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UV excision repair protein RAD23

 RAD23_YEAST             Reviewed;         398 AA.
P32628; D3DLL2;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
01-OCT-1993, sequence version 1.
22-NOV-2017, entry version 169.
RecName: Full=UV excision repair protein RAD23;
Name=RAD23; OrderedLocusNames=YEL037C; ORFNames=SYGP-ORF29;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=8246991; DOI=10.1128/MCB.13.12.7757;
Watkins J.F., Sung P., Prakash L., Prakash S.;
"The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear
protein containing a ubiquitin-like domain required for biological
function.";
Mol. Cell. Biol. 13:7757-7765(1993).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
STRAIN=B-6441;
PubMed=8411151; DOI=10.1006/jmbi.1993.1518;
Melnick L., Sherman F.;
"The gene clusters ARC and COR on chromosomes 5 and 10, respectively,
of Saccharomyces cerevisiae share a common ancestry.";
J. Mol. Biol. 233:372-388(1993).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169868;
Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G.,
Hunicke-Smith S., Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H.,
Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P.,
Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T.,
Smith V., Taylor P., Wei Y., Botstein D., Davis R.W.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
Nature 387:78-81(1997).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[6]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[7]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[8]
INTERACTION WITH PNG1.
PubMed=15351714; DOI=10.1016/j.bbrc.2004.08.061;
Biswas S., Katiyar S., Li G., Zhou X., Lennarz W.J., Schindelin H.;
"The N-terminus of yeast peptide: N-glycanase interacts with the DNA
repair protein Rad23.";
Biochem. Biophys. Res. Commun. 323:149-155(2004).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-139, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ADR376;
PubMed=17330950; DOI=10.1021/pr060559j;
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,
Elias J.E., Gygi S.P.;
"Large-scale phosphorylation analysis of alpha-factor-arrested
Saccharomyces cerevisiae.";
J. Proteome Res. 6:1190-1197(2007).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-121, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-94 AND THR-139, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
[12]
UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-49, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22106047; DOI=10.1002/pmic.201100166;
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;
"Sites of ubiquitin attachment in Saccharomyces cerevisiae.";
Proteomics 12:236-240(2012).
[13]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 238-309 IN COMPLEX WITH PNG1.
PubMed=15964983; DOI=10.1073/pnas.0502082102;
Lee J.-H., Choi J.M., Lee C., Yi K.J., Cho Y.;
"Structure of a peptide:N-glycanase-Rad23 complex: insight into the
deglycosylation for denatured glycoproteins.";
Proc. Natl. Acad. Sci. U.S.A. 102:9144-9149(2005).
-!- FUNCTION: Plays a central role both in proteasomal degradation of
misfolded proteins and DNA repair. Central component of a complex
required to couple deglycosylation and proteasome-mediated
degradation of misfolded proteins in the endoplasmic reticulum
that are retrotranslocated in the cytosol. Involved in DNA
excision repair. May play a part in DNA damage recognition and/or
in altering chromatin structure to allow access by damage-
processing enzymes.
-!- SUBUNIT: Interacts directly with PNG1.
{ECO:0000269|PubMed:15351714, ECO:0000269|PubMed:15964983}.
-!- INTERACTION:
P25694:CDC48; NbExp=2; IntAct=EBI-14668, EBI-4308;
P22141:PRE1; NbExp=3; IntAct=EBI-14668, EBI-13988;
P34222:PTH2; NbExp=5; IntAct=EBI-14668, EBI-2345448;
P14736:RAD4; NbExp=7; IntAct=EBI-14668, EBI-14766;
P38764:RPN1; NbExp=10; IntAct=EBI-14668, EBI-15913;
P33299:RPT1; NbExp=7; IntAct=EBI-14668, EBI-13910;
P33298:RPT3; NbExp=2; IntAct=EBI-14668, EBI-13905;
Q01939:RPT6; NbExp=6; IntAct=EBI-14668, EBI-13914;
P18888:SNF6; NbExp=2; IntAct=EBI-14668, EBI-17550;
P0CG48:UBC (xeno); NbExp=4; IntAct=EBI-14668, EBI-3390054;
P0CG63:UBI4; NbExp=4; IntAct=EBI-14668, EBI-7000452;
P61864:UBI4 (xeno); NbExp=11; IntAct=EBI-14668, EBI-19797;
P54860:UFD2; NbExp=5; IntAct=EBI-14668, EBI-20003;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
Cytoplasm {ECO:0000269|PubMed:14562095}.
-!- MISCELLANEOUS: Present with 10900 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-----------------------------------------------------------------------
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EMBL; L25428; AAA16070.1; -; Unassigned_DNA.
EMBL; L22172; AAA34935.1; -; Genomic_DNA.
EMBL; L22173; AAA34938.1; -; Genomic_DNA.
EMBL; S65964; AAD13972.1; -; Genomic_DNA.
EMBL; S66117; AAB28441.1; -; mRNA.
EMBL; U18779; AAB65005.1; -; Genomic_DNA.
EMBL; AY693018; AAT93037.1; -; Genomic_DNA.
EMBL; BK006939; DAA07616.1; -; Genomic_DNA.
PIR; S50507; S50507.
RefSeq; NP_010877.3; NM_001178852.3.
PDB; 1X3W; X-ray; 3.00 A; B=238-309.
PDB; 1X3Z; X-ray; 2.80 A; B=238-309.
PDB; 2NBU; NMR; -; A=1-78.
PDB; 2NBW; NMR; -; B=1-78.
PDB; 2QSF; X-ray; 2.35 A; X=230-398.
PDB; 2QSG; X-ray; 3.10 A; X=230-398.
PDB; 2QSH; X-ray; 2.81 A; X=230-398.
PDB; 3ESW; X-ray; 3.40 A; B=254-308.
PDB; 3M62; X-ray; 2.40 A; B=1-84.
PDB; 4YIR; X-ray; 3.05 A; X=230-398.
PDBsum; 1X3W; -.
PDBsum; 1X3Z; -.
PDBsum; 2NBU; -.
PDBsum; 2NBW; -.
PDBsum; 2QSF; -.
PDBsum; 2QSG; -.
PDBsum; 2QSH; -.
PDBsum; 3ESW; -.
PDBsum; 3M62; -.
PDBsum; 4YIR; -.
ProteinModelPortal; P32628; -.
SMR; P32628; -.
BioGrid; 36692; 206.
DIP; DIP-1548N; -.
IntAct; P32628; 38.
MINT; MINT-404213; -.
STRING; 4932.YEL037C; -.
iPTMnet; P32628; -.
MaxQB; P32628; -.
PRIDE; P32628; -.
EnsemblFungi; YEL037C; YEL037C; YEL037C.
GeneID; 856674; -.
KEGG; sce:YEL037C; -.
EuPathDB; FungiDB:YEL037C; -.
SGD; S000000763; RAD23.
GeneTree; ENSGT00390000012078; -.
HOGENOM; HOG000172162; -.
InParanoid; P32628; -.
KO; K10839; -.
OMA; NFLFDQP; -.
OrthoDB; EOG092C4GFV; -.
BioCyc; YEAST:G3O-30158-MONOMER; -.
Reactome; R-SCE-5696394; DNA Damage Recognition in GG-NER.
Reactome; R-SCE-5696395; Formation of Incision Complex in GG-NER.
EvolutionaryTrace; P32628; -.
PRO; PR:P32628; -.
Proteomes; UP000002311; Chromosome V.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0000111; C:nucleotide-excision repair factor 2 complex; IDA:SGD.
GO; GO:0000502; C:proteasome complex; IMP:SGD.
GO; GO:0003684; F:damaged DNA binding; IDA:SGD.
GO; GO:0070628; F:proteasome binding; IDA:SGD.
GO; GO:0030674; F:protein binding, bridging; IPI:SGD.
GO; GO:0043130; F:ubiquitin binding; IDA:SGD.
GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:SGD.
GO; GO:0006289; P:nucleotide-excision repair; IEA:InterPro.
GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IMP:SGD.
GO; GO:0006517; P:protein deglycosylation; IDA:SGD.
GO; GO:0030433; P:ubiquitin-dependent ERAD pathway; IMP:SGD.
InterPro; IPR004806; Rad23.
InterPro; IPR006636; STI1_HS-bd.
InterPro; IPR015940; UBA.
InterPro; IPR009060; UBA-like_sf.
InterPro; IPR029071; Ubiquitin-like_domsf.
InterPro; IPR000626; Ubiquitin_dom.
InterPro; IPR015360; XPC-bd.
InterPro; IPR036353; XPC-bd_sf.
Pfam; PF00627; UBA; 2.
Pfam; PF00240; ubiquitin; 1.
Pfam; PF09280; XPC-binding; 1.
PRINTS; PR01839; RAD23PROTEIN.
SMART; SM00727; STI1; 1.
SMART; SM00165; UBA; 2.
SMART; SM00213; UBQ; 1.
SUPFAM; SSF101238; SSF101238; 1.
SUPFAM; SSF46934; SSF46934; 2.
SUPFAM; SSF54236; SSF54236; 1.
TIGRFAMs; TIGR00601; rad23; 1.
PROSITE; PS50030; UBA; 2.
PROSITE; PS50053; UBIQUITIN_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; DNA damage; DNA repair;
Isopeptide bond; Nucleus; Phosphoprotein; Reference proteome; Repeat;
Ubl conjugation; Ubl conjugation pathway.
CHAIN 1 398 UV excision repair protein RAD23.
/FTId=PRO_0000114902.
DOMAIN 1 77 Ubiquitin-like. {ECO:0000255|PROSITE-
ProRule:PRU00214}.
DOMAIN 146 186 UBA 1. {ECO:0000255|PROSITE-
ProRule:PRU00212}.
DOMAIN 355 395 UBA 2. {ECO:0000255|PROSITE-
ProRule:PRU00212}.
MOD_RES 94 94 Phosphothreonine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 121 121 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 139 139 Phosphothreonine.
{ECO:0000244|PubMed:17330950,
ECO:0000244|PubMed:19779198}.
CROSSLNK 49 49 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000244|PubMed:22106047}.
CONFLICT 277 277 A -> R (in Ref. 2; AAA34935/AAA34938/
AAD13972/AAB28441). {ECO:0000305}.
STRAND 4 7 {ECO:0000244|PDB:3M62}.
STRAND 9 11 {ECO:0000244|PDB:2NBW}.
STRAND 13 16 {ECO:0000244|PDB:3M62}.
HELIX 24 33 {ECO:0000244|PDB:3M62}.
TURN 34 36 {ECO:0000244|PDB:3M62}.
HELIX 39 41 {ECO:0000244|PDB:3M62}.
STRAND 43 46 {ECO:0000244|PDB:3M62}.
TURN 57 61 {ECO:0000244|PDB:3M62}.
STRAND 67 71 {ECO:0000244|PDB:3M62}.
HELIX 259 270 {ECO:0000244|PDB:2QSF}.
HELIX 273 275 {ECO:0000244|PDB:2QSF}.
HELIX 276 286 {ECO:0000244|PDB:2QSF}.
HELIX 290 296 {ECO:0000244|PDB:2QSF}.
HELIX 298 307 {ECO:0000244|PDB:2QSF}.
HELIX 355 365 {ECO:0000244|PDB:2QSF}.
TURN 366 368 {ECO:0000244|PDB:2QSF}.
HELIX 371 380 {ECO:0000244|PDB:2QSF}.
TURN 381 383 {ECO:0000244|PDB:2QSF}.
HELIX 385 392 {ECO:0000244|PDB:2QSF}.
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


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