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P49723 (RIR4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 146. 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 2

EC=1.17.4.1
Alternative name(s):
Ribonucleotide reductase R2 subunit 2
Ribonucleotide reductase small subunit 2
Gene names
Name:RNR4
Synonyms:CRT3
Ordered Locus Names:YGR180C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length345 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. RNR4 is required for proper folding of RNR2 and assembly with the large subunits. Ref.6

Catalytic activity

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

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.6 Ref.7 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.9 Ref.12

Induction

Induced by DNA-damage. Ref.1

Miscellaneous

Present with 88884 molecules/cell in log phase SD medium.

Lacks 3 iron-binding residues conserved in all other R2 subunits.

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.7

Temperature dependence:

Optimum temperature is 30 degrees Celsius.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 345345Ribonucleoside-diphosphate reductase small chain 2
PRO_0000190465

Sites

Active site1311 By similarity

Amino acid modifications

Modified residue11N-acetylmethionine Ref.5 Ref.15
Modified residue1691Phosphoserine Ref.11 Ref.13
Modified residue3321Phosphoserine Ref.14
Modified residue3341Phosphothreonine Ref.14
Modified residue3361Phosphoserine Ref.14

Experimental info

Sequence conflict1271Y → H in AAU09736. Ref.4

Secondary structure

.............................................. 345
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P49723 [UniParc].

Last modified October 1, 1996. Version 1.
Checksum: 712853F2D87D3972

FASTA34540,055
        10         20         30         40         50         60 
MEAHNQFLKT FQKERHDMKE AEKDEILLME NSRRFVMFPI KYHEIWAAYK KVEASFWTAE 

        70         80         90        100        110        120 
EIELAKDTED FQKLTDDQKT YIGNLLALSI SSDNLVNKYL IENFSAQLQN PEGKSFYGFQ 

       130        140        150        160        170        180 
IMMENIYSEV YSMMVDAFFK DPKNIPLFKE IANLPEVKHK AAFIERWISN DDSLYAERLV 

       190        200        210        220        230        240 
AFAAKEGIFQ AGNYASMFWL TDKKIMPGLA MANRNICRDR GAYTDFSCLL FAHLRTKPNP 

       250        260        270        280        290        300 
KIIEKIITEA VEIEKEYYSN SLPVEKFGMD LKSIHTYIEF VADGLLQGFG NEKYYNAVNP 

       310        320        330        340 
FEFMEDVATA GKTTFFEKKV SDYQKASDMS KSATPSKEIN FDDDF 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
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]"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].
[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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
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]"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).
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U30385 Genomic DNA. Translation: AAB72236.1.
Z72965 Genomic DNA. Translation: CAA97206.1.
AY723819 Genomic DNA. Translation: AAU09736.1.
BK006941 Genomic DNA. Translation: DAA08275.1.
PIRS59744.
RefSeqNP_011696.3. NM_001181309.3.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1JK0X-ray2.80B1-345[»]
1SMSX-ray3.10A/B1-345[»]
1ZZDX-ray2.60B337-345[»]
DisProtDP00488.
ProteinModelPortalP49723.
SMRP49723. Positions 3-325.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid33432. 88 interactions.
DIPDIP-5381N.
IntActP49723. 16 interactions.
MINTMINT-537732.
STRING4932.YGR180C.

Proteomic databases

PaxDbP49723.
PeptideAtlasP49723.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYGR180C; YGR180C; YGR180C.
GeneID853091.
KEGGsce:YGR180C.

Organism-specific databases

CYGDYGR180c.
SGDS000003412. RNR4.

Phylogenomic databases

eggNOGCOG0208.
HOGENOMHOG000255975.
KOK10808.
OrthoDBEOG7T1RMH.

Enzyme and pathway databases

BioCycMetaCyc:YGR180C-MONOMER.
YEAST:YGR180C-MONOMER.
UniPathwayUPA00326.

Gene expression databases

GenevestigatorP49723.

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

EvolutionaryTraceP49723.
NextBio973076.

Entry information

Entry nameRIR4_YEAST
AccessionPrimary (citable) accession number: P49723
Secondary accession number(s): D6VUW4, Q66R92
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: October 1, 1996
Last modified: April 16, 2014
This is version 146 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VII

Yeast (Saccharomyces cerevisiae) chromosome VII: 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