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P49723 - RIR4_YEAST

UniProt

P49723 - RIR4_YEAST

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Protein

Ribonucleoside-diphosphate reductase small chain 2

Gene

RNR4

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. RNR4 is required for proper folding of RNR2 and assembly with the large subunits.1 Publication

Catalytic activityi

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

Kineticsi

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

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.1 Publication

    Pathwayi

    Genetic information processing; DNA replication.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei131 – 1311PROSITE-ProRule annotation

    GO - Molecular functioni

    1. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: SGD

    GO - Biological processi

    1. cofactor biosynthetic process Source: SGD
    2. deoxyribonucleoside diphosphate metabolic process Source: InterPro
    3. deoxyribonucleotide biosynthetic process Source: SGD
    4. DNA replication Source: UniProtKB-UniPathway
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    DNA replication

    Enzyme and pathway databases

    BioCyciMetaCyc:YGR180C-MONOMER.
    YEAST:YGR180C-MONOMER.
    ReactomeiREACT_189247. G1/S-Specific Transcription.
    REACT_238684. Synthesis and interconversion of nucleotide di- and triphosphates.
    REACT_252897. E2F mediated regulation of DNA replication.
    UniPathwayiUPA00326.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonucleoside-diphosphate reductase small chain 2 (EC:1.17.4.1)
    Alternative name(s):
    Ribonucleotide reductase R2 subunit 2
    Ribonucleotide reductase small subunit 2
    Gene namesi
    Name:RNR4
    Synonyms:CRT3
    Ordered Locus Names:YGR180C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›
    ProteomesiUP000002311: Chromosome VII

    Organism-specific databases

    CYGDiYGR180c.
    SGDiS000003412. RNR4.

    Subcellular locationi

    Nucleus 2 Publications
    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 – 345345Ribonucleoside-diphosphate reductase small chain 2PRO_0000190465Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine2 Publications
    Modified residuei169 – 1691Phosphoserine2 Publications
    Modified residuei332 – 3321Phosphoserine1 Publication
    Modified residuei334 – 3341Phosphothreonine1 Publication
    Modified residuei336 – 3361Phosphoserine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP49723.
    PaxDbiP49723.
    PeptideAtlasiP49723.

    Expressioni

    Inductioni

    Induced by DNA-damage.1 Publication

    Gene expression databases

    GenevestigatoriP49723.

    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
    RNR2P099386EBI-15251,EBI-15240
    WTM1Q123634EBI-15251,EBI-20563

    Protein-protein interaction databases

    BioGridi33432. 91 interactions.
    DIPiDIP-5381N.
    IntActiP49723. 16 interactions.
    MINTiMINT-537732.
    STRINGi4932.YGR180C.

    Structurei

    Secondary structure

    1
    345
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 96Combined sources
    Helixi13 – 219Combined sources
    Turni22 – 243Combined sources
    Turni26 – 283Combined sources
    Helixi43 – 5412Combined sources
    Helixi59 – 613Combined sources
    Turni65 – 673Combined sources
    Turni69 – 735Combined sources
    Helixi78 – 8912Combined sources
    Helixi101 – 1077Combined sources
    Helixi111 – 13828Combined sources
    Helixi142 – 1443Combined sources
    Helixi148 – 1514Combined sources
    Helixi155 – 16612Combined sources
    Beta strandi169 – 1724Combined sources
    Helixi175 – 18713Combined sources
    Turni188 – 1903Combined sources
    Helixi191 – 20010Combined sources
    Beta strandi202 – 2054Combined sources
    Helixi207 – 23226Combined sources
    Helixi240 – 25819Combined sources
    Turni265 – 2684Combined sources
    Helixi277 – 28812Combined sources
    Helixi316 – 3227Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80B1-345[»]
    1SMSX-ray3.10A/B1-345[»]
    1ZZDX-ray2.60B337-345[»]
    DisProtiDP00488.
    ProteinModelPortaliP49723.
    SMRiP49723. Positions 3-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP49723.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the ribonucleoside diphosphate reductase small chain family.Curated

    Phylogenomic databases

    eggNOGiCOG0208.
    HOGENOMiHOG000255975.
    InParanoidiP49723.
    KOiK10808.
    OrthoDBiEOG7T1RMH.

    Family and domain databases

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

    P49723-1 [UniParc]FASTAAdd to Basket

    « Hide

            10         20         30         40         50
    MEAHNQFLKT FQKERHDMKE AEKDEILLME NSRRFVMFPI KYHEIWAAYK 
            60         70         80         90        100
    KVEASFWTAE EIELAKDTED FQKLTDDQKT YIGNLLALSI SSDNLVNKYL 
           110        120        130        140        150
    IENFSAQLQN PEGKSFYGFQ IMMENIYSEV YSMMVDAFFK DPKNIPLFKE 
           160        170        180        190        200
    IANLPEVKHK AAFIERWISN DDSLYAERLV AFAAKEGIFQ AGNYASMFWL 
           210        220        230        240        250
    TDKKIMPGLA MANRNICRDR GAYTDFSCLL FAHLRTKPNP KIIEKIITEA 
           260        270        280        290        300
    VEIEKEYYSN SLPVEKFGMD LKSIHTYIEF VADGLLQGFG NEKYYNAVNP 
           310        320        330        340 
    FEFMEDVATA GKTTFFEKKV SDYQKASDMS KSATPSKEIN FDDDF
    Length:345
    Mass (Da):40,055
    Last modified:October 1, 1996 - v1
    Checksum:i712853F2D87D3972
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti127 – 1271Y → H in AAU09736. (PubMed:17322287)Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    		U30385 Genomic DNA. Translation: AAB72236.1.
    Z72965 Genomic DNA. Translation: CAA97206.1.
    AY723819 Genomic DNA. Translation: AAU09736.1.
    BK006941 Genomic DNA. Translation: DAA08275.1.
    PIRiS59744.
    RefSeqiNP_011696.3. NM_001181309.3.

    Genome annotation databases

    EnsemblFungiiYGR180C; YGR180C; YGR180C.
    GeneIDi853091.
    KEGGisce:YGR180C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    		U30385 Genomic DNA. Translation: AAB72236.1.
    Z72965 Genomic DNA. Translation: CAA97206.1.
    AY723819 Genomic DNA. Translation: AAU09736.1.
    BK006941 Genomic DNA. Translation: DAA08275.1.
    PIRiS59744.
    RefSeqiNP_011696.3. NM_001181309.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1JK0X-ray2.80B1-345[»]
    1SMSX-ray3.10A/B1-345[»]
    1ZZDX-ray2.60B337-345[»]
    DisProtiDP00488.
    ProteinModelPortaliP49723.
    SMRiP49723. Positions 3-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi33432. 91 interactions.
    DIPiDIP-5381N.
    IntActiP49723. 16 interactions.
    MINTiMINT-537732.
    STRINGi4932.YGR180C.

    Proteomic databases

    MaxQBiP49723.
    PaxDbiP49723.
    PeptideAtlasiP49723.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYGR180C; YGR180C; YGR180C.
    GeneIDi853091.
    KEGGisce:YGR180C.

    Organism-specific databases

    CYGDiYGR180c.
    SGDiS000003412. RNR4.

    Phylogenomic databases

    eggNOGiCOG0208.
    HOGENOMiHOG000255975.
    InParanoidiP49723.
    KOiK10808.
    OrthoDBiEOG7T1RMH.

    Enzyme and pathway databases

    UniPathwayiUPA00326.
    BioCyciMetaCyc:YGR180C-MONOMER.
    YEAST:YGR180C-MONOMER.
    ReactomeiREACT_189247. G1/S-Specific Transcription.
    REACT_238684. Synthesis and interconversion of nucleotide di- and triphosphates.
    REACT_252897. E2F mediated regulation of DNA replication.

    Miscellaneous databases

    EvolutionaryTraceiP49723.
    NextBioi973076.

    Gene expression databases

    GenevestigatoriP49723.

    Family and domain databases

    Gene3Di1.10.620.20. 1 hit.
    InterProiIPR009078. Ferritin-like_SF.
    IPR012348. RNR-rel.
    IPR000358. RNR_small.
    [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. "Rnr4p, a novel ribonucleotide reductase small-subunit protein."
      Wang P.J., Chabes A., Casagrande R., Tian X.C., Thelander L., Huffaker T.C.
      Mol. Cell. Biol. 17:6114-6121(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INDUCTION.
      Strain: ATCC 204508 / S288c.
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII."
      Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E.
      , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K.
      Nature 387:81-84(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    5. Bienvenut W.V., Peters C.
      Submitted (JUN-2005) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 1-9; 150-158; 167-178; 219-235 AND 294-312, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY.
    6. "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.
    7. "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.
    8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    9. "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.
    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: 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-169, 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-169, 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-332; THR-334 AND SER-336, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    15. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "Sites of ubiquitin attachment in Saccharomyces cerevisiae."
      Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
      Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    17. Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
    18. "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).
    +Additional computationally mapped references.

    Entry informationi

    Entry nameiRIR4_YEAST
    AccessioniPrimary (citable) accession number: P49723
    Secondary accession number(s): D6VUW4, Q66R92
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: October 1, 1996
    Last modified: January 7, 2015
    This is version 153 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 88884 molecules/cell in log phase SD medium.1 Publication
    Lacks 3 iron-binding residues conserved in all other R2 subunits.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, 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 VII
      Yeast (Saccharomyces cerevisiae) chromosome VII: 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.