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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

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

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi145 – 1451Iron 1
    Metal bindingi176 – 1761Iron 1
    Metal bindingi176 – 1761Iron 2
    Metal bindingi179 – 1791Iron 1
    Active sitei183 – 1831
    Metal bindingi239 – 2391Iron 2
    Metal bindingi273 – 2731Iron 2
    Metal bindingi276 – 2761Iron 2

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: SGD

    GO - Biological processi

    1. deoxyribonucleoside diphosphate metabolic process Source: InterPro
    2. deoxyribonucleotide biosynthetic process Source: SGD
    3. 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.
    ReactomeiREACT_275578. Synthesis and interconversion of nucleotide di- and triphosphates.
    REACT_303865. E2F mediated regulation of DNA replication.
    REACT_345909. 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
    ProteomesiUP000002311 Componenti: Chromosome X

    Organism-specific databases

    CYGDiYJL026w.
    EuPathDBiFungiDB:YJL026W.
    SGDiS000003563. RNR2.

    Subcellular locationi

    1. Nucleus 2 Publications

    2. Note: Found predominantly in the nucleus under normal growth conditions and is redistributed to the cytoplasm in damaged cells in a DNA replication and damage checkpoint-dependent manner. Nuclear localization is mediated by DIF1.

    GO - Cellular componenti

    1. cytoplasm Source: SGD
    2. nucleus Source: SGD
    3. ribonucleoside-diphosphate reductase complex Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 399399Ribonucleoside-diphosphate reductase small chain 1PRO_0000190464Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei15 – 151Phosphoserine4 Publications
    Modified residuei24 – 241Phosphoserine1 Publication
    Modified residuei41 – 411Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP09938.
    PaxDbiP09938.
    PeptideAtlasiP09938.

    Expressioni

    Inductioni

    Induced by DNA-damage.2 Publications

    Gene expression databases

    GenevestigatoriP09938.

    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. 51 interactions.
    DIPiDIP-5671N.
    IntActiP09938. 16 interactions.
    MINTiMINT-547064.
    STRINGi4932.YJL026W.

    Structurei

    Secondary structure

    1
    399
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi27 – 3610Combined sources
    Helixi38 – 4912Combined sources
    Helixi51 – 6111Combined sources
    Helixi63 – 7210Combined sources
    Helixi73 – 753Combined sources
    Helixi77 – 793Combined sources
    Helixi94 – 10411Combined sources
    Helixi110 – 1123Combined sources
    Helixi118 – 1247Combined sources
    Helixi128 – 14215Combined sources
    Helixi147 – 1526Combined sources
    Helixi153 – 1575Combined sources
    Helixi163 – 19028Combined sources
    Helixi194 – 20411Combined sources
    Helixi208 – 22013Combined sources
    Beta strandi223 – 2253Combined sources
    Helixi228 – 24013Combined sources
    Turni241 – 2433Combined sources
    Helixi244 – 25512Combined sources
    Helixi260 – 28526Combined sources
    Helixi293 – 31220Combined sources
    Helixi317 – 3204Combined sources
    Helixi324 – 34017Combined sources
    Turni341 – 3433Combined sources
    Helixi355 – 3584Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80A1-399[»]
    1SMQX-ray3.10A/B/C/D1-399[»]
    2CVYX-ray2.40B391-399[»]
    DisProtiDP00487.
    ProteinModelPortaliP09938.
    SMRiP09938. Positions 26-359.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP09938.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG0208.
    GeneTreeiENSGT00390000013305.
    HOGENOMiHOG000255975.
    InParanoidiP09938.
    KOiK10808.
    OMAiLNIEREF.
    OrthoDBiEOG7T1RMH.

    Family and domain databases

    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR000358. RNR_small.
    IPR030475. RNR_small_AS.
    [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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti101 – 1033Missing in AAA34987 (PubMed:3313004).Curated
    Sequence conflicti111 – 1111E → ETAE (PubMed:3313004).Curated

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80A1-399[»]
    1SMQX-ray3.10A/B/C/D1-399[»]
    2CVYX-ray2.40B391-399[»]
    DisProtiDP00487.
    ProteinModelPortaliP09938.
    SMRiP09938. Positions 26-359.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33733. 51 interactions.
    DIPiDIP-5671N.
    IntActiP09938. 16 interactions.
    MINTiMINT-547064.
    STRINGi4932.YJL026W.

    Proteomic databases

    MaxQBiP09938.
    PaxDbiP09938.
    PeptideAtlasiP09938.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    CYGDiYJL026w.
    EuPathDBiFungiDB:YJL026W.
    SGDiS000003563. RNR2.

    Phylogenomic databases

    eggNOGiCOG0208.
    GeneTreeiENSGT00390000013305.
    HOGENOMiHOG000255975.
    InParanoidiP09938.
    KOiK10808.
    OMAiLNIEREF.
    OrthoDBiEOG7T1RMH.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BioCyciMetaCyc:YJL026W-MONOMER.
    YEAST:YJL026W-MONOMER.
    ReactomeiREACT_275578. Synthesis and interconversion of nucleotide di- and triphosphates.
    REACT_303865. E2F mediated regulation of DNA replication.
    REACT_345909. G1/S-Specific Transcription.

    Miscellaneous databases

    EvolutionaryTraceiP09938.
    NextBioi973962.
    PROiP09938.

    Gene expression databases

    GenevestigatoriP09938.

    Family and domain databases

    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR000358. RNR_small.
    IPR030475. RNR_small_AS.
    [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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Identification and isolation of the gene encoding the small subunit of ribonucleotide reductase from Saccharomyces cerevisiae: DNA damage-inducible gene required for mitotic viability."
      Elledge S.J., Davis R.W.
      Mol. Cell. Biol. 7:2783-2793(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
    2. "Identification of the gene for the yeast ribonucleotide reductase small subunit and its inducibility by methyl methanesulfonate."
      Hurd H.K., Roberts C.W., Roberts J.W.
      Mol. Cell. Biol. 7:3673-3677(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
    3. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
      Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
      , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
      EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    4. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    5. "Purification of ribonucleotide reductase subunits Y1, Y2, Y3, and Y4 from yeast: Y4 plays a key role in diiron cluster assembly."
      Nguyen H.-H.T., Ge J., Perlstein D.L., Stubbe J.
      Proc. Natl. Acad. Sci. U.S.A. 96:12339-12344(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBUNIT.
    6. "Yeast ribonucleotide reductase has a heterodimeric iron-radical-containing subunit."
      Chabes A., Domkin V., Larsson G., Liu A., Graeslund A., Wijmenga S., Thelander L.
      Proc. Natl. Acad. Sci. U.S.A. 97:2474-2479(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES.
    7. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    8. "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.
    9. "Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway."
      Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N.
      Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: YAL6B.
    10. "Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
      Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
      J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ADR376.
    11. "Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
      Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
      Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-41, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    12. "Dif1 is a DNA-damage-regulated facilitator of nuclear import for ribonucleotide reductase."
      Lee Y.D., Wang J., Stubbe J., Elledge S.J.
      Mol. Cell 32:70-80(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, INTERACTION WITH DIF1 AND RNR4.
    13. "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-15, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-15 AND SER-24, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    16. "Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4 homodimers."
      Sommerhalter M., Voegtli W.C., Perlstein D.L., Ge J., Stubbe J., Rosenzweig A.C.
      Biochemistry 43:7736-7742(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).

    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: April 29, 2015
    This is version 166 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

    External Data

    Dasty 3

    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 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.