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P49723

- RIR4_YEAST

UniProt

P49723 - RIR4_YEAST

Protein

Ribonucleoside-diphosphate reductase small chain 2

Gene

RNR4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 150 (01 Oct 2014)
      Sequence version 1 (01 Oct 1996)
      Previous versions | rss
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    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

      Sites

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

      GO - Molecular functioni

      1. protein binding Source: IntAct
      2. 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

      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.
      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 lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
      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

      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. 88 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 – 96
      Helixi13 – 219
      Turni22 – 243
      Turni26 – 283
      Helixi43 – 5412
      Helixi59 – 613
      Turni65 – 673
      Turni69 – 735
      Helixi78 – 8912
      Helixi101 – 1077
      Helixi111 – 13828
      Helixi142 – 1443
      Helixi148 – 1514
      Helixi155 – 16612
      Beta strandi169 – 1724
      Helixi175 – 18713
      Turni188 – 1903
      Helixi191 – 20010
      Beta strandi202 – 2054
      Helixi207 – 23226
      Helixi240 – 25819
      Turni265 – 2684
      Helixi277 – 28812
      Helixi316 – 3227

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      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

      Phylogenomic databases

      eggNOGiCOG0208.
      HOGENOMiHOG000255975.
      KOiK10808.
      OMAiMANRNIC.
      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

      MEAHNQFLKT FQKERHDMKE AEKDEILLME NSRRFVMFPI KYHEIWAAYK    50
      KVEASFWTAE EIELAKDTED FQKLTDDQKT YIGNLLALSI SSDNLVNKYL 100
      IENFSAQLQN PEGKSFYGFQ IMMENIYSEV YSMMVDAFFK DPKNIPLFKE 150
      IANLPEVKHK AAFIERWISN DDSLYAERLV AFAAKEGIFQ AGNYASMFWL 200
      TDKKIMPGLA MANRNICRDR GAYTDFSCLL FAHLRTKPNP KIIEKIITEA 250
      VEIEKEYYSN SLPVEKFGMD LKSIHTYIEF VADGLLQGFG NEKYYNAVNP 300
      FEFMEDVATA GKTTFFEKKV SDYQKASDMS KSATPSKEIN FDDDF 345
      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:
      EMBL
      GenBank
      DDBJ
      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:
      EMBL
      GenBank
      DDBJ
      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 .
      PIRi S59744.
      RefSeqi NP_011696.3. NM_001181309.3.

      3D structure databases

      Select the link destinations:
      PDBe
      RCSB PDB
      PDBj
      Links Updated
      Entry Method Resolution (Å) Chain Positions PDBsum
      1JK0 X-ray 2.80 B 1-345 [» ]
      1SMS X-ray 3.10 A/B 1-345 [» ]
      1ZZD X-ray 2.60 B 337-345 [» ]
      DisProti DP00488.
      ProteinModelPortali P49723.
      SMRi P49723. Positions 3-325.
      ModBasei Search...
      MobiDBi Search...

      Protein-protein interaction databases

      BioGridi 33432. 88 interactions.
      DIPi DIP-5381N.
      IntActi P49723. 16 interactions.
      MINTi MINT-537732.
      STRINGi 4932.YGR180C.

      Proteomic databases

      MaxQBi P49723.
      PaxDbi P49723.
      PeptideAtlasi P49723.

      Protocols and materials databases

      Structural Biology Knowledgebase Search...

      Genome annotation databases

      EnsemblFungii YGR180C ; YGR180C ; YGR180C .
      GeneIDi 853091.
      KEGGi sce:YGR180C.

      Organism-specific databases

      CYGDi YGR180c.
      SGDi S000003412. RNR4.

      Phylogenomic databases

      eggNOGi COG0208.
      HOGENOMi HOG000255975.
      KOi K10808.
      OMAi MANRNIC.
      OrthoDBi EOG7T1RMH.

      Enzyme and pathway databases

      UniPathwayi UPA00326 .
      BioCyci MetaCyc:YGR180C-MONOMER.
      YEAST:YGR180C-MONOMER.
      Reactomei REACT_189247. G1/S-Specific Transcription.

      Miscellaneous databases

      EvolutionaryTracei P49723.
      NextBioi 973076.

      Gene expression databases

      Genevestigatori P49723.

      Family and domain databases

      Gene3Di 1.10.620.20. 1 hit.
      InterProi IPR009078. Ferritin-like_SF.
      IPR012348. RNR-rel.
      IPR000358. RNR_small.
      [Graphical view ]
      PANTHERi PTHR23409. PTHR23409. 1 hit.
      Pfami PF00268. Ribonuc_red_sm. 1 hit.
      [Graphical view ]
      SUPFAMi SSF47240. SSF47240. 1 hit.
      PROSITEi PS00368. RIBORED_SMALL. 1 hit.
      [Graphical view ]
      ProtoNeti Search...

      Publicationsi

      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).

      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: October 1, 2014
      This is version 150 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