RIR3_YEAST
ID RIR3_YEAST Reviewed; 869 AA.
AC P21672; D6VVL8;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 4.
DT 03-AUG-2022, entry version 202.
DE RecName: Full=Ribonucleoside-diphosphate reductase large chain 2;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase DNA damage-inducible regulatory subunit 2;
DE AltName: Full=Ribonucleotide reductase R1 subunit 2;
DE AltName: Full=Ribonucleotide reductase large subunit 2;
GN Name=RNR3; Synonyms=DIN1; OrderedLocusNames=YIL066C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169870;
RA Churcher C.M., Bowman S., Badcock K., Bankier A.T., Brown D.,
RA Chillingworth T., Connor R., Devlin K., Gentles S., Hamlin N., Harris D.E.,
RA Horsnell T., Hunt S., Jagels K., Jones M., Lye G., Moule S., Odell C.,
RA Pearson D., Rajandream M.A., Rice P., Rowley N., Skelton J., Smith V.,
RA Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.";
RL Nature 387:84-87(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-758, AND INDUCTION.
RX PubMed=2204819; DOI=10.1128/mcb.10.10.5553-5557.1990;
RA Yagle K., McEntee K.;
RT "The DNA damage-inducible gene DIN1 of Saccharomyces cerevisiae encodes a
RT regulatory subunit of ribonucleotide reductase and is identical to RNR3.";
RL Mol. Cell. Biol. 10:5553-5557(1990).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-101 AND 652-711, AND INDUCTION.
RX PubMed=2199320; DOI=10.1101/gad.4.5.740;
RA Elledge S.J., Davis R.W.;
RT "Two genes differentially regulated in the cell cycle and by DNA-damaging
RT agents encode alternative regulatory subunits of ribonucleotide
RT reductase.";
RL Genes Dev. 4:740-751(1990).
RN [5]
RP FUNCTION.
RX PubMed=11893751; DOI=10.1074/jbc.m201553200;
RA Domkin V., Thelander L., Chabes A.;
RT "Yeast DNA damage-inducible Rnr3 has a very low catalytic activity strongly
RT stimulated after the formation of a cross-talking Rnr1/Rnr3 complex.";
RL J. Biol. Chem. 277:18574-18578(2002).
RN [6]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [7]
RP SUBCELLULAR LOCATION.
RX PubMed=12732713; DOI=10.1073/pnas.1131932100;
RA Yao R., Zhang Z., An X., Bucci B., Perlstein D.L., Stubbe J., Huang M.;
RT "Subcellular localization of yeast ribonucleotide reductase regulated by
RT the DNA replication and damage checkpoint pathways.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:6628-6633(2003).
RN [8]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-806, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. {ECO:0000269|PubMed:11893751}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[thioredoxin]-disulfide + a 2'-deoxyribonucleoside 5'-
CC diphosphate + H2O = [thioredoxin]-dithiol + a ribonucleoside 5'-
CC diphosphate; Xref=Rhea:RHEA:23252, Rhea:RHEA-COMP:10698, Rhea:RHEA-
CC COMP:10700, ChEBI:CHEBI:15377, ChEBI:CHEBI:29950, ChEBI:CHEBI:50058,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:73316; EC=1.17.4.1;
CC -!- ACTIVITY REGULATION: Under complex allosteric control mediated by
CC deoxynucleoside triphosphates and ATP binding to separate specificity
CC and activation sites on the large subunit. The type of nucleotide bound
CC at the specificity site determines substrate preference. It seems
CC probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP
CC reduction and dTTP favors GDP reduction. Stimulated by ATP and
CC inhibited by dATP binding to the activity site (By similarity).
CC {ECO:0000250}.
CC -!- PATHWAY: Genetic information processing; DNA replication.
CC -!- SUBUNIT: Heterotetramer of two large (R1) and two small (R2) subunits.
CC S.cerevisiae has two different R1 subunits (RNR1 and RNR3) and two
CC different R2 subunits (RNR2 and RNR4). The functional form of the small
CC subunits is a RNR2-RNR4 heterodimer, where RNR2 provides the iron-
CC radical center and RNR4 is required for proper folding of RNR2 and
CC assembly with the large subunits. Under normal growth conditions, the
CC active form of the large subunits is a homodimer of the constitutively
CC expressed RNR1. In damaged cells or cells arrested for DNA synthesis,
CC the reductase consists of multiple species because of the association
CC of the small subunits (RNR2-RNR4) with either the RNR1 homodimer or a
CC heterodimer of RNR1 and the damage-inducible RNR3.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:12732713}.
CC -!- INDUCTION: Highly induced by DNA-damage. {ECO:0000269|PubMed:2199320,
CC ECO:0000269|PubMed:2204819}.
CC -!- MISCELLANEOUS: Two distinct regulatory sites have been defined: the
CC specificity site, which controls substrate specificity, and the
CC activity site which regulates overall catalytic activity. A substrate-
CC binding catalytic site, located on R1, is formed only in the presence
CC of the second subunit R2 (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: Present with 1364 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase large
CC chain family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA34569.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA86157.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; Z38060; CAA86157.1; ALT_INIT; Genomic_DNA.
DR EMBL; M58012; AAA34569.1; ALT_FRAME; Genomic_DNA.
DR EMBL; BK006942; DAA08484.1; -; Genomic_DNA.
DR PIR; S48413; WMBY3L.
DR RefSeq; NP_012198.3; NM_001179416.3.
DR AlphaFoldDB; P21672; -.
DR SMR; P21672; -.
DR BioGRID; 34926; 93.
DR ComplexPortal; CPX-1103; Ribonucleoside-diphosphate reductase variant 2.
DR DIP; DIP-2563N; -.
DR IntAct; P21672; 32.
DR MINT; P21672; -.
DR STRING; 4932.YIL066C; -.
DR iPTMnet; P21672; -.
DR MaxQB; P21672; -.
DR PaxDb; P21672; -.
DR PRIDE; P21672; -.
DR EnsemblFungi; YIL066C_mRNA; YIL066C; YIL066C.
DR GeneID; 854744; -.
DR KEGG; sce:YIL066C; -.
DR SGD; S000001328; RNR3.
DR VEuPathDB; FungiDB:YIL066C; -.
DR eggNOG; KOG1112; Eukaryota.
DR GeneTree; ENSGT00910000144246; -.
DR HOGENOM; CLU_000404_1_2_1; -.
DR InParanoid; P21672; -.
DR OMA; RNYAWTK; -.
DR BioCyc; MetaCyc:YIL066C-MON; -.
DR BioCyc; YEAST:YIL066C-MON; -.
DR UniPathway; UPA00326; -.
DR PRO; PR:P21672; -.
DR Proteomes; UP000002311; Chromosome IX.
DR RNAct; P21672; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:UniProtKB-EC.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IDA:SGD.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR GO; GO:0043457; P:regulation of cellular respiration; IMP:SGD.
DR InterPro; IPR005144; ATP-cone_dom.
DR InterPro; IPR013346; NrdE_NrdA.
DR InterPro; IPR000788; RNR_lg_C.
DR InterPro; IPR013509; RNR_lsu_N.
DR InterPro; IPR008926; RNR_R1-su_N.
DR InterPro; IPR039718; Rrm1.
DR PANTHER; PTHR11573; PTHR11573; 1.
DR Pfam; PF03477; ATP-cone; 1.
DR Pfam; PF02867; Ribonuc_red_lgC; 1.
DR Pfam; PF00317; Ribonuc_red_lgN; 1.
DR PRINTS; PR01183; RIBORDTASEM1.
DR SUPFAM; SSF48168; SSF48168; 1.
DR TIGRFAMs; TIGR02506; NrdE_NrdA; 1.
DR PROSITE; PS51161; ATP_CONE; 1.
DR PROSITE; PS00089; RIBORED_LARGE; 1.
PE 1: Evidence at protein level;
KW Allosteric enzyme; ATP-binding; Cytoplasm; Deoxyribonucleotide synthesis;
KW Disulfide bond; Isopeptide bond; Nucleotide-binding; Oxidoreductase;
KW Phosphoprotein; Reference proteome; Ubl conjugation.
FT CHAIN 1..869
FT /note="Ribonucleoside-diphosphate reductase large chain 2"
FT /id="PRO_0000187204"
FT DOMAIN 1..92
FT /note="ATP-cone"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00492"
FT REGION 793..843
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 793..823
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 426
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 428
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250"
FT ACT_SITE 430
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 5..6
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 11..17
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 53
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /ligand_note="allosteric activator"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 202
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 217
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 226..228
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 243
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 256
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 263..264
FT /ligand="dTTP"
FT /ligand_id="ChEBI:CHEBI:37568"
FT /ligand_note="allosteric effector that controls substrate
FT specificity"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 426
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 430
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT BINDING 608..611
FT /ligand="GDP"
FT /ligand_id="ChEBI:CHEBI:58189"
FT /evidence="ECO:0000250|UniProtKB:P23921"
FT SITE 218
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 443
FT /note="Important for hydrogen atom transfer"
FT /evidence="ECO:0000250"
FT SITE 741
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 742
FT /note="Important for electron transfer"
FT /evidence="ECO:0000250"
FT SITE 864
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT SITE 867
FT /note="Interacts with thioredoxin/glutaredoxin"
FT /evidence="ECO:0000250"
FT MOD_RES 227
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P21524"
FT MOD_RES 806
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 827
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P21524"
FT MOD_RES 868
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P21524"
FT DISULFID 218..443
FT /note="Redox-active"
FT /evidence="ECO:0000250"
FT CROSSLNK 387
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:P21524"
FT CONFLICT 21..22
FT /note="RI -> VL (in Ref. 4; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 37
FT /note="V -> F (in Ref. 4; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 58
FT /note="N -> I (in Ref. 4; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 69
FT /note="T -> H (in Ref. 4; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 83
FT /note="I -> T (in Ref. 4; no nucleotide entry)"
FT /evidence="ECO:0000305"
FT CONFLICT 212
FT /note="H -> L (in Ref. 3; AAA34569)"
FT /evidence="ECO:0000305"
FT CONFLICT 249
FT /note="G -> V (in Ref. 3; AAA34569)"
FT /evidence="ECO:0000305"
FT CONFLICT 311
FT /note="F -> K (in Ref. 3; AAA34569)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 869 AA; 97515 MW; BEE8DEDE41D7049A CRC64;
MYVIKRDGRK EPVQFDKITS RITRLSYGLD PNRIDAVKVT QRIISGVYSG VTTVELDNLA
AETCAYMTTV HPDYATLAAR IAISNLHKQT TKQFSKVIED LHDWINPATG KHAPMISDEI
YNIVMENKDT LNSAIVYDRD FQYTYFGFKT LERSYLLRLN GEVAERPQHL VMRVALGIHG
SDIESVLKTY NLMSLRYFTH ASPTLFNAGT PHPQMSSCFL IAMKDDSIEG IYDTLKECAM
ISKTAGGVGL HINNIRSTGS YIAGTNGTSN GLIPMIRVFN NTARYVDQGG NKRPGAFALF
LEPWHADIFD FVDIRKTHGK EEIRARDLFP ALWIPDLFMK RVQEDGPWTL FSPSAAPGLD
DVWGDEFEEL YTRYEREGRG KTIKAQKLWY AILQAQTETG TPFMVYKDAC NRKTNQQNLG
TIKSSNLCCE IVEYSSPDET AVCNLASIAL PAFVEVSEDG KTASYNFERL HEIAKVITHN
LNRVIDRNYY PVPEARNSNM KHRPIALGVQ GLADTYMMLR LPFESEEAQT LNKQIFETIY
HATLEASCEL AQKEGKYSTF EGSPASKGIL QFDMWNAKPF GMWDWETLRK DIVKHGLRNS
LTMAPMPTAS TSQILGYNEC FEPVTSNMYS RRVLSGEFQV VNPYLLRDLV DLGIWDDSMK
QYLITQNGSI QGLPNVPQEL KELYKTVWEI SQKTIINMAA DRAIYIDQSH SLNLFLQAPS
MGKITSMHFY GWKKGLKTGM YYLRTQAASA AIQFTIDQEV ADQAATHIAS VSELDRPVYV
PKGTKFSEQK AASALTESSD NEKDASPVPS EQSSVSSAMS NVKLEDSVAP AVPTETIKED
SDEKKCDIYN EKVIACTAPT PEACESCSG
