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P21672 (RIR3_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 138. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ribonucleoside-diphosphate reductase large chain 2

EC=1.17.4.1
Alternative name(s):
Ribonucleotide reductase DNA damage-inducible regulatory subunit 2
Ribonucleotide reductase R1 subunit 2
Ribonucleotide reductase large subunit 2
Gene names
Name:RNR3
Synonyms:DIN1
Ordered Locus Names:YIL066C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length869 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. Ref.5

Catalytic activity

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

Enzyme regulation

Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the large subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site By similarity.

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.

Subcellular location

Cytoplasm Ref.7.

Induction

Highly induced by DNA-damage. Ref.3 Ref.4

Miscellaneous

Two distinct regulatory sites have been defined: the specificity site, which controls substrate specificity, and the activity site which regulates overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2 By similarity.

Present with 1364 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase large chain family.

Contains 1 ATP-cone domain.

Sequence caution

The sequence AAA34569.1 differs from that shown. Reason: Frameshift at positions 127, 129, 130, 247, 250, 287 and 313.

The sequence CAA86157.1 differs from that shown. Reason: Erroneous initiation.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 869869Ribonucleoside-diphosphate reductase large chain 2
PRO_0000187204

Regions

Domain1 – 9292ATP-cone
Region11 – 177Allosteric activator binding By similarity
Region217 – 2182Substrate binding By similarity
Region285 – 2884Allosteric effector binding, determines substrate specificity By similarity
Region426 – 4305Substrate binding By similarity
Region607 – 6115Substrate binding By similarity

Sites

Active site4261Proton acceptor By similarity
Active site4281Cysteine radical intermediate By similarity
Active site4301Proton acceptor By similarity
Binding site51Allosteric activator By similarity
Binding site531Allosteric activator By similarity
Binding site881Allosteric activator By similarity
Binding site2021Substrate By similarity
Binding site2471Substrate; via amide nitrogen By similarity
Site2181Important for hydrogen atom transfer By similarity
Site2261Allosteric effector binding, determines substrate specificity By similarity
Site2561Allosteric effector binding, determines substrate specificity By similarity
Site4431Important for hydrogen atom transfer By similarity
Site7411Important for electron transfer By similarity
Site7421Important for electron transfer By similarity
Site8641Interacts with thioredoxin/glutaredoxin By similarity
Site8671Interacts with thioredoxin/glutaredoxin By similarity

Amino acid modifications

Modified residue8061Phosphoserine Ref.8
Disulfide bond218 ↔ 443Redox-active By similarity

Experimental info

Sequence conflict21 – 222RI → VL no nucleotide entry Ref.4
Sequence conflict371V → F no nucleotide entry Ref.4
Sequence conflict581N → I no nucleotide entry Ref.4
Sequence conflict691T → H no nucleotide entry Ref.4
Sequence conflict831I → T no nucleotide entry Ref.4
Sequence conflict2121H → L in AAA34569. Ref.3
Sequence conflict2491G → V in AAA34569. Ref.3
Sequence conflict3111F → K in AAA34569. Ref.3

Sequences

Sequence LengthMass (Da)Tools
P21672 [UniParc].

Last modified February 1, 1995. Version 4.
Checksum: BEE8DEDE41D7049A

FASTA86997,515
        10         20         30         40         50         60 
MYVIKRDGRK EPVQFDKITS RITRLSYGLD PNRIDAVKVT QRIISGVYSG VTTVELDNLA 

        70         80         90        100        110        120 
AETCAYMTTV HPDYATLAAR IAISNLHKQT TKQFSKVIED LHDWINPATG KHAPMISDEI 

       130        140        150        160        170        180 
YNIVMENKDT LNSAIVYDRD FQYTYFGFKT LERSYLLRLN GEVAERPQHL VMRVALGIHG 

       190        200        210        220        230        240 
SDIESVLKTY NLMSLRYFTH ASPTLFNAGT PHPQMSSCFL IAMKDDSIEG IYDTLKECAM 

       250        260        270        280        290        300 
ISKTAGGVGL HINNIRSTGS YIAGTNGTSN GLIPMIRVFN NTARYVDQGG NKRPGAFALF 

       310        320        330        340        350        360 
LEPWHADIFD FVDIRKTHGK EEIRARDLFP ALWIPDLFMK RVQEDGPWTL FSPSAAPGLD 

       370        380        390        400        410        420 
DVWGDEFEEL YTRYEREGRG KTIKAQKLWY AILQAQTETG TPFMVYKDAC NRKTNQQNLG 

       430        440        450        460        470        480 
TIKSSNLCCE IVEYSSPDET AVCNLASIAL PAFVEVSEDG KTASYNFERL HEIAKVITHN 

       490        500        510        520        530        540 
LNRVIDRNYY PVPEARNSNM KHRPIALGVQ GLADTYMMLR LPFESEEAQT LNKQIFETIY 

       550        560        570        580        590        600 
HATLEASCEL AQKEGKYSTF EGSPASKGIL QFDMWNAKPF GMWDWETLRK DIVKHGLRNS 

       610        620        630        640        650        660 
LTMAPMPTAS TSQILGYNEC FEPVTSNMYS RRVLSGEFQV VNPYLLRDLV DLGIWDDSMK 

       670        680        690        700        710        720 
QYLITQNGSI QGLPNVPQEL KELYKTVWEI SQKTIINMAA DRAIYIDQSH SLNLFLQAPS 

       730        740        750        760        770        780 
MGKITSMHFY GWKKGLKTGM YYLRTQAASA AIQFTIDQEV ADQAATHIAS VSELDRPVYV 

       790        800        810        820        830        840 
PKGTKFSEQK AASALTESSD NEKDASPVPS EQSSVSSAMS NVKLEDSVAP AVPTETIKED 

       850        860 
SDEKKCDIYN EKVIACTAPT PEACESCSG 

« Hide

References

« Hide 'large scale' references
[1]"The nucleotide sequence of Saccharomyces cerevisiae chromosome IX."
Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D., Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E., Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C. expand/collapse author list , Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V., Walsh S.V., Whitehead S., Barrell B.G.
Nature 387:84-87(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[3]"The DNA damage-inducible gene DIN1 of Saccharomyces cerevisiae encodes a regulatory subunit of ribonucleotide reductase and is identical to RNR3."
Yagle K., McEntee K.
Mol. Cell. Biol. 10:5553-5557(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-758, INDUCTION.
[4]"Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase."
Elledge S.J., Davis R.W.
Genes Dev. 4:740-751(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-101 AND 652-711, INDUCTION.
[5]"Yeast DNA damage-inducible Rnr3 has a very low catalytic activity strongly stimulated after the formation of a cross-talking Rnr1/Rnr3 complex."
Domkin V., Thelander L., Chabes A.
J. Biol. Chem. 277:18574-18578(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[6]"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].
[7]"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.
[8]"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-806, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
Z38060 Genomic DNA. Translation: CAA86157.1. Different initiation.
M58012 Genomic DNA. Translation: AAA34569.1. Frameshift.
BK006942 Genomic DNA. Translation: DAA08484.1.
PIRWMBY3L. S48413.
RefSeqNP_012198.3. NM_001179416.3.

3D structure databases

ProteinModelPortalP21672.
SMRP21672. Positions 1-787.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34926. 29 interactions.
DIPDIP-2563N.
IntActP21672. 1 interaction.
MINTMINT-425113.
STRING4932.YIL066C.

Proteomic databases

PaxDbP21672.
PeptideAtlasP21672.
PRIDEP21672.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYIL066C; YIL066C; YIL066C.
GeneID854744.
KEGGsce:YIL066C.

Organism-specific databases

CYGDYIL066c.
SGDS000001328. RNR3.

Phylogenomic databases

eggNOGCOG0209.
GeneTreeENSGT00740000115975.
HOGENOMHOG000057035.
KOK10807.
OMAVAVGIHQ.
OrthoDBEOG7C5MHR.

Enzyme and pathway databases

BioCycMetaCyc:YIL066C-MONOMER.
YEAST:YIL066C-MONOMER.
UniPathwayUPA00326.

Gene expression databases

GenevestigatorP21672.

Family and domain databases

InterProIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSPR01183. RIBORDTASEM1.
SUPFAMSSF48168. SSF48168. 1 hit.
TIGRFAMsTIGR02506. NrdE_NrdA. 1 hit.
PROSITEPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio977464.

Entry information

Entry nameRIR3_YEAST
AccessionPrimary (citable) accession number: P21672
Secondary accession number(s): D6VVL8
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: February 1, 1995
Last modified: March 19, 2014
This is version 138 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome IX

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

Yeast

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

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways