RAD4_YEAST
ID RAD4_YEAST Reviewed; 754 AA.
AC P14736; D3DM70;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 21-SEP-2011, sequence version 3.
DT 03-AUG-2022, entry version 189.
DE RecName: Full=DNA repair protein RAD4;
GN Name=RAD4; OrderedLocusNames=YER162C;
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].
RX PubMed=3073107; DOI=10.1016/0378-1119(88)90186-2;
RA Gietz R.D., Prakash S.;
RT "Cloning and nucleotide sequence analysis of the Saccharomyces cerevisiae
RT RAD4 gene required for excision repair of UV-damaged DNA.";
RL Gene 74:535-541(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2649477; DOI=10.1128/jb.171.4.1862-1869.1989;
RA Couto L.B., Friedberg E.C.;
RT "Nucleotide sequence of the wild-type RAD4 gene of Saccharomyces cerevisiae
RT and characterization of mutant rad4 alleles.";
RL J. Bacteriol. 171:1862-1869(1989).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [4]
RP GENOME REANNOTATION, AND SEQUENCE REVISION TO 223.
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 [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
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 IDENTIFICATION BY MASS 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).
CC -!- FUNCTION: Involved in nucleotide excision repair of DNA damaged with UV
CC light, bulky adducts, or cross-linking agents.
CC -!- INTERACTION:
CC P14736; P32628: RAD23; NbExp=8; IntAct=EBI-14766, EBI-14668;
CC P14736; P18888: SNF6; NbExp=2; IntAct=EBI-14766, EBI-17550;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. Nucleus
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 876 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the XPC family. {ECO:0000305}.
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DR EMBL; M26050; AAA34944.1; -; Genomic_DNA.
DR EMBL; M24928; AAA34945.1; -; Genomic_DNA.
DR EMBL; U18917; AAB64689.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07824.2; -; Genomic_DNA.
DR PIR; S30814; DDBYD4.
DR RefSeq; NP_011089.4; NM_001179052.4.
DR PDB; 2M14; NMR; -; B=76-115.
DR PDB; 2QSF; X-ray; 2.35 A; A=101-632.
DR PDB; 2QSG; X-ray; 3.10 A; A=101-632.
DR PDB; 2QSH; X-ray; 2.81 A; A=101-632.
DR PDB; 4YIR; X-ray; 3.05 A; A=101-632.
DR PDB; 6CFI; X-ray; 3.36 A; A=101-632.
DR PDB; 6UBF; X-ray; 4.60 A; A=101-632.
DR PDB; 6UG1; X-ray; 2.83 A; A=129-632.
DR PDB; 6UIN; X-ray; 3.35 A; A=101-632.
DR PDB; 7K04; EM; 9.25 A; A=1-754.
DR PDB; 7M2U; EM; 8.20 A; A=1-754.
DR PDBsum; 2M14; -.
DR PDBsum; 2QSF; -.
DR PDBsum; 2QSG; -.
DR PDBsum; 2QSH; -.
DR PDBsum; 4YIR; -.
DR PDBsum; 6CFI; -.
DR PDBsum; 6UBF; -.
DR PDBsum; 6UG1; -.
DR PDBsum; 6UIN; -.
DR PDBsum; 7K04; -.
DR PDBsum; 7M2U; -.
DR AlphaFoldDB; P14736; -.
DR BMRB; P14736; -.
DR SMR; P14736; -.
DR BioGRID; 36915; 442.
DR ComplexPortal; CPX-1640; Nucleotide excision repair factor 2 complex.
DR DIP; DIP-1547N; -.
DR IntAct; P14736; 6.
DR MINT; P14736; -.
DR STRING; 4932.YER162C; -.
DR MaxQB; P14736; -.
DR PaxDb; P14736; -.
DR PRIDE; P14736; -.
DR EnsemblFungi; YER162C_mRNA; YER162C; YER162C.
DR GeneID; 856909; -.
DR KEGG; sce:YER162C; -.
DR SGD; S000000964; RAD4.
DR VEuPathDB; FungiDB:YER162C; -.
DR eggNOG; KOG2179; Eukaryota.
DR GeneTree; ENSGT00390000005194; -.
DR HOGENOM; CLU_003639_1_2_1; -.
DR InParanoid; P14736; -.
DR OMA; SYVIAFE; -.
DR BioCyc; YEAST:G3O-30323-MON; -.
DR EvolutionaryTrace; P14736; -.
DR PRO; PR:P14736; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P14736; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0000111; C:nucleotide-excision repair factor 2 complex; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0071942; C:XPC complex; IBA:GO_Central.
DR GO; GO:0003684; F:damaged DNA binding; IDA:SGD.
DR GO; GO:1990165; F:single-strand break-containing DNA binding; IDA:SGD.
DR GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR GO; GO:0006265; P:DNA topological change; IDA:SGD.
DR GO; GO:0006298; P:mismatch repair; IBA:GO_Central.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0006289; P:nucleotide-excision repair; IMP:SGD.
DR GO; GO:0000715; P:nucleotide-excision repair, DNA damage recognition; IC:ComplexPortal.
DR GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR DisProt; DP01628; -.
DR Gene3D; 3.30.70.2460; -; 1.
DR Gene3D; 3.90.260.10; -; 1.
DR IDEAL; IID50167; -.
DR InterPro; IPR018327; BHD_2.
DR InterPro; IPR004583; DNA_repair_Rad4.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR InterPro; IPR018325; Rad4/PNGase_transGLS-fold.
DR InterPro; IPR018326; Rad4_beta-hairpin_dom1.
DR InterPro; IPR018328; Rad4_beta-hairpin_dom3.
DR InterPro; IPR042488; Rad4_BHD3_sf.
DR InterPro; IPR036985; Transglutaminase-like_sf.
DR PANTHER; PTHR12135; PTHR12135; 2.
DR Pfam; PF10403; BHD_1; 1.
DR Pfam; PF10405; BHD_3; 1.
DR Pfam; PF03835; Rad4; 1.
DR SMART; SM01030; BHD_1; 1.
DR SMART; SM01031; BHD_2; 1.
DR SMART; SM01032; BHD_3; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA damage; DNA repair; DNA-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..754
FT /note="DNA repair protein RAD4"
FT /id="PRO_0000218298"
FT DNA_BIND 250..269
FT /evidence="ECO:0000255"
FT REGION 23..51
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 701..754
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 709..730
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 223
FT /note="V -> E (in Ref. 3; AAB64689)"
FT /evidence="ECO:0000305"
FT CONFLICT 225
FT /note="L -> I (in Ref. 1; AAA34944 and 2; AAA34945)"
FT /evidence="ECO:0000305"
FT TURN 91..94
FT /evidence="ECO:0007829|PDB:2M14"
FT HELIX 124..129
FT /evidence="ECO:0007829|PDB:2QSH"
FT HELIX 134..162
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 165..171
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 177..182
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 193..213
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:2QSH"
FT HELIX 230..235
FT /evidence="ECO:0007829|PDB:2QSF"
FT TURN 236..239
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 248..257
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 262..275
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 280..286
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:6UIN"
FT HELIX 306..309
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 314..321
FT /evidence="ECO:0007829|PDB:2QSF"
FT TURN 322..325
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 326..335
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:2QSF"
FT TURN 352..355
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 362..366
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 372..374
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 376..379
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 383..387
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 388..390
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 392..394
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 396..409
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 416..431
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 436..438
FT /evidence="ECO:0007829|PDB:2QSH"
FT HELIX 439..441
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 445..449
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 450..452
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 457..459
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 466..470
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 478..483
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 487..489
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 493..497
FT /evidence="ECO:0007829|PDB:2QSF"
FT TURN 498..500
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 501..503
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 510..513
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 529..532
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 534..536
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 537..539
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 564..566
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 571..575
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 579..585
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 591..597
FT /evidence="ECO:0007829|PDB:2QSF"
FT STRAND 601..603
FT /evidence="ECO:0007829|PDB:4YIR"
FT STRAND 607..615
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 616..618
FT /evidence="ECO:0007829|PDB:2QSH"
FT HELIX 619..627
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 629..631
FT /evidence="ECO:0007829|PDB:2QSF"
SQ SEQUENCE 754 AA; 87174 MW; 788D3B6F580D2BF8 CRC64;
MNEDLPKEYF ELIRKALNEK EAEKAPLSRR RRVRRKNQPL PDAKKKFKTG LNELPRESVV
TVNLDSSDDG VVTVPTDDSV EEIQSSEEDY DSEEFEDVTD GNEVAGVEDI SVEIKPSSKR
NSDARRTSRN VCSNEERKRR KYFHMLYLVC LMVHGFIRNE WINSKRLSRK LSNLVPEKVF
ELLHPQKDEE LPLRSTRKLL DGLKKCMELW QKHWKITKKY DNVGLYMRTW KEIEMSANNK
RKFKTLKRSD FLRAVSKGHG DPDISVQGFV AMLRACNVNA RLIMSCQPPD FTNMKIDTSL
NGNNAYKDMV KYPIFWCEVW DKFSKKWITV DPVNLKTIEQ VRLHSKLAPK GVACCERNML
RYVIAYDRKY GCRDVTRRYA QWMNSKVRKR RITKDDFGEK WFRKVITALH HRKRTKIDDY
EDQYFFQRDE SEGIPDSVQD LKNHPYYVLE QDIKQTQIVK PGCKECGYLK VHGKVGKVLK
VYAKRDIADL KSARQWYMNG RILKTGSRCK KVIKRTVGRP KGEAEEEDER LYSFEDTELY
IPPLASASGE ITKNTFGNIE VFAPTMIPGN CCLVENPVAI KAARFLGVEF APAVTSFKFE
RGSTVKPVLS GIVVAKWLRE AIETAIDGIE FIQEDDNRKE HLLGALESWN TLLLKLRIRS
KLNSTYGKIA EEEPNVTKEQ NIADNHDNTE TFMGGGFLPG IANHEARPYS EPSEPEDSLD
YVSVDKAEES ATDDDVGEDY SDFMKELEMS EESD
