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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: 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. RNR2 provides the diiron-tyrosyl radical center.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

    GO - Biological processi

    • deoxyribonucleotide biosynthetic process Source: SGD
    • DNA replication Source: UniProtKB-UniPathway
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:YJL026W-MONOMER.
    YEAST:YJL026W-MONOMER.
    ReactomeiR-SCE-113510. E2F mediated regulation of DNA replication.
    R-SCE-499943. Synthesis and interconversion of nucleotide di- and triphosphates.
    R-SCE-69205. G1/S-Specific Transcription.
    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
    • UP000002311 Componenti: Chromosome X

    Organism-specific databases

    EuPathDBiFungiDB:YJL026W.
    SGDiS000003563. RNR2.

    Subcellular locationi

    GO - Cellular componenti

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

    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.
    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

    WithEntry#Exp.IntActNotes
    RNR4P497236EBI-15240,EBI-15251

    Protein-protein interaction databases

    BioGridi33733. 58 interactors.
    DIPiDIP-5671N.
    IntActiP09938. 16 interactors.
    MINTiMINT-547064.

    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.
    OMAiHEIWQAY.
    OrthoDBiEOG092C3G06.

    Family and domain databases

    CDDicd01049. RNRR2. 1 hit.
    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR033909. RNR_small.
    IPR030475. RNR_small_AS.
    IPR000358. RNR_small_fam.
    [Graphical view]
    PANTHERiPTHR23409. PTHR23409. 1 hit.
    PfamiPF00268. Ribonuc_red_sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF47240. SSF47240. 1 hit.
    PROSITEiPS00368. RIBORED_SMALL. 1 hit.
    [Graphical view]

    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.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    BioGridi33733. 58 interactors.
    DIPiDIP-5671N.
    IntActiP09938. 16 interactors.
    MINTiMINT-547064.

    PTM databases

    iPTMnetiP09938.

    Proteomic databases

    MaxQBiP09938.
    PRIDEiP09938.
    TopDownProteomicsiP09938.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYJL026W; YJL026W; YJL026W.
    GeneIDi853427.
    KEGGisce:YJL026W.

    Organism-specific databases

    EuPathDBiFungiDB:YJL026W.
    SGDiS000003563. RNR2.

    Phylogenomic databases

    GeneTreeiENSGT00390000013305.
    HOGENOMiHOG000255975.
    InParanoidiP09938.
    KOiK10808.
    OMAiHEIWQAY.
    OrthoDBiEOG092C3G06.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BioCyciMetaCyc:YJL026W-MONOMER.
    YEAST:YJL026W-MONOMER.
    ReactomeiR-SCE-113510. E2F mediated regulation of DNA replication.
    R-SCE-499943. Synthesis and interconversion of nucleotide di- and triphosphates.
    R-SCE-69205. G1/S-Specific Transcription.

    Miscellaneous databases

    EvolutionaryTraceiP09938.
    PROiP09938.

    Family and domain databases

    CDDicd01049. RNRR2. 1 hit.
    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR033909. RNR_small.
    IPR030475. RNR_small_AS.
    IPR000358. RNR_small_fam.
    [Graphical view]
    PANTHERiPTHR23409. PTHR23409. 1 hit.
    PfamiPF00268. Ribonuc_red_sm. 1 hit.
    [Graphical view]
    SUPFAMiSSF47240. SSF47240. 1 hit.
    PROSITEiPS00368. RIBORED_SMALL. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIR2_YEAST
    AccessioniPrimary (citable) accession number: P09938
    Secondary accession number(s): D6VWF6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1989
    Last sequence update: November 1, 1995
    Last modified: November 30, 2016
    This is version 184 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

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

    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

    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.