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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: 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: DNA replication

This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei5Allosteric activatorBy similarity1
Binding sitei53Allosteric activatorBy similarity1
Binding sitei88Allosteric activatorBy similarity1
Binding sitei202SubstrateBy similarity1
Sitei218Important for hydrogen atom transferBy similarity1
Sitei226Allosteric effector binding, determines substrate specificityBy similarity1
Binding sitei247Substrate; via amide nitrogenBy similarity1
Sitei256Allosteric effector binding, determines substrate specificityBy similarity1
Active sitei426Proton acceptorBy similarity1
Active sitei428Cysteine radical intermediateBy similarity1
Active sitei430Proton acceptorBy similarity1
Sitei443Important for hydrogen atom transferBy similarity1
Sitei741Important for electron transferBy similarity1
Sitei742Important for electron transferBy similarity1
Sitei864Interacts with thioredoxin/glutaredoxinBy similarity1
Sitei867Interacts with thioredoxin/glutaredoxinBy similarity1

GO - Molecular functioni

GO - Biological processi

  • deoxyribonucleotide biosynthetic process Source: SGD
  • 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.
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
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

EuPathDBiFungiDB:YIL066C.
SGDiS000001328. RNR3.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001872041 – 869Ribonucleoside-diphosphate reductase large chain 2Add BLAST869

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi218 ↔ 443Redox-activeBy similarity
Modified residuei227PhosphoserineBy similarity1
Cross-linki387Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei806PhosphoserineCombined sources1
Modified residuei827PhosphoserineBy similarity1
Modified residuei868PhosphoserineBy similarity1

Keywords - PTMi

Disulfide bond, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP21672.
PRIDEiP21672.

PTM databases

iPTMnetiP21672.

Expressioni

Inductioni

Highly induced by DNA-damage.2 Publications

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 interactors.
DIPiDIP-2563N.
IntActiP21672. 2 interactors.
MINTiMINT-425113.

Structurei

3D structure databases

ProteinModelPortaliP21672.
SMRiP21672.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 92ATP-conePROSITE-ProRule annotationAdd BLAST92

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni11 – 17Allosteric activator bindingBy similarity7
Regioni217 – 218Substrate bindingBy similarity2
Regioni285 – 288Allosteric effector binding, determines substrate specificityBy similarity4
Regioni426 – 430Substrate bindingBy similarity5
Regioni607 – 611Substrate bindingBy similarity5

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

GeneTreeiENSGT00860000134166.
HOGENOMiHOG000057035.
InParanoidiP21672.
KOiK10807.
OMAiIIAMTLM.
OrthoDBiEOG092C0QYB.

Family and domain databases

InterProiIPR005144. ATP-cone_dom.
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 differs from that shown. Reason: Frameshift at positions 127, 129, 130, 247, 250, 287 and 313.Curated
The sequence CAA86157 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti21 – 22RI → VL no nucleotide entry (PubMed:2199320).Curated2
Sequence conflicti37V → F no nucleotide entry (PubMed:2199320).Curated1
Sequence conflicti58N → I no nucleotide entry (PubMed:2199320).Curated1
Sequence conflicti69T → H no nucleotide entry (PubMed:2199320).Curated1
Sequence conflicti83I → T no nucleotide entry (PubMed:2199320).Curated1
Sequence conflicti212H → L in AAA34569 (PubMed:2204819).Curated1
Sequence conflicti249G → V in AAA34569 (PubMed:2204819).Curated1
Sequence conflicti311F → K in AAA34569 (PubMed:2204819).Curated1

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.
PIRiS48413. WMBY3L.
RefSeqiNP_012198.3. NM_001179416.3.

3D structure databases

ProteinModelPortaliP21672.
SMRiP21672.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34926. 30 interactors.
DIPiDIP-2563N.
IntActiP21672. 2 interactors.
MINTiMINT-425113.

PTM databases

iPTMnetiP21672.

Proteomic databases

MaxQBiP21672.
PRIDEiP21672.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EuPathDBiFungiDB:YIL066C.
SGDiS000001328. RNR3.

Phylogenomic databases

GeneTreeiENSGT00860000134166.
HOGENOMiHOG000057035.
InParanoidiP21672.
KOiK10807.
OMAiIIAMTLM.
OrthoDBiEOG092C0QYB.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciMetaCyc:YIL066C-MONOMER.
YEAST:YIL066C-MONOMER.

Miscellaneous databases

PROiP21672.

Family and domain databases

InterProiIPR005144. ATP-cone_dom.
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]
ProtoNetiSearch...

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 30, 2016
This is version 165 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.