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Protein

Ribonucleoside-diphosphate reductase small chain 1

Gene

RNR2

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

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center.1 Publication

Miscellaneous

Present with 538 molecules/cell in log phase SD medium.1 Publication

Catalytic activityi

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

Cofactori

Fe cationNote: Binds 2 iron ions per subunit.

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
    Metal bindingi145Iron 11
    Metal bindingi176Iron 11
    Metal bindingi176Iron 21
    Metal bindingi179Iron 11
    Active sitei1831
    Metal bindingi239Iron 21
    Metal bindingi273Iron 21
    Metal bindingi276Iron 21

    GO - Molecular functioni

    • ferrous iron binding Source: CAFA
    • protein heterodimerization activity Source: CAFA
    • ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: SGD
    • zinc ion binding Source: CAFA

    GO - Biological processi

    • deoxyribonucleotide biosynthetic process Source: SGD
    • DNA replication Source: UniProtKB-UniPathway

    Keywordsi

    Molecular functionOxidoreductase
    Biological processDNA replication
    LigandIron, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:YJL026W-MONOMER
    YEAST:YJL026W-MONOMER
    ReactomeiR-SCE-499943 Interconversion of nucleotide di- and triphosphates
    UniPathwayiUPA00326

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase small chain 1 (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase R2 subunit 1
    Ribonucleotide reductase small subunit 1
    Gene namesi
    Name:RNR2
    Synonyms:CRT6
    Ordered Locus Names:YJL026W
    ORF Names:J1271
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi

    Organism-specific databases

    EuPathDBiFungiDB:YJL026W
    SGDiS000003563 RNR2

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001904641 – 399Ribonucleoside-diphosphate reductase small chain 1Add BLAST399

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei15PhosphoserineCombined sources1
    Modified residuei24PhosphoserineCombined sources1
    Modified residuei41PhosphoserineCombined sources1

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP09938
    PaxDbiP09938
    PRIDEiP09938
    TopDownProteomicsiP09938

    PTM databases

    iPTMnetiP09938

    Expressioni

    Inductioni

    Induced by DNA-damage.2 Publications

    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. Interacts with DIF1.3 Publications

    Binary interactionsi

    Show more details

    GO - Molecular functioni

    • protein heterodimerization activity Source: CAFA

    Protein-protein interaction databases

    BioGridi33733, 65 interactors
    DIPiDIP-5671N
    IntActiP09938, 28 interactors
    MINTiP09938
    STRINGi4932.YJL026W

    Structurei

    Secondary structure

    1399
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi27 – 36Combined sources10
    Helixi38 – 49Combined sources12
    Helixi51 – 61Combined sources11
    Helixi63 – 72Combined sources10
    Helixi73 – 75Combined sources3
    Helixi77 – 79Combined sources3
    Helixi94 – 104Combined sources11
    Helixi110 – 112Combined sources3
    Helixi118 – 124Combined sources7
    Helixi128 – 142Combined sources15
    Helixi147 – 152Combined sources6
    Helixi153 – 157Combined sources5
    Helixi163 – 190Combined sources28
    Helixi194 – 204Combined sources11
    Helixi208 – 220Combined sources13
    Beta strandi223 – 225Combined sources3
    Helixi228 – 240Combined sources13
    Turni241 – 243Combined sources3
    Helixi244 – 255Combined sources12
    Helixi260 – 285Combined sources26
    Helixi293 – 312Combined sources20
    Helixi317 – 320Combined sources4
    Helixi324 – 340Combined sources17
    Turni341 – 343Combined sources3
    Helixi355 – 358Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80A1-399[»]
    1SMQX-ray3.10A/B/C/D1-399[»]
    2CVYX-ray2.40B391-399[»]
    DisProtiDP00487
    ProteinModelPortaliP09938
    SMRiP09938
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP09938

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    GeneTreeiENSGT00390000013305
    HOGENOMiHOG000255975
    InParanoidiP09938
    KOiK10808
    OMAiFYVGFVQ
    OrthoDBiEOG092C3G06

    Family and domain databases

    CDDicd01049 RNRR2, 1 hit
    Gene3Di1.10.620.20, 1 hit
    InterProiView protein in InterPro
    IPR009078 Ferritin-like_SF
    IPR012348 RNR-like
    IPR033909 RNR_small
    IPR030475 RNR_small_AS
    IPR000358 RNR_small_fam
    PANTHERiPTHR23409 PTHR23409, 1 hit
    PfamiView protein in Pfam
    PF00268 Ribonuc_red_sm, 1 hit
    SUPFAMiSSF47240 SSF47240, 1 hit
    PROSITEiView protein in PROSITE
    PS00368 RIBORED_SMALL, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P09938-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPKETPSKAA ADALSDLEIK DSKSNLNKEL ETLREENRVK SDMLKEKLSK
    60 70 80 90 100
    DAENHKAYLK SHQVHRHKLK EMEKEEPLLN EDKERTVLFP IKYHEIWQAY
    110 120 130 140 150
    KRAEASFWTA EEIDLSKDIH DWNNRMNENE RFFISRVLAF FAASDGIVNE
    160 170 180 190 200
    NLVENFSTEV QIPEAKSFYG FQIMIENIHS ETYSLLIDTY IKDPKESEFL
    210 220 230 240 250
    FNAIHTIPEI GEKAEWALRW IQDADALFGE RLVAFASIEG VFFSGSFASI
    260 270 280 290 300
    FWLKKRGMMP GLTFSNELIC RDEGLHTDFA CLLFAHLKNK PDPAIVEKIV
    310 320 330 340 350
    TEAVEIEQRY FLDALPVALL GMNADLMNQY VEFVADRLLV AFGNKKYYKV
    360 370 380 390
    ENPFDFMENI SLAGKTNFFE KRVSDYQKAG VMSKSTKQEA GAFTFNEDF
    Length:399
    Mass (Da):46,147
    Last modified:November 1, 1995 - v2
    Checksum:iDB98028408292042
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti101 – 103Missing in AAA34987 (PubMed:3313004).Curated3
    Sequence conflicti111E → ETAE (PubMed:3313004).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M17221 Genomic DNA Translation: AAA34987.1
    M17789 Genomic DNA Translation: AAA34988.1
    Z49301 Genomic DNA Translation: CAA89317.1
    BK006943 Genomic DNA Translation: DAA08772.1
    PIRiA26916
    RefSeqiNP_012508.1, NM_001181460.1

    Genome annotation databases

    EnsemblFungiiYJL026W; YJL026W; YJL026W
    GeneIDi853427
    KEGGisce:YJL026W

    Similar proteinsi

    Entry informationi

    Entry nameiRIR2_YEAST
    AccessioniPrimary (citable) accession number: P09938
    Secondary accession number(s): D6VWF6
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
    Last sequence update: November 1, 1995
    Last modified: May 23, 2018
    This is version 195 of the entry and version 2 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, 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 X
      Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

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