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P21672

- RIR3_YEAST

UniProt

P21672 - RIR3_YEAST

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Protein

Ribonucleoside-diphosphate reductase large chain 2

Gene

RNR3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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.1 Publication

Catalytic activityi

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

Enzyme regulationi

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).By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei5 – 51Allosteric activatorBy similarity
Binding sitei53 – 531Allosteric activatorBy similarity
Binding sitei88 – 881Allosteric activatorBy similarity
Binding sitei202 – 2021SubstrateBy similarity
Sitei218 – 2181Important for hydrogen atom transferBy similarity
Sitei226 – 2261Allosteric effector binding, determines substrate specificityBy similarity
Binding sitei247 – 2471Substrate; via amide nitrogenBy similarity
Sitei256 – 2561Allosteric effector binding, determines substrate specificityBy similarity
Active sitei426 – 4261Proton acceptorBy similarity
Active sitei428 – 4281Cysteine radical intermediateBy similarity
Active sitei430 – 4301Proton acceptorBy similarity
Sitei443 – 4431Important for hydrogen atom transferBy similarity
Sitei741 – 7411Important for electron transferBy similarity
Sitei742 – 7421Important for electron transferBy similarity
Sitei864 – 8641Interacts with thioredoxin/glutaredoxinBy similarity
Sitei867 – 8671Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. deoxyribonucleotide biosynthetic process Source: SGD
  2. DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:YIL066C-MONOMER.
YEAST:YIL066C-MONOMER.
ReactomeiREACT_238684. Synthesis and interconversion of nucleotide di- and triphosphates.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:RNR3
Synonyms:DIN1
Ordered Locus Names:YIL066C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome IX

Organism-specific databases

CYGDiYIL066c.
SGDiS000001328. RNR3.

Subcellular locationi

Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: SGD
  2. ribonucleoside-diphosphate reductase complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 869869Ribonucleoside-diphosphate reductase large chain 2PRO_0000187204Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi218 ↔ 443Redox-activeBy similarity
Modified residuei806 – 8061Phosphoserine1 Publication

Keywords - PTMi

Disulfide bond, Phosphoprotein

Proteomic databases

MaxQBiP21672.
PaxDbiP21672.
PeptideAtlasiP21672.
PRIDEiP21672.

Expressioni

Inductioni

Highly induced by DNA-damage.2 Publications

Gene expression databases

GenevestigatoriP21672.

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.

Protein-protein interaction databases

BioGridi34926. 30 interactions.
DIPiDIP-2563N.
IntActiP21672. 1 interaction.
MINTiMINT-425113.
STRINGi4932.YIL066C.

Structurei

3D structure databases

ProteinModelPortaliP21672.
SMRiP21672. Positions 1-787.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 9292ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 177Allosteric activator bindingBy similarity
Regioni217 – 2182Substrate bindingBy similarity
Regioni285 – 2884Allosteric effector binding, determines substrate specificityBy similarity
Regioni426 – 4305Substrate bindingBy similarity
Regioni607 – 6115Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
GeneTreeiENSGT00750000117986.
HOGENOMiHOG000057035.
InParanoidiP21672.
KOiK10807.
OMAiKECAMIS.
OrthoDBiEOG7C5MHR.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P21672-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MYVIKRDGRK EPVQFDKITS RITRLSYGLD PNRIDAVKVT QRIISGVYSG
60 70 80 90 100
VTTVELDNLA AETCAYMTTV HPDYATLAAR IAISNLHKQT TKQFSKVIED
110 120 130 140 150
LHDWINPATG KHAPMISDEI YNIVMENKDT LNSAIVYDRD FQYTYFGFKT
160 170 180 190 200
LERSYLLRLN GEVAERPQHL VMRVALGIHG SDIESVLKTY NLMSLRYFTH
210 220 230 240 250
ASPTLFNAGT PHPQMSSCFL IAMKDDSIEG IYDTLKECAM ISKTAGGVGL
260 270 280 290 300
HINNIRSTGS YIAGTNGTSN GLIPMIRVFN NTARYVDQGG NKRPGAFALF
310 320 330 340 350
LEPWHADIFD FVDIRKTHGK EEIRARDLFP ALWIPDLFMK RVQEDGPWTL
360 370 380 390 400
FSPSAAPGLD DVWGDEFEEL YTRYEREGRG KTIKAQKLWY AILQAQTETG
410 420 430 440 450
TPFMVYKDAC NRKTNQQNLG TIKSSNLCCE IVEYSSPDET AVCNLASIAL
460 470 480 490 500
PAFVEVSEDG KTASYNFERL HEIAKVITHN LNRVIDRNYY PVPEARNSNM
510 520 530 540 550
KHRPIALGVQ GLADTYMMLR LPFESEEAQT LNKQIFETIY HATLEASCEL
560 570 580 590 600
AQKEGKYSTF EGSPASKGIL QFDMWNAKPF GMWDWETLRK DIVKHGLRNS
610 620 630 640 650
LTMAPMPTAS TSQILGYNEC FEPVTSNMYS RRVLSGEFQV VNPYLLRDLV
660 670 680 690 700
DLGIWDDSMK QYLITQNGSI QGLPNVPQEL KELYKTVWEI SQKTIINMAA
710 720 730 740 750
DRAIYIDQSH SLNLFLQAPS MGKITSMHFY GWKKGLKTGM YYLRTQAASA
760 770 780 790 800
AIQFTIDQEV ADQAATHIAS VSELDRPVYV PKGTKFSEQK AASALTESSD
810 820 830 840 850
NEKDASPVPS EQSSVSSAMS NVKLEDSVAP AVPTETIKED SDEKKCDIYN
860
EKVIACTAPT PEACESCSG
Length:869
Mass (Da):97,515
Last modified:February 1, 1995 - v4
Checksum:iBEE8DEDE41D7049A
GO

Sequence cautioni

The sequence AAA34569.1 differs from that shown. Reason: Frameshift at positions 127, 129, 130, 247, 250, 287 and 313. Curated
The sequence CAA86157.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti21 – 222RI → VL no nucleotide entry (PubMed:2199320)Curated
Sequence conflicti37 – 371V → F no nucleotide entry (PubMed:2199320)Curated
Sequence conflicti58 – 581N → I no nucleotide entry (PubMed:2199320)Curated
Sequence conflicti69 – 691T → H no nucleotide entry (PubMed:2199320)Curated
Sequence conflicti83 – 831I → T no nucleotide entry (PubMed:2199320)Curated
Sequence conflicti212 – 2121H → L in AAA34569. (PubMed:2204819)Curated
Sequence conflicti249 – 2491G → V in AAA34569. (PubMed:2204819)Curated
Sequence conflicti311 – 3111F → K in AAA34569. (PubMed:2204819)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38060 Genomic DNA. Translation: CAA86157.1. Different initiation.
M58012 Genomic DNA. Translation: AAA34569.1. Frameshift.
BK006942 Genomic DNA. Translation: DAA08484.1.
PIRiS48413. WMBY3L.
RefSeqiNP_012198.3. NM_001179416.3.

Genome annotation databases

EnsemblFungiiYIL066C; YIL066C; YIL066C.
GeneIDi854744.
KEGGisce:YIL066C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z38060 Genomic DNA. Translation: CAA86157.1 . Different initiation.
M58012 Genomic DNA. Translation: AAA34569.1 . Frameshift.
BK006942 Genomic DNA. Translation: DAA08484.1 .
PIRi S48413. WMBY3L.
RefSeqi NP_012198.3. NM_001179416.3.

3D structure databases

ProteinModelPortali P21672.
SMRi P21672. Positions 1-787.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34926. 30 interactions.
DIPi DIP-2563N.
IntActi P21672. 1 interaction.
MINTi MINT-425113.
STRINGi 4932.YIL066C.

Proteomic databases

MaxQBi P21672.
PaxDbi P21672.
PeptideAtlasi P21672.
PRIDEi P21672.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YIL066C ; YIL066C ; YIL066C .
GeneIDi 854744.
KEGGi sce:YIL066C.

Organism-specific databases

CYGDi YIL066c.
SGDi S000001328. RNR3.

Phylogenomic databases

eggNOGi COG0209.
GeneTreei ENSGT00750000117986.
HOGENOMi HOG000057035.
InParanoidi P21672.
KOi K10807.
OMAi KECAMIS.
OrthoDBi EOG7C5MHR.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci MetaCyc:YIL066C-MONOMER.
YEAST:YIL066C-MONOMER.
Reactomei REACT_238684. Synthesis and interconversion of nucleotide di- and triphosphates.

Miscellaneous databases

NextBioi 977464.

Gene expression databases

Genevestigatori P21672.

Family and domain databases

InterProi IPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view ]
Pfami PF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view ]
PRINTSi PR01183. RIBORDTASEM1.
SUPFAMi SSF48168. SSF48168. 1 hit.
TIGRFAMsi TIGR02506. NrdE_NrdA. 1 hit.
PROSITEi PS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. 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. 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].

Entry informationi

Entry nameiRIR3_YEAST
AccessioniPrimary (citable) accession number: P21672
Secondary accession number(s): D6VVL8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: February 1, 1995
Last modified: November 26, 2014
This is version 144 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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).By similarity
Present with 1364 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

External Data

Dasty 3