Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P21672

- RIR3_YEAST

UniProt

P21672 - RIR3_YEAST

Protein

Ribonucleoside-diphosphate reductase large chain 2

Gene

RNR3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 142 (01 Oct 2014)
      Sequence version 4 (01 Feb 1995)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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 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 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 sitei426 – 4261Proton acceptorBy similarity
    Active sitei428 – 4281Cysteine radical intermediateBy similarity
    Active sitei430 – 4301Proton acceptorBy similarity
    Sitei443 – 4431Important for hydrogen atom transferBy similarity
    Sitei741 – 7411Important for electron transferBy similarity
    Sitei742 – 7421Important for electron transferBy similarity
    Sitei864 – 8641Interacts with thioredoxin/glutaredoxinBy similarity
    Sitei867 – 8671Interacts with thioredoxin/glutaredoxinBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. deoxyribonucleotide biosynthetic process Source: SGD
    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

    BioCyciMetaCyc:YIL066C-MONOMER.
    YEAST:YIL066C-MONOMER.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase large chain 2 (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase DNA damage-inducible regulatory subunit 2
    Ribonucleotide reductase R1 subunit 2
    Ribonucleotide reductase large subunit 2
    Gene namesi
    Name:RNR3
    Synonyms:DIN1
    Ordered Locus Names:YIL066C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IX

    Organism-specific databases

    CYGDiYIL066c.
    SGDiS000001328. RNR3.

    Subcellular locationi

    Cytoplasm 1 Publication

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. ribonucleoside-diphosphate reductase complex Source: SGD

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 869869Ribonucleoside-diphosphate reductase large chain 2PRO_0000187204Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi218 ↔ 443Redox-activeBy similarity
    Modified residuei806 – 8061Phosphoserine1 Publication

    Keywords - PTMi

    Disulfide bond, Phosphoprotein

    Proteomic databases

    MaxQBiP21672.
    PaxDbiP21672.
    PeptideAtlasiP21672.
    PRIDEiP21672.

    Expressioni

    Inductioni

    Highly induced by DNA-damage.2 Publications

    Gene expression databases

    GenevestigatoriP21672.

    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.

    Protein-protein interaction databases

    BioGridi34926. 29 interactions.
    DIPiDIP-2563N.
    IntActiP21672. 1 interaction.
    MINTiMINT-425113.
    STRINGi4932.YIL066C.

    Structurei

    3D structure databases

    ProteinModelPortaliP21672.
    SMRiP21672. Positions 1-787.
    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
    Regioni426 – 4305Substrate bindingBy similarity
    Regioni607 – 6115Substrate bindingBy similarity

    Sequence similaritiesi

    Contains 1 ATP-cone domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0209.
    GeneTreeiENSGT00390000001372.
    HOGENOMiHOG000057035.
    KOiK10807.
    OMAiKECAMIS.
    OrthoDBiEOG7C5MHR.

    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.

    P21672-1 [UniParc]FASTAAdd to Basket

    « Hide

    MYVIKRDGRK EPVQFDKITS RITRLSYGLD PNRIDAVKVT QRIISGVYSG    50
    VTTVELDNLA AETCAYMTTV HPDYATLAAR IAISNLHKQT TKQFSKVIED 100
    LHDWINPATG KHAPMISDEI YNIVMENKDT LNSAIVYDRD FQYTYFGFKT 150
    LERSYLLRLN GEVAERPQHL VMRVALGIHG SDIESVLKTY NLMSLRYFTH 200
    ASPTLFNAGT PHPQMSSCFL IAMKDDSIEG IYDTLKECAM ISKTAGGVGL 250
    HINNIRSTGS YIAGTNGTSN GLIPMIRVFN NTARYVDQGG NKRPGAFALF 300
    LEPWHADIFD FVDIRKTHGK EEIRARDLFP ALWIPDLFMK RVQEDGPWTL 350
    FSPSAAPGLD DVWGDEFEEL YTRYEREGRG KTIKAQKLWY AILQAQTETG 400
    TPFMVYKDAC NRKTNQQNLG TIKSSNLCCE IVEYSSPDET AVCNLASIAL 450
    PAFVEVSEDG KTASYNFERL HEIAKVITHN LNRVIDRNYY PVPEARNSNM 500
    KHRPIALGVQ GLADTYMMLR LPFESEEAQT LNKQIFETIY HATLEASCEL 550
    AQKEGKYSTF EGSPASKGIL QFDMWNAKPF GMWDWETLRK DIVKHGLRNS 600
    LTMAPMPTAS TSQILGYNEC FEPVTSNMYS RRVLSGEFQV VNPYLLRDLV 650
    DLGIWDDSMK QYLITQNGSI QGLPNVPQEL KELYKTVWEI SQKTIINMAA 700
    DRAIYIDQSH SLNLFLQAPS MGKITSMHFY GWKKGLKTGM YYLRTQAASA 750
    AIQFTIDQEV ADQAATHIAS VSELDRPVYV PKGTKFSEQK AASALTESSD 800
    NEKDASPVPS EQSSVSSAMS NVKLEDSVAP AVPTETIKED SDEKKCDIYN 850
    EKVIACTAPT PEACESCSG 869
    Length:869
    Mass (Da):97,515
    Last modified:February 1, 1995 - v4
    Checksum:iBEE8DEDE41D7049A
    GO

    Sequence cautioni

    The sequence AAA34569.1 differs from that shown. Reason: Frameshift at positions 127, 129, 130, 247, 250, 287 and 313.
    The sequence CAA86157.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti21 – 222RI → VL no nucleotide entry (PubMed:2199320)Curated
    Sequence conflicti37 – 371V → F no nucleotide entry (PubMed:2199320)Curated
    Sequence conflicti58 – 581N → I no nucleotide entry (PubMed:2199320)Curated
    Sequence conflicti69 – 691T → H no nucleotide entry (PubMed:2199320)Curated
    Sequence conflicti83 – 831I → T no nucleotide entry (PubMed:2199320)Curated
    Sequence conflicti212 – 2121H → L in AAA34569. (PubMed:2204819)Curated
    Sequence conflicti249 – 2491G → V in AAA34569. (PubMed:2204819)Curated
    Sequence conflicti311 – 3111F → K in AAA34569. (PubMed:2204819)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z38060 Genomic DNA. Translation: CAA86157.1. Different initiation.
    M58012 Genomic DNA. Translation: AAA34569.1. Frameshift.
    BK006942 Genomic DNA. Translation: DAA08484.1.
    PIRiS48413. WMBY3L.
    RefSeqiNP_012198.3. NM_001179416.3.

    Genome annotation databases

    EnsemblFungiiYIL066C; YIL066C; YIL066C.
    GeneIDi854744.
    KEGGisce:YIL066C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Z38060 Genomic DNA. Translation: CAA86157.1 . Different initiation.
    M58012 Genomic DNA. Translation: AAA34569.1 . Frameshift.
    BK006942 Genomic DNA. Translation: DAA08484.1 .
    PIRi S48413. WMBY3L.
    RefSeqi NP_012198.3. NM_001179416.3.

    3D structure databases

    ProteinModelPortali P21672.
    SMRi P21672. Positions 1-787.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34926. 29 interactions.
    DIPi DIP-2563N.
    IntActi P21672. 1 interaction.
    MINTi MINT-425113.
    STRINGi 4932.YIL066C.

    Proteomic databases

    MaxQBi P21672.
    PaxDbi P21672.
    PeptideAtlasi P21672.
    PRIDEi P21672.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YIL066C ; YIL066C ; YIL066C .
    GeneIDi 854744.
    KEGGi sce:YIL066C.

    Organism-specific databases

    CYGDi YIL066c.
    SGDi S000001328. RNR3.

    Phylogenomic databases

    eggNOGi COG0209.
    GeneTreei ENSGT00390000001372.
    HOGENOMi HOG000057035.
    KOi K10807.
    OMAi KECAMIS.
    OrthoDBi EOG7C5MHR.

    Enzyme and pathway databases

    UniPathwayi UPA00326 .
    BioCyci MetaCyc:YIL066C-MONOMER.
    YEAST:YIL066C-MONOMER.

    Miscellaneous databases

    NextBioi 977464.

    Gene expression databases

    Genevestigatori P21672.

    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: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. "The DNA damage-inducible gene DIN1 of Saccharomyces cerevisiae encodes a regulatory subunit of ribonucleotide reductase and is identical to RNR3."
      Yagle K., McEntee K.
      Mol. Cell. Biol. 10:5553-5557(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-758, INDUCTION.
    4. "Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase."
      Elledge S.J., Davis R.W.
      Genes Dev. 4:740-751(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-101 AND 652-711, INDUCTION.
    5. "Yeast DNA damage-inducible Rnr3 has a very low catalytic activity strongly stimulated after the formation of a cross-talking Rnr1/Rnr3 complex."
      Domkin V., Thelander L., Chabes A.
      J. Biol. Chem. 277:18574-18578(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    6. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    7. "Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways."
      Yao R., Zhang Z., An X., Bucci B., Perlstein D.L., Stubbe J., Huang M.
      Proc. Natl. Acad. Sci. U.S.A. 100:6628-6633(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION.
    8. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
      Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
      Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-806, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiRIR3_YEAST
    AccessioniPrimary (citable) accession number: P21672
    Secondary accession number(s): D6VVL8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 1991
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 142 of the entry and version 4 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 1364 molecules/cell in log phase SD medium.1 Publication

    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
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome IX
      Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

    External Data

    Dasty 3