RAD23_YEAST
ID RAD23_YEAST Reviewed; 398 AA.
AC P32628; D3DLL2;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 201.
DE RecName: Full=UV excision repair protein RAD23;
GN Name=RAD23; OrderedLocusNames=YEL037C; ORFNames=SYGP-ORF29;
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=8246991; DOI=10.1128/mcb.13.12.7757-7765.1993;
RA Watkins J.F., Sung P., Prakash L., Prakash S.;
RT "The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear
RT protein containing a ubiquitin-like domain required for biological
RT function.";
RL Mol. Cell. Biol. 13:7757-7765(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
RC STRAIN=B-6441;
RX PubMed=8411151; DOI=10.1006/jmbi.1993.1518;
RA Melnick L., Sherman F.;
RT "The gene clusters ARC and COR on chromosomes 5 and 10, respectively, of
RT Saccharomyces cerevisiae share a common ancestry.";
RL J. Mol. Biol. 233:372-388(1993).
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.
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 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 [6]
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 [7]
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 [8]
RP INTERACTION WITH PNG1.
RX PubMed=15351714; DOI=10.1016/j.bbrc.2004.08.061;
RA Biswas S., Katiyar S., Li G., Zhou X., Lennarz W.J., Schindelin H.;
RT "The N-terminus of yeast peptide: N-glycanase interacts with the DNA repair
RT protein Rad23.";
RL Biochem. Biophys. Res. Commun. 323:149-155(2004).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-139, AND IDENTIFICATION BY
RP 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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-121, 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 [11]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-94 AND THR-139, 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 [12]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-49, AND IDENTIFICATION BY MASS
RP 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 [13]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 238-309 IN COMPLEX WITH PNG1.
RX PubMed=15964983; DOI=10.1073/pnas.0502082102;
RA Lee J.-H., Choi J.M., Lee C., Yi K.J., Cho Y.;
RT "Structure of a peptide:N-glycanase-Rad23 complex: insight into the
RT deglycosylation for denatured glycoproteins.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:9144-9149(2005).
CC -!- FUNCTION: Plays a central role both in proteasomal degradation of
CC misfolded proteins and DNA repair. Central component of a complex
CC required to couple deglycosylation and proteasome-mediated degradation
CC of misfolded proteins in the endoplasmic reticulum that are
CC retrotranslocated in the cytosol. Involved in DNA excision repair. May
CC play a part in DNA damage recognition and/or in altering chromatin
CC structure to allow access by damage-processing enzymes.
CC -!- SUBUNIT: Interacts directly with PNG1. {ECO:0000269|PubMed:15351714,
CC ECO:0000269|PubMed:15964983}.
CC -!- INTERACTION:
CC P32628; P25694: CDC48; NbExp=2; IntAct=EBI-14668, EBI-4308;
CC P32628; Q02890: PNG1; NbExp=3; IntAct=EBI-14668, EBI-38139;
CC P32628; P22141: PRE1; NbExp=3; IntAct=EBI-14668, EBI-13988;
CC P32628; P34222: PTH2; NbExp=5; IntAct=EBI-14668, EBI-2345448;
CC P32628; P14736: RAD4; NbExp=8; IntAct=EBI-14668, EBI-14766;
CC P32628; P38764: RPN1; NbExp=11; IntAct=EBI-14668, EBI-15913;
CC P32628; P33299: RPT1; NbExp=7; IntAct=EBI-14668, EBI-13910;
CC P32628; P33298: RPT3; NbExp=2; IntAct=EBI-14668, EBI-13905;
CC P32628; Q01939: RPT6; NbExp=6; IntAct=EBI-14668, EBI-13914;
CC P32628; P18888: SNF6; NbExp=2; IntAct=EBI-14668, EBI-17550;
CC P32628; P0CG63: UBI4; NbExp=4; IntAct=EBI-14668, EBI-7000452;
CC P32628; P54860: UFD2; NbExp=7; IntAct=EBI-14668, EBI-20003;
CC P32628; P0CG48: UBC; Xeno; NbExp=2; IntAct=EBI-14668, EBI-3390054;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}. Cytoplasm
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 10900 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
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DR EMBL; L25428; AAA16070.1; -; Unassigned_DNA.
DR EMBL; L22172; AAA34935.1; -; Genomic_DNA.
DR EMBL; L22173; AAA34938.1; -; Genomic_DNA.
DR EMBL; S65964; AAD13972.1; -; Genomic_DNA.
DR EMBL; S66117; AAB28441.1; -; mRNA.
DR EMBL; U18779; AAB65005.1; -; Genomic_DNA.
DR EMBL; AY693018; AAT93037.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07616.1; -; Genomic_DNA.
DR PIR; S50507; S50507.
DR RefSeq; NP_010877.3; NM_001178852.3.
DR PDB; 1X3W; X-ray; 3.00 A; B=238-309.
DR PDB; 1X3Z; X-ray; 2.80 A; B=238-309.
DR PDB; 2NBU; NMR; -; A=1-78.
DR PDB; 2NBW; NMR; -; B=1-78.
DR PDB; 2QSF; X-ray; 2.35 A; X=230-398.
DR PDB; 2QSG; X-ray; 3.10 A; X=230-398.
DR PDB; 2QSH; X-ray; 2.81 A; X=230-398.
DR PDB; 3ESW; X-ray; 3.40 A; B=254-308.
DR PDB; 3M62; X-ray; 2.40 A; B=1-84.
DR PDB; 4YIR; X-ray; 3.05 A; X=230-398.
DR PDB; 6CFI; X-ray; 3.36 A; X=230-398.
DR PDB; 6UBF; X-ray; 4.60 A; X=230-398.
DR PDB; 6UG1; X-ray; 2.83 A; X=256-311.
DR PDB; 6UIN; X-ray; 3.35 A; X=230-398.
DR PDBsum; 1X3W; -.
DR PDBsum; 1X3Z; -.
DR PDBsum; 2NBU; -.
DR PDBsum; 2NBW; -.
DR PDBsum; 2QSF; -.
DR PDBsum; 2QSG; -.
DR PDBsum; 2QSH; -.
DR PDBsum; 3ESW; -.
DR PDBsum; 3M62; -.
DR PDBsum; 4YIR; -.
DR PDBsum; 6CFI; -.
DR PDBsum; 6UBF; -.
DR PDBsum; 6UG1; -.
DR PDBsum; 6UIN; -.
DR AlphaFoldDB; P32628; -.
DR SMR; P32628; -.
DR BioGRID; 36692; 247.
DR ComplexPortal; CPX-1320; Peptide:N-glycanase-Rad23 complex.
DR ComplexPortal; CPX-1323; CDC48-RAD23-UFD2 complex.
DR ComplexPortal; CPX-1640; Nucleotide excision repair factor 2 complex.
DR DIP; DIP-1548N; -.
DR IntAct; P32628; 38.
DR MINT; P32628; -.
DR STRING; 4932.YEL037C; -.
DR iPTMnet; P32628; -.
DR MaxQB; P32628; -.
DR PaxDb; P32628; -.
DR PRIDE; P32628; -.
DR EnsemblFungi; YEL037C_mRNA; YEL037C; YEL037C.
DR GeneID; 856674; -.
DR KEGG; sce:YEL037C; -.
DR SGD; S000000763; RAD23.
DR VEuPathDB; FungiDB:YEL037C; -.
DR eggNOG; KOG0011; Eukaryota.
DR GeneTree; ENSGT00390000012078; -.
DR HOGENOM; CLU_040364_0_0_1; -.
DR InParanoid; P32628; -.
DR OMA; ANTVESY; -.
DR BioCyc; YEAST:G3O-30158-MON; -.
DR Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
DR EvolutionaryTrace; P32628; -.
DR PRO; PR:P32628; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P32628; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:ComplexPortal.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IBA:GO_Central.
DR GO; GO:0000111; C:nucleotide-excision repair factor 2 complex; IDA:SGD.
DR GO; GO:0120125; C:PNGase complex; IPI:ComplexPortal.
DR GO; GO:0003684; F:damaged DNA binding; IDA:SGD.
DR GO; GO:0031593; F:polyubiquitin modification-dependent protein binding; IBA:GO_Central.
DR GO; GO:0070628; F:proteasome binding; IDA:SGD.
DR GO; GO:0030674; F:protein-macromolecule adaptor activity; IPI:SGD.
DR GO; GO:0043130; F:ubiquitin binding; IDA:SGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; 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 GO; GO:0006517; P:protein deglycosylation; IDA:SGD.
DR GO; GO:0035977; P:protein deglycosylation involved in glycoprotein catabolic process; IDA:ComplexPortal.
DR GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; IMP:SGD.
DR GO; GO:0097466; P:ubiquitin-dependent glycoprotein ERAD pathway; IDA:ComplexPortal.
DR DisProt; DP01629; -.
DR Gene3D; 1.10.10.540; -; 1.
DR InterPro; IPR004806; Rad23.
DR InterPro; IPR006636; STI1_HS-bd.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR015360; XPC-bd.
DR InterPro; IPR036353; XPC-bd_sf.
DR Pfam; PF00627; UBA; 2.
DR Pfam; PF00240; ubiquitin; 1.
DR Pfam; PF09280; XPC-binding; 1.
DR PRINTS; PR01839; RAD23PROTEIN.
DR SMART; SM00727; STI1; 1.
DR SMART; SM00165; UBA; 2.
DR SMART; SM00213; UBQ; 1.
DR SUPFAM; SSF101238; SSF101238; 1.
DR SUPFAM; SSF46934; SSF46934; 2.
DR SUPFAM; SSF54236; SSF54236; 1.
DR TIGRFAMs; TIGR00601; rad23; 1.
DR PROSITE; PS50030; UBA; 2.
DR PROSITE; PS50053; UBIQUITIN_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA damage; DNA repair; Isopeptide bond; Nucleus;
KW Phosphoprotein; Reference proteome; Repeat; Ubl conjugation;
KW Ubl conjugation pathway.
FT CHAIN 1..398
FT /note="UV excision repair protein RAD23"
FT /id="PRO_0000114902"
FT DOMAIN 1..77
FT /note="Ubiquitin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT DOMAIN 146..186
FT /note="UBA 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT DOMAIN 355..395
FT /note="UBA 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00212"
FT REGION 75..149
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 195..216
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 229..252
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 93..111
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 120..145
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 195..215
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 94
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:19779198"
FT MOD_RES 121
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MOD_RES 139
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:17330950,
FT ECO:0007744|PubMed:19779198"
FT CROSSLNK 49
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0007744|PubMed:22106047"
FT CONFLICT 277
FT /note="A -> R (in Ref. 2; AAA34935/AAA34938/AAD13972/
FT AAB28441)"
FT /evidence="ECO:0000305"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:3M62"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:2NBW"
FT STRAND 13..16
FT /evidence="ECO:0007829|PDB:3M62"
FT HELIX 24..33
FT /evidence="ECO:0007829|PDB:3M62"
FT TURN 34..36
FT /evidence="ECO:0007829|PDB:3M62"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:3M62"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:3M62"
FT TURN 57..61
FT /evidence="ECO:0007829|PDB:3M62"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:3M62"
FT HELIX 259..270
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 273..275
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 276..286
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 290..296
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 298..307
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 355..365
FT /evidence="ECO:0007829|PDB:2QSF"
FT TURN 366..368
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 371..380
FT /evidence="ECO:0007829|PDB:2QSF"
FT TURN 381..383
FT /evidence="ECO:0007829|PDB:2QSF"
FT HELIX 385..392
FT /evidence="ECO:0007829|PDB:2QSF"
SQ SEQUENCE 398 AA; 42367 MW; B3F0436DAB60B833 CRC64;
MVSLTFKNFK KEKVPLDLEP SNTILETKTK LAQSISCEES QIKLIYSGKV LQDSKTVSEC
GLKDGDQVVF MVSQKKSTKT KVTEPPIAPE SATTPGRENS TEASPSTDAS AAPAATAPEG
SQPQEEQTAT TERTESASTP GFVVGTERNE TIERIMEMGY QREEVERALR AAFNNPDRAV
EYLLMGIPEN LRQPEPQQQT AAAAEQPSTA ATTAEQPAED DLFAQAAQGG NASSGALGTT
GGATDAAQGG PPGSIGLTVE DLLSLRQVVS GNPEALAPLL ENISARYPQL REHIMANPEV
FVSMLLEAVG DNMQDVMEGA DDMVEGEDIE VTGEAAAAGL GQGEGEGSFQ VDYTPEDDQA
ISRLCELGFE RDLVIQVYFA CDKNEEAAAN ILFSDHAD
