RIR4_YEAST
ID RIR4_YEAST Reviewed; 345 AA.
AC P49723; D6VUW4; Q66R92;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 212.
DE RecName: Full=Ribonucleoside-diphosphate reductase small chain 2;
DE EC=1.17.4.1;
DE AltName: Full=Ribonucleotide reductase R2 subunit 2;
DE AltName: Full=Ribonucleotide reductase small subunit 2;
GN Name=RNR4; Synonyms=CRT3; OrderedLocusNames=YGR180C;
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 [GENOMIC DNA], AND INDUCTION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9315671; DOI=10.1128/mcb.17.10.6114;
RA Wang P.J., Chabes A., Casagrande R., Tian X.C., Thelander L.,
RA Huffaker T.C.;
RT "Rnr4p, a novel ribonucleotide reductase small-subunit protein.";
RL Mol. Cell. Biol. 17:6114-6121(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(1997).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP PROTEIN SEQUENCE OF 1-9; 150-158; 167-178; 219-235 AND 294-312, CLEAVAGE OF
RP INITIATOR METHIONINE, ACETYLATION AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RA Bienvenut W.V., Peters C.;
RL Submitted (JUN-2005) to UniProtKB.
RN [6]
RP FUNCTION, AND SUBUNIT.
RX PubMed=10535923; DOI=10.1073/pnas.96.22.12339;
RA Nguyen H.-H.T., Ge J., Perlstein D.L., Stubbe J.;
RT "Purification of ribonucleotide reductase subunits Y1, Y2, Y3, and Y4 from
RT yeast: Y4 plays a key role in diiron cluster assembly.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:12339-12344(1999).
RN [7]
RP SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=10716984; DOI=10.1073/pnas.97.6.2474;
RA Chabes A., Domkin V., Larsson G., Liu A., Graeslund A., Wijmenga S.,
RA Thelander L.;
RT "Yeast ribonucleotide reductase has a heterodimeric iron-radical-containing
RT subunit.";
RL Proc. Natl. Acad. Sci. U.S.A. 97:2474-2479(2000).
RN [8]
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 [9]
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 [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ADR376;
RX PubMed=17330950; DOI=10.1021/pr060559j;
RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
RA Elias J.E., Gygi S.P.;
RT "Large-scale phosphorylation analysis of alpha-factor-arrested
RT Saccharomyces cerevisiae.";
RL J. Proteome Res. 6:1190-1197(2007).
RN [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-169, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT "Analysis of phosphorylation sites on proteins from Saccharomyces
RT cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN [12]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH DIF1 AND RNR4.
RX PubMed=18851834; DOI=10.1016/j.molcel.2008.08.018;
RA Lee Y.D., Wang J., Stubbe J., Elledge S.J.;
RT "Dif1 is a DNA-damage-regulated facilitator of nuclear import for
RT ribonucleotide reductase.";
RL Mol. Cell 32:70-80(2008).
RN [13]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-169, 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).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-332; THR-334 AND SER-336, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19779198; DOI=10.1126/science.1172867;
RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights
RT into evolution.";
RL Science 325:1682-1686(2009).
RN [15]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [16]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-337, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22106047; DOI=10.1002/pmic.201100166;
RA Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
RT "Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
RL Proteomics 12:236-240(2012).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RX PubMed=11526233; DOI=10.1073/pnas.181336398;
RA Voegtli W.C., Ge J., Perlstein D.L., Stubbe J., Rosenzweig A.C.;
RT "Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:10073-10078(2001).
RN [18]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS).
RX PubMed=15196016; DOI=10.1021/bi049510m;
RA Sommerhalter M., Voegtli W.C., Perlstein D.L., Ge J., Stubbe J.,
RA Rosenzweig A.C.;
RT "Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4
RT homodimers.";
RL Biochemistry 43:7736-7742(2004).
CC -!- FUNCTION: Provides the precursors necessary for DNA synthesis.
CC Catalyzes the biosynthesis of deoxyribonucleotides from the
CC corresponding ribonucleotides. RNR4 is required for proper folding of
CC RNR2 and assembly with the large subunits.
CC {ECO:0000269|PubMed:10535923}.
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 Evidence={ECO:0000255|PROSITE-ProRule:PRU10014};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=2250 nmol/min/mg enzyme for cytidine 5'-diphosphate
CC {ECO:0000269|PubMed:10716984};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:10716984};
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. Interacts with DIF1.
CC {ECO:0000269|PubMed:10535923, ECO:0000269|PubMed:10716984,
CC ECO:0000269|PubMed:18851834}.
CC -!- INTERACTION:
CC P49723; P21524: RNR1; NbExp=5; IntAct=EBI-15251, EBI-15234;
CC P49723; P09938: RNR2; NbExp=8; IntAct=EBI-15251, EBI-15240;
CC P49723; Q12363: WTM1; NbExp=5; IntAct=EBI-15251, EBI-20563;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12732713,
CC ECO:0000269|PubMed:18851834}. Note=Found predominantly in the nucleus
CC under normal growth conditions and is redistributed to the cytoplasm in
CC damaged cells in a DNA replication and damage checkpoint-dependent
CC manner. Nuclear localization is mediated by DIF1.
CC -!- INDUCTION: Induced by DNA-damage. {ECO:0000269|PubMed:9315671}.
CC -!- MISCELLANEOUS: Present with 88884 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- MISCELLANEOUS: Lacks 3 iron-binding residues conserved in all other R2
CC subunits.
CC -!- SIMILARITY: Belongs to the ribonucleoside diphosphate reductase small
CC chain family. {ECO:0000305}.
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DR EMBL; U30385; AAB72236.1; -; Genomic_DNA.
DR EMBL; Z72965; CAA97206.1; -; Genomic_DNA.
DR EMBL; AY723819; AAU09736.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA08275.1; -; Genomic_DNA.
DR PIR; S59744; S59744.
DR RefSeq; NP_011696.3; NM_001181309.3.
DR PDB; 1JK0; X-ray; 2.80 A; B=1-345.
DR PDB; 1SMS; X-ray; 3.10 A; A/B=1-345.
DR PDB; 1ZZD; X-ray; 2.60 A; B=337-345.
DR PDBsum; 1JK0; -.
DR PDBsum; 1SMS; -.
DR PDBsum; 1ZZD; -.
DR AlphaFoldDB; P49723; -.
DR SMR; P49723; -.
DR BioGRID; 33432; 208.
DR ComplexPortal; CPX-1102; Ribonucleoside-diphosphate reductase variant 1.
DR ComplexPortal; CPX-1103; Ribonucleoside-diphosphate reductase variant 2.
DR DIP; DIP-5381N; -.
DR IntAct; P49723; 24.
DR MINT; P49723; -.
DR STRING; 4932.YGR180C; -.
DR iPTMnet; P49723; -.
DR MaxQB; P49723; -.
DR PaxDb; P49723; -.
DR PRIDE; P49723; -.
DR TopDownProteomics; P49723; -.
DR EnsemblFungi; YGR180C_mRNA; YGR180C; YGR180C.
DR GeneID; 853091; -.
DR KEGG; sce:YGR180C; -.
DR SGD; S000003412; RNR4.
DR VEuPathDB; FungiDB:YGR180C; -.
DR eggNOG; KOG1567; Eukaryota.
DR GeneTree; ENSGT00390000013305; -.
DR HOGENOM; CLU_035339_2_1_1; -.
DR InParanoid; P49723; -.
DR OMA; MMENIYD; -.
DR BioCyc; MetaCyc:YGR180C-MON; -.
DR BioCyc; YEAST:YGR180C-MON; -.
DR UniPathway; UPA00326; -.
DR EvolutionaryTrace; P49723; -.
DR PRO; PR:P49723; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P49723; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0005971; C:ribonucleoside-diphosphate reductase complex; IDA:SGD.
DR GO; GO:0046982; F:protein heterodimerization activity; IDA:CAFA.
DR GO; GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IMP:SGD.
DR GO; GO:0009263; P:deoxyribonucleotide biosynthetic process; IDA:SGD.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
DR CDD; cd01049; RNRR2; 1.
DR DisProt; DP00488; -.
DR Gene3D; 1.10.620.20; -; 1.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR012348; RNR-like.
DR InterPro; IPR033909; RNR_small.
DR InterPro; IPR030475; RNR_small_AS.
DR InterPro; IPR000358; RNR_small_fam.
DR PANTHER; PTHR23409; PTHR23409; 1.
DR Pfam; PF00268; Ribonuc_red_sm; 1.
DR SUPFAM; SSF47240; SSF47240; 1.
DR PROSITE; PS00368; RIBORED_SMALL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Deoxyribonucleotide synthesis;
KW Direct protein sequencing; Isopeptide bond; Nucleus; Oxidoreductase;
KW Phosphoprotein; Reference proteome; Ubl conjugation.
FT CHAIN 1..345
FT /note="Ribonucleoside-diphosphate reductase small chain 2"
FT /id="PRO_0000190465"
FT ACT_SITE 131
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10014"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PubMed:22814378"
FT MOD_RES 169
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17287358,
FT ECO:0007744|PubMed:18407956"
FT MOD_RES 332
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 334
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 336
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT CROSSLNK 337
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT CONFLICT 127
FT /note="Y -> H (in Ref. 4; AAU09736)"
FT /evidence="ECO:0000305"
FT HELIX 4..9
FT /evidence="ECO:0007829|PDB:1SMS"
FT HELIX 13..21
FT /evidence="ECO:0007829|PDB:1JK0"
FT TURN 22..24
FT /evidence="ECO:0007829|PDB:1JK0"
FT TURN 26..28
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 43..54
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 59..61
FT /evidence="ECO:0007829|PDB:1JK0"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:1JK0"
FT TURN 69..73
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 78..89
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 101..107
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 111..138
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:1SMS"
FT HELIX 148..151
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 155..166
FT /evidence="ECO:0007829|PDB:1JK0"
FT STRAND 169..172
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 175..187
FT /evidence="ECO:0007829|PDB:1JK0"
FT TURN 188..190
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 191..200
FT /evidence="ECO:0007829|PDB:1JK0"
FT STRAND 202..205
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 207..232
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 240..258
FT /evidence="ECO:0007829|PDB:1JK0"
FT TURN 265..268
FT /evidence="ECO:0007829|PDB:1SMS"
FT HELIX 277..288
FT /evidence="ECO:0007829|PDB:1JK0"
FT HELIX 316..322
FT /evidence="ECO:0007829|PDB:1SMS"
SQ SEQUENCE 345 AA; 40055 MW; 712853F2D87D3972 CRC64;
MEAHNQFLKT FQKERHDMKE AEKDEILLME NSRRFVMFPI KYHEIWAAYK KVEASFWTAE
EIELAKDTED FQKLTDDQKT YIGNLLALSI SSDNLVNKYL IENFSAQLQN PEGKSFYGFQ
IMMENIYSEV YSMMVDAFFK DPKNIPLFKE IANLPEVKHK AAFIERWISN DDSLYAERLV
AFAAKEGIFQ AGNYASMFWL TDKKIMPGLA MANRNICRDR GAYTDFSCLL FAHLRTKPNP
KIIEKIITEA VEIEKEYYSN SLPVEKFGMD LKSIHTYIEF VADGLLQGFG NEKYYNAVNP
FEFMEDVATA GKTTFFEKKV SDYQKASDMS KSATPSKEIN FDDDF
