS 794
    Length:794
    Mass (Da):89,816
    Last modified:May 1, 1997 - v1
    Checksum:i128355C073B3908C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U57964 mRNA. Translation: AAB37102.1.
    UniGeneiDr.33356.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U57964 mRNA. Translation: AAB37102.1 .
    UniGenei Dr.33356.

    3D structure databases

    ProteinModelPortali P79732.
    SMRi P79732. Positions 15-755.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 7955.ENSDARP00000010800.

    Proteomic databases

    PRIDEi P79732.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Organism-specific databases

    ZFINi ZDB-GENE-990415-247. rrm1.

    Phylogenomic databases

    eggNOGi COG0209.
    HOGENOMi HOG000057035.
    HOVERGENi HBG003447.
    InParanoidi P79732.
    PhylomeDBi P79732.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .

    Miscellaneous databases

    NextBioi 20807088.
    PROi P79732.

    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. "Cloning and sequencing of cDNAs encoding ribonucleotide reductase from zebrafish Danio rerio."
      Mathews C.Z., Sjoeberg B.-M., Karlsson M.
      Mol. Mar. Biol. Biotechnol. 5:284-287(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].

    Entry informationi

    Entry nameiRIR1_DANRE
    AccessioniPrimary (citable) accession number: P79732
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: May 1, 1997
    Last modified: October 1, 2014
    This is version 100 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3