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P09938 (RIR2_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 158. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:RNR2
Synonyms:CRT6
Ordered Locus Names:YJL026W
ORF Names:J1271
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length399 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center. Ref.5

Catalytic activity

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

Cofactor

Binds 2 iron ions per subunit.

Pathway

Genetic information processing; DNA replication.

Subunit structure

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. Ref.5 Ref.6 Ref.12

Subcellular location

Nucleus. 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. Ref.8 Ref.12

Induction

Induced by DNA-damage. Ref.1 Ref.2

Miscellaneous

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

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase small chain family.

Biophysicochemical properties

Kinetic parameters:

Vmax=2250 nmol/min/mg enzyme for cytidine 5'-diphosphate Ref.6

Temperature dependence:

Optimum temperature is 30 degrees Celsius.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

RNR4P497236EBI-15240,EBI-15251

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 399399Ribonucleoside-diphosphate reductase small chain 1
PRO_0000190464

Sites

Active site1831
Metal binding1451Iron 1
Metal binding1761Iron 1
Metal binding1761Iron 2
Metal binding1791Iron 1
Metal binding2391Iron 2
Metal binding2731Iron 2
Metal binding2761Iron 2

Amino acid modifications

Modified residue151Phosphoserine Ref.9 Ref.10 Ref.13 Ref.14
Modified residue241Phosphoserine Ref.14
Modified residue411Phosphoserine Ref.11

Experimental info

Sequence conflict101 – 1033Missing in AAA34987. Ref.1
Sequence conflict1111E → ETAE Ref.1

Secondary structure

.............................................. 399
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P09938 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: DB98028408292042

FASTA39946,147
        10         20         30         40         50         60 
MPKETPSKAA ADALSDLEIK DSKSNLNKEL ETLREENRVK SDMLKEKLSK DAENHKAYLK 

        70         80         90        100        110        120 
SHQVHRHKLK EMEKEEPLLN EDKERTVLFP IKYHEIWQAY KRAEASFWTA EEIDLSKDIH 

       130        140        150        160        170        180 
DWNNRMNENE RFFISRVLAF FAASDGIVNE NLVENFSTEV QIPEAKSFYG FQIMIENIHS 

       190        200        210        220        230        240 
ETYSLLIDTY IKDPKESEFL FNAIHTIPEI GEKAEWALRW IQDADALFGE RLVAFASIEG 

       250        260        270        280        290        300 
VFFSGSFASI FWLKKRGMMP GLTFSNELIC RDEGLHTDFA CLLFAHLKNK PDPAIVEKIV 

       310        320        330        340        350        360 
TEAVEIEQRY FLDALPVALL GMNADLMNQY VEFVADRLLV AFGNKKYYKV ENPFDFMENI 

       370        380        390 
SLAGKTNFFE KRVSDYQKAG VMSKSTKQEA GAFTFNEDF 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
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]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
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]"Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer."
Voegtli W.C., Ge J., Perlstein D.L., Stubbe J., Rosenzweig A.C.
Proc. Natl. Acad. Sci. U.S.A. 98:10073-10078(2001) [PubMed] [Europe PMC] [Abstract]
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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M17221 Genomic DNA. Translation: AAA34987.1.
M17789 Genomic DNA. Translation: AAA34988.1.
Z49301 Genomic DNA. Translation: CAA89317.1.
BK006943 Genomic DNA. Translation: DAA08772.1.
PIRA26916.
RefSeqNP_012508.1. NM_001181460.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JK0X-ray2.80A1-399[»]
1SMQX-ray3.10A/B/C/D1-399[»]
2CVYX-ray2.40B391-399[»]
DisProtDP00487.
ProteinModelPortalP09938.
SMRP09938. Positions 26-359.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33733. 50 interactions.
DIPDIP-5671N.
IntActP09938. 15 interactions.
MINTMINT-547064.
STRING4932.YJL026W.

Proteomic databases

MaxQBP09938.
PaxDbP09938.
PeptideAtlasP09938.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYJL026W; YJL026W; YJL026W.
GeneID853427.
KEGGsce:YJL026W.

Organism-specific databases

CYGDYJL026w.
SGDS000003563. RNR2.

Phylogenomic databases

eggNOGCOG0208.
GeneTreeENSGT00390000013305.
HOGENOMHOG000255975.
KOK10808.
OMAGVMNSTK.
OrthoDBEOG7T1RMH.

Enzyme and pathway databases

BioCycMetaCyc:YJL026W-MONOMER.
YEAST:YJL026W-MONOMER.
UniPathwayUPA00326.

Gene expression databases

GenevestigatorP09938.

Family and domain databases

Gene3D1.10.620.20. 1 hit.
InterProIPR009078. Ferritin-like_SF.
IPR012348. RNR-rel.
IPR000358. RNR_small.
[Graphical view]
PANTHERPTHR23409. PTHR23409. 1 hit.
PfamPF00268. Ribonuc_red_sm. 1 hit.
[Graphical view]
SUPFAMSSF47240. SSF47240. 1 hit.
PROSITEPS00368. RIBORED_SMALL. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP09938.
NextBio973962.
PROP09938.

Entry information

Entry nameRIR2_YEAST
AccessionPrimary (citable) accession number: P09938
Secondary accession number(s): D6VWF6
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: November 1, 1995
Last modified: June 11, 2014
This is version 158 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome X

Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways