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Protein

Ribonucleoside-diphosphate reductase large chain 1

Gene

RNR1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.1 Publication

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 R1 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. Inhibited by SML1.1 Publication

Kineticsi

    1. Vmax=2250 nmol/min/mg enzyme for cytidine 5'-diphosphate1 Publication

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.1 Publication

    Pathwayi: DNA replication

    This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
    View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei5Allosteric activatorBy similarity1
    Binding sitei53Allosteric activatorBy similarity1
    Binding sitei88Allosteric activatorBy similarity1
    Binding sitei202Substrate1
    Sitei218Important for hydrogen atom transferBy similarity1
    Sitei226Allosteric effector binding, determines substrate specificity1
    Binding sitei247Substrate; via amide nitrogen1
    Sitei256Allosteric effector binding, determines substrate specificity1
    Active sitei426Proton acceptor1
    Active sitei428Cysteine radical intermediate1
    Active sitei430Proton acceptor1
    Sitei443Important for hydrogen atom transferBy similarity1
    Sitei741Important for electron transferBy similarity1
    Sitei742Important for electron transferBy similarity1
    Sitei883Interacts with thioredoxin/glutaredoxinBy similarity1
    Sitei886Interacts with thioredoxin/glutaredoxinBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:YER070W-MONOMER.
    YEAST:YER070W-MONOMER.
    BRENDAi1.17.4.1. 984.
    ReactomeiR-SCE-499943. Synthesis and interconversion of nucleotide di- and triphosphates.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase large chain 1 (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase R1 subunit 1
    Ribonucleotide reductase large subunit 1
    Gene namesi
    Name:RNR1
    Synonyms:CRT7, RIR1, SDS12
    Ordered Locus Names:YER070W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome V

    Organism-specific databases

    EuPathDBiFungiDB:YER070W.
    SGDiS000000872. RNR1.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: SGD
    • ribonucleoside-diphosphate reductase complex Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi428C → A: Completely abolishes reductase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001872031 – 888Ribonucleoside-diphosphate reductase large chain 1Add BLAST888

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi218 ↔ 443Redox-active1 Publication
    Modified residuei227PhosphoserineCombined sources1
    Cross-linki387Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei816PhosphoserineBy similarity1
    Modified residuei837PhosphoserineCombined sources1
    Cross-linki853Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
    Modified residuei887PhosphoserineCombined sources1

    Keywords - PTMi

    Disulfide bond, Isopeptide bond, Phosphoprotein, Ubl conjugation

    Proteomic databases

    MaxQBiP21524.
    PRIDEiP21524.

    PTM databases

    iPTMnetiP21524.

    Expressioni

    Inductioni

    Cell cycle-regulated with highest activity in S phase. Moderately induced by DNA-damage.1 Publication

    Interactioni

    Subunit structurei

    Heterotetramer of two large (R1) and two small (R2) subunits. S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two different R2 subunits (RNR2 and RNR4). The functional form of the small subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-radical center and RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Under normal growth conditions, the active form of the large subunits is a homodimer of the constitutively expressed RNR1. In damaged cells or cells arrested for DNA synthesis, the reductase consists of multiple species because of the association of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a heterodimer of RNR1 and the damage-inducible RNR3. RNR1 interacts with the ribonucleotide reductase inhibitor SML1.4 Publications

    Protein-protein interaction databases

    BioGridi36813. 63 interactors.
    DIPiDIP-6299N.
    IntActiP21524. 10 interactors.
    MINTiMINT-680321.

    Structurei

    Secondary structure

    1888
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi19 – 23Combined sources5
    Turni31 – 33Combined sources3
    Helixi36 – 41Combined sources6
    Helixi53 – 66Combined sources14
    Turni67 – 70Combined sources4
    Helixi79 – 89Combined sources11
    Helixi94 – 102Combined sources9
    Turni107 – 110Combined sources4
    Helixi118 – 126Combined sources9
    Helixi128 – 132Combined sources5
    Helixi137 – 142Combined sources6
    Helixi145 – 154Combined sources10
    Beta strandi158 – 163Combined sources6
    Helixi167 – 179Combined sources13
    Helixi183 – 194Combined sources12
    Beta strandi197 – 200Combined sources4
    Helixi202 – 207Combined sources6
    Beta strandi210 – 212Combined sources3
    Beta strandi218 – 222Combined sources5
    Helixi228 – 242Combined sources15
    Turni243 – 245Combined sources3
    Beta strandi247 – 251Combined sources5
    Turni263 – 266Combined sources4
    Helixi272 – 285Combined sources14
    Turni288 – 291Combined sources4
    Beta strandi297 – 301Combined sources5
    Helixi308 – 311Combined sources4
    Turni312 – 315Combined sources4
    Beta strandi317 – 319Combined sources3
    Helixi321 – 323Combined sources3
    Beta strandi328 – 334Combined sources7
    Helixi336 – 343Combined sources8
    Beta strandi347 – 351Combined sources5
    Turni353 – 355Combined sources3
    Helixi359 – 361Combined sources3
    Helixi364 – 376Combined sources13
    Beta strandi380 – 384Combined sources5
    Helixi385 – 399Combined sources15
    Beta strandi403 – 406Combined sources4
    Helixi407 – 412Combined sources6
    Turni415 – 419Combined sources5
    Beta strandi427 – 429Combined sources3
    Beta strandi441 – 443Combined sources3
    Beta strandi445 – 449Combined sources5
    Helixi450 – 453Combined sources4
    Beta strandi454 – 456Combined sources3
    Beta strandi458 – 462Combined sources5
    Beta strandi463 – 465Combined sources3
    Helixi467 – 487Combined sources21
    Helixi493 – 502Combined sources10
    Beta strandi506 – 510Combined sources5
    Helixi512 – 519Combined sources8
    Helixi526 – 554Combined sources29
    Helixi564 – 567Combined sources4
    Helixi571 – 574Combined sources4
    Beta strandi581 – 583Combined sources3
    Helixi585 – 595Combined sources11
    Helixi611 – 615Combined sources5
    Beta strandi619 – 622Combined sources4
    Beta strandi627 – 629Combined sources3
    Beta strandi634 – 636Combined sources3
    Beta strandi638 – 641Combined sources4
    Helixi643 – 651Combined sources9
    Helixi657 – 664Combined sources8
    Turni665 – 668Combined sources4
    Helixi678 – 683Combined sources6
    Helixi687 – 689Combined sources3
    Helixi692 – 703Combined sources12
    Beta strandi714 – 718Combined sources5
    Helixi721 – 734Combined sources14
    Beta strandi737 – 741Combined sources5
    Beta strandi743 – 745Combined sources3
    Turni748 – 751Combined sources4
    Helixi760 – 763Combined sources4
    Helixi764 – 766Combined sources3
    Turni789 – 791Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ZYZX-ray2.90A/B1-888[»]
    1ZZDX-ray2.60A1-888[»]
    2CVSX-ray2.60A1-888[»]
    2CVTX-ray3.20A1-888[»]
    2CVUX-ray2.90A1-888[»]
    2CVVX-ray2.90A1-888[»]
    2CVWX-ray2.40A1-888[»]
    2CVXX-ray2.20A1-888[»]
    2CVYX-ray2.40A1-888[»]
    2EUDX-ray2.30A1-888[»]
    2ZLFX-ray2.59A1-888[»]
    2ZLGX-ray2.52A1-888[»]
    3K8TX-ray2.10A1-888[»]
    3PAWX-ray6.61A/B/C/D1-888[»]
    3RSRX-ray2.30A1-888[»]
    3S87X-ray2.25A1-888[»]
    3S8AX-ray2.90A1-888[»]
    3S8BX-ray2.80A1-888[»]
    3S8CX-ray2.77A1-888[»]
    3TB9X-ray2.53A1-888[»]
    3TBAX-ray2.80A1-888[»]
    ProteinModelPortaliP21524.
    SMRiP21524.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP21524.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini1 – 92ATP-conePROSITE-ProRule annotationAdd BLAST92

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni11 – 17Allosteric activator bindingBy similarity7
    Regioni217 – 218Substrate binding2
    Regioni285 – 288Allosteric effector binding, determines substrate specificity4
    Regioni426 – 430Substrate binding5
    Regioni607 – 611Substrate binding5

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    GeneTreeiENSGT00390000001372.
    HOGENOMiHOG000057035.
    InParanoidiP21524.
    KOiK10807.
    OMAiTLFMTDK.
    OrthoDBiEOG092C0QYB.

    Family and domain databases

    InterProiIPR005144. ATP-cone_dom.
    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.

    P21524-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MYVYKRDGRK EPVQFDKITA RISRLCYGLD PKHIDAVKVT QRIISGVYEG
    60 70 80 90 100
    VTTIELDNLA AETCAYMTTV HPDYATLAAR IAISNLHKQT TKQFSKVVED
    110 120 130 140 150
    LYRYVNAATG KPAPMISDDV YNIVMENKDK LNSAIVYDRD FQYSYFGFKT
    160 170 180 190 200
    LERSYLLRIN GQVAERPQHL IMRVALGIHG RDIEAALETY NLMSLKYFTH
    210 220 230 240 250
    ASPTLFNAGT PKPQMSSCFL VAMKEDSIEG IYDTLKECAL ISKTAGGIGL
    260 270 280 290 300
    HIHNIRSTGS YIAGTNGTSN GLIPMIRVFN NTARYVDQGG NKRPGAFALY
    310 320 330 340 350
    LEPWHADIFD FIDIRKNHGK EEIRARDLFP ALWIPDLFMK RVEENGTWTL
    360 370 380 390 400
    FSPTSAPGLS DCYGDEFEAL YTRYEKEGRG KTIKAQKLWY SILEAQTETG
    410 420 430 440 450
    TPFVVYKDAC NRKSNQKNLG VIKSSNLCCE IVEYSAPDET AVCNLASVAL
    460 470 480 490 500
    PAFIETSEDG KTSTYNFKKL HEIAKVVTRN LNRVIDRNYY PVEEARKSNM
    510 520 530 540 550
    RHRPIALGVQ GLADTFMLLR LPFDSEEARL LNIQIFETIY HASMEASCEL
    560 570 580 590 600
    AQKDGPYETF QGSPASQGIL QFDMWDQKPY GMWDWDTLRK DIMKHGVRNS
    610 620 630 640 650
    LTMAPMPTAS TSQILGYNEC FEPVTSNMYS RRVLSGEFQV VNPYLLRDLV
    660 670 680 690 700
    DLGIWDEGMK QYLITQNGSI QGLPNVPQEL KDLYKTVWEI SQKTIINMAA
    710 720 730 740 750
    DRSVYIDQSH SLNLFLRAPT MGKLTSMHFY GWKKGLKTGM YYLRTQAASA
    760 770 780 790 800
    AIQFTIDQKI ADQATENVAD ISNLKRPSYM PSSASYAASD FVPAAVTANA
    810 820 830 840 850
    TIPSLDSSSE ASREASPAPT GSHSLTKGMA ELNVQESKVE VPEVPAPTKN
    860 870 880
    EEKAAPIVDD EETEFDIYNS KVIACAIDNP EACEMCSG
    Length:888
    Mass (Da):99,561
    Last modified:February 1, 1995 - v2
    Checksum:i56BE1B077916E419
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti329F → L in CAA49151 (PubMed:8121398).Curated1
    Sequence conflicti587 – 589TLR → NLK in CAA49150 (PubMed:8121398).Curated3
    Sequence conflicti666Q → E no nucleotide entry (PubMed:2199320).Curated1
    Sequence conflicti679E → Q no nucleotide entry (PubMed:2199320).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18813 Genomic DNA. Translation: AAB64606.1.
    X69216 Genomic DNA. Translation: CAA49150.1.
    X69217 Genomic DNA. Translation: CAA49151.1.
    BK006939 Genomic DNA. Translation: DAA07729.1.
    PIRiS50573.
    RefSeqiNP_010993.1. NM_001178961.1.

    Genome annotation databases

    EnsemblFungiiYER070W; YER070W; YER070W.
    GeneIDi856801.
    KEGGisce:YER070W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18813 Genomic DNA. Translation: AAB64606.1.
    X69216 Genomic DNA. Translation: CAA49150.1.
    X69217 Genomic DNA. Translation: CAA49151.1.
    BK006939 Genomic DNA. Translation: DAA07729.1.
    PIRiS50573.
    RefSeqiNP_010993.1. NM_001178961.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ZYZX-ray2.90A/B1-888[»]
    1ZZDX-ray2.60A1-888[»]
    2CVSX-ray2.60A1-888[»]
    2CVTX-ray3.20A1-888[»]
    2CVUX-ray2.90A1-888[»]
    2CVVX-ray2.90A1-888[»]
    2CVWX-ray2.40A1-888[»]
    2CVXX-ray2.20A1-888[»]
    2CVYX-ray2.40A1-888[»]
    2EUDX-ray2.30A1-888[»]
    2ZLFX-ray2.59A1-888[»]
    2ZLGX-ray2.52A1-888[»]
    3K8TX-ray2.10A1-888[»]
    3PAWX-ray6.61A/B/C/D1-888[»]
    3RSRX-ray2.30A1-888[»]
    3S87X-ray2.25A1-888[»]
    3S8AX-ray2.90A1-888[»]
    3S8BX-ray2.80A1-888[»]
    3S8CX-ray2.77A1-888[»]
    3TB9X-ray2.53A1-888[»]
    3TBAX-ray2.80A1-888[»]
    ProteinModelPortaliP21524.
    SMRiP21524.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36813. 63 interactors.
    DIPiDIP-6299N.
    IntActiP21524. 10 interactors.
    MINTiMINT-680321.

    PTM databases

    iPTMnetiP21524.

    Proteomic databases

    MaxQBiP21524.
    PRIDEiP21524.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYER070W; YER070W; YER070W.
    GeneIDi856801.
    KEGGisce:YER070W.

    Organism-specific databases

    EuPathDBiFungiDB:YER070W.
    SGDiS000000872. RNR1.

    Phylogenomic databases

    GeneTreeiENSGT00390000001372.
    HOGENOMiHOG000057035.
    InParanoidiP21524.
    KOiK10807.
    OMAiTLFMTDK.
    OrthoDBiEOG092C0QYB.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BioCyciMetaCyc:YER070W-MONOMER.
    YEAST:YER070W-MONOMER.
    BRENDAi1.17.4.1. 984.
    ReactomeiR-SCE-499943. Synthesis and interconversion of nucleotide di- and triphosphates.

    Miscellaneous databases

    EvolutionaryTraceiP21524.
    PROiP21524.

    Family and domain databases

    InterProiIPR005144. ATP-cone_dom.
    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]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIR1_YEAST
    AccessioniPrimary (citable) accession number: P21524
    Secondary accession number(s): D3DLX5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: February 1, 1995
    Last modified: November 2, 2016
    This is version 167 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Two distinct regulatory sites have been defined: the specificity site, which controls substrate specificity, and the activity site which regulates overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2 (By similarity).By similarity
    Present with 293000 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    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.