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UV excision repair protein RAD23 homolog B (HR23B) (mHR23B) (XP-C repair-complementing complex 58 kDa protein) (p58)

 RD23B_MOUSE             Reviewed;         416 AA.
P54728; Q3TUA4;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
27-JUL-2011, sequence version 2.
22-NOV-2017, entry version 153.
RecName: Full=UV excision repair protein RAD23 homolog B;
Short=HR23B;
Short=mHR23B;
AltName: Full=XP-C repair-complementing complex 58 kDa protein;
Short=p58;
Name=Rad23b; Synonyms=Mhr23b;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=BALB/cJ; TISSUE=Testis;
PubMed=8808275; DOI=10.1006/geno.1996.0004;
van der Spek P.J., Visser C.E., Hanaoka F., Smit B., Hagemeijer A.,
Bootsma D., Hoeijmakers J.H.J.;
"Cloning, comparative mapping, and RNA expression of the mouse
homologues of the Saccharomyces cerevisiae nucleotide excision repair
gene RAD23.";
Genomics 31:20-27(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J; TISSUE=Bone marrow, Embryo, and Head;
PubMed=16141072; DOI=10.1126/science.1112014;
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M.,
Davis M.J., Wilming L.G., Aidinis V., Allen J.E.,
Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L.,
Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M.,
Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R.,
Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G.,
di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G.,
Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M.,
Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N.,
Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T.,
Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H.,
Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K.,
Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J.,
Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L.,
Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K.,
Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P.,
Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B.,
Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K.,
Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A.,
Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K.,
Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C.,
Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J.,
Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y.,
Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T.,
Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N.,
Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N.,
Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S.,
Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J.,
Hayashizaki Y.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=C57BL/6J;
PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
Lindblad-Toh K., Eichler E.E., Ponting C.P.;
"Lineage-specific biology revealed by a finished genome assembly of
the mouse.";
PLoS Biol. 7:E1000112-E1000112(2009).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=FVB/N; TISSUE=Mammary gland;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
INTERACTION WITH NGLY1.
PubMed=11562482; DOI=10.1073/pnas.201393498;
Park H., Suzuki T., Lennarz W.J.;
"Identification of proteins that interact with mammalian peptide:N-
glycanase and implicate this hydrolase in the proteasome-dependent
pathway for protein degradation.";
Proc. Natl. Acad. Sci. U.S.A. 98:11163-11168(2001).
[6]
DISRUPTION PHENOTYPE.
PubMed=11809813; DOI=10.1128/MCB.22.4.1233-1245.2002;
Ng J.M., Vrieling H., Sugasawa K., Ooms M.P., Grootegoed J.A.,
Vreeburg J.T., Visser P., Beems R.B., Gorgels T.G., Hanaoka F.,
Hoeijmakers J.H., van der Horst G.T.;
"Developmental defects and male sterility in mice lacking the
ubiquitin-like DNA repair gene mHR23B.";
Mol. Cell. Biol. 22:1233-1245(2002).
[7]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=12815074; DOI=10.1101/gad.260003;
Ng J.M., Vermeulen W., van der Horst G.T., Bergink S., Sugasawa K.,
Vrieling H., Hoeijmakers J.H.;
"A novel regulation mechanism of DNA repair by damage-induced and
RAD23-dependent stabilization of xeroderma pigmentosum group C
protein.";
Genes Dev. 17:1630-1645(2003).
[8]
FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
PubMed=15336624; DOI=10.1016/j.dnarep.2004.06.010;
Okuda Y., Nishi R., Ng J.M., Vermeulen W., van der Horst G.T.,
Mori T., Hoeijmakers J.H., Hanaoka F., Sugasawa K.;
"Relative levels of the two mammalian Rad23 homologs determine
composition and stability of the xeroderma pigmentosum group C protein
complex.";
DNA Repair 3:1285-1295(2004).
[9]
INTERACTION WITH NGLY1.
PubMed=15358861; DOI=10.1073/pnas.0405663101;
Katiyar S., Li G., Lennarz W.J.;
"A complex between peptide:N-glycanase and two proteasome-linked
proteins suggests a mechanism for the degradation of misfolded
glycoproteins.";
Proc. Natl. Acad. Sci. U.S.A. 101:13774-13779(2004).
[10]
INTERACTION WITH NGLY1.
PubMed=16249333; DOI=10.1073/pnas.0507155102;
Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J.;
"Multiple modes of interaction of the deglycosylation enzyme, mouse
peptide N-glycanase, with the proteasome.";
Proc. Natl. Acad. Sci. U.S.A. 102:15809-15814(2005).
[11]
ERRATUM.
Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J.;
Proc. Natl. Acad. Sci. U.S.A. 103:1153-1153(2006).
[12]
FUNCTION IN ERAD, AND INTERACTION WITH AMFR; NGLY1 AND DEGLYCOSYLATED
PROTEINS.
PubMed=16709668; DOI=10.1073/pnas.0602747103;
Li G., Zhao G., Zhou X., Schindelin H., Lennarz W.J.;
"The AAA ATPase p97 links peptide N-glycanase to the endoplasmic
reticulum-associated E3 ligase autocrine motility factor receptor.";
Proc. Natl. Acad. Sci. U.S.A. 103:8348-8353(2006).
[13]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung,
Pancreas, Spleen, and Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
[14]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 273-332 IN COMPLEX WITH
NGLY1.
PubMed=16500903; DOI=10.1074/jbc.M600137200;
Zhao G., Zhou X., Wang L., Li G., Kisker C., Lennarz W.J.,
Schindelin H.;
"Structure of the mouse peptide N-glycanase-HR23 complex suggests co-
evolution of the endoplasmic reticulum-associated degradation and DNA
repair pathways.";
J. Biol. Chem. 281:13751-13761(2006).
-!- FUNCTION: Multiubiquitin chain receptor involved in modulation of
proteasomal degradation. Binds to polyubiquitin chains. Proposed
to be capable to bind simultaneously to the 26S proteasome and to
polyubiquitinated substrates and to deliver ubiquitinated proteins
to the proteasome. May play a role in endoplasmic reticulum-
associated degradation (ERAD) of misfolded glycoproteins by
association with PNGase and delivering deglycosylated proteins to
the proteasome. {ECO:0000269|PubMed:12815074,
ECO:0000269|PubMed:15336624, ECO:0000269|PubMed:16709668}.
-!- FUNCTION: Involved in global genome nucleotide excision repair
(GG-NER) by acting as component of the XPC complex. Cooperatively
with Cetn2 appears to stabilize Xpc. May protect Xpc from
proteasomal degradation (By similarity). {ECO:0000250}.
-!- FUNCTION: The XPC complex is proposed to represent the first
factor bound at the sites of DNA damage and together with other
core recognition factors, Xpa, RPA and the TFIIH complex, is part
of the pre-incision (or initial recognition) complex. The XPC
complex recognizes a wide spectrum of damaged DNA characterized by
distortions of the DNA helix such as single-stranded loops,
mismatched bubbles or single-stranded overhangs. The orientation
of XPC complex binding appears to be crucial for inducing a
productive NER. XPC complex is proposed to recognize and to
interact with unpaired bases on the undamaged DNA strand which is
followed by recruitment of the TFIIH complex and subsequent
scanning for lesions in the opposite strand in a 5'-to-3'
direction by the NER machinery. Cyclobutane pyrimidine dimers
(CPDs) which are formed upon UV-induced DNA damage esacpe
detection by the XPC complex due to a low degree of structural
perurbation. Instead they are detected by the UV-DDB complex which
in turn recruits and cooperates with the XPC complex in the
respective DNA repair. In vitro, the Xpc:Rad23b dimer is
sufficient to initiate NER; it preferentially binds to cisplatin
and UV-damaged double-stranded DNA and also binds to a variety of
chemically and structurally diverse DNA adducts. Xpc:Rad23b
contacts DNA both 5' and 3' of a cisplatin lesion with a
preference for the 5' side. Xpc:Rad23bB induces a bend in DNA upon
binding. Xpc:Rad23b stimulates the activity of DNA glycosylases
Tdg and Smug1 (By similarity). {ECO:0000250}.
-!- SUBUNIT: Component of the XPC complex composed of XPC, RAD23B and
CETN2. Interacts with NGLY1 and PSMC1. Interacts with ATXN3 (By
similarity). Interacts with AMFR. Interacts with VCP; the
interaction is indirect and mediated by NGLY1. {ECO:0000250,
ECO:0000269|PubMed:11562482, ECO:0000269|PubMed:15358861,
ECO:0000269|PubMed:16249333, ECO:0000269|PubMed:16500903,
ECO:0000269|PubMed:16709668}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15336624}.
Cytoplasm {ECO:0000269|PubMed:15336624}.
-!- DISRUPTION PHENOTYPE: Impaired embryonic development with a 90 %
rate of intrauterine or neonatal death. Surviving animals display
a variety of abnormalities, including retarded growth, facial
dysmorphology and male sterility. The effect on NER competence is
reported conflictingly: According PubMed:11809813 no change in NER
activity is found and according PubMed:15336624 a reduced NER
activity is seen. Embryonic lethal with Rad23a and Rad23b double
deficiency. Double deficient cells show reduced cell survival
upopn UV radiation and reduced steady-state level of Xpc
indicating a reduced NER capacity. {ECO:0000269|PubMed:11809813,
ECO:0000269|PubMed:12815074, ECO:0000269|PubMed:15336624}.
-!- SIMILARITY: Belongs to the RAD23 family. {ECO:0000305}.
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EMBL; X92411; CAA63146.1; -; mRNA.
EMBL; AK150089; BAE29298.1; -; mRNA.
EMBL; AK160880; BAE36067.1; -; mRNA.
EMBL; AK160890; BAE36071.1; -; mRNA.
EMBL; AK160973; BAE36124.1; -; mRNA.
EMBL; AL683890; CAM13976.1; -; Genomic_DNA.
EMBL; BC027747; AAH27747.1; -; mRNA.
CCDS; CCDS18194.1; -.
RefSeq; NP_033037.2; NM_009011.4.
UniGene; Mm.196846; -.
PDB; 2F4M; X-ray; 1.85 A; B=273-332.
PDB; 2F4O; X-ray; 2.26 A; B=273-332.
PDBsum; 2F4M; -.
PDBsum; 2F4O; -.
ProteinModelPortal; P54728; -.
SMR; P54728; -.
BioGrid; 202562; 8.
IntAct; P54728; 8.
MINT; MINT-214731; -.
STRING; 10090.ENSMUSP00000030134; -.
iPTMnet; P54728; -.
PhosphoSitePlus; P54728; -.
EPD; P54728; -.
MaxQB; P54728; -.
PaxDb; P54728; -.
PeptideAtlas; P54728; -.
PRIDE; P54728; -.
Ensembl; ENSMUST00000030134; ENSMUSP00000030134; ENSMUSG00000028426.
GeneID; 19359; -.
KEGG; mmu:19359; -.
UCSC; uc012dej.1; mouse.
CTD; 5887; -.
MGI; MGI:105128; Rad23b.
eggNOG; KOG0011; Eukaryota.
eggNOG; COG5272; LUCA.
GeneTree; ENSGT00390000012078; -.
HOGENOM; HOG000172162; -.
HOVERGEN; HBG055042; -.
InParanoid; P54728; -.
KO; K10839; -.
OMA; NFLFDQP; -.
OrthoDB; EOG091G0DVL; -.
TreeFam; TF101216; -.
Reactome; R-MMU-532668; N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
Reactome; R-MMU-5696394; DNA Damage Recognition in GG-NER.
Reactome; R-MMU-5696395; Formation of Incision Complex in GG-NER.
ChiTaRS; Rad23b; mouse.
EvolutionaryTrace; P54728; -.
PRO; PR:P54728; -.
Proteomes; UP000000589; Chromosome 4.
Bgee; ENSMUSG00000028426; -.
CleanEx; MM_RAD23B; -.
Genevisible; P54728; MM.
GO; GO:0005829; C:cytosol; ISO:MGI.
GO; GO:0005654; C:nucleoplasm; ISO:MGI.
GO; GO:0000502; C:proteasome complex; IEA:UniProtKB-KW.
GO; GO:0071942; C:XPC complex; ISS:UniProtKB.
GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
GO; GO:0031593; F:polyubiquitin modification-dependent protein binding; ISO:MGI.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IDA:MGI.
GO; GO:0048568; P:embryonic organ development; IEA:Ensembl.
GO; GO:0006289; P:nucleotide-excision repair; ISO:MGI.
GO; GO:0000715; P:nucleotide-excision repair, DNA damage recognition; ISO:MGI.
GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; IEA:InterPro.
GO; GO:0032434; P:regulation of proteasomal ubiquitin-dependent protein catabolic process; ISO:MGI.
GO; GO:0007283; P:spermatogenesis; IMP:MGI.
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;
Nucleus; Phosphoprotein; Proteasome; Reference proteome; Repeat;
Ubl conjugation pathway.
CHAIN 1 416 UV excision repair protein RAD23 homolog
B.
/FTId=PRO_0000114907.
DOMAIN 1 79 Ubiquitin-like. {ECO:0000255|PROSITE-
ProRule:PRU00214}.
DOMAIN 188 228 UBA 1. {ECO:0000255|PROSITE-
ProRule:PRU00212}.
DOMAIN 274 317 STI1.
DOMAIN 371 411 UBA 2. {ECO:0000255|PROSITE-
ProRule:PRU00212}.
COMPBIAS 255 261 Poly-Ala.
COMPBIAS 262 270 Poly-Thr.
COMPBIAS 336 355 Poly-Gly.
MOD_RES 155 155 Phosphothreonine.
{ECO:0000250|UniProtKB:P54727}.
MOD_RES 160 160 Phosphoserine.
{ECO:0000250|UniProtKB:P54727}.
MOD_RES 174 174 Phosphoserine.
{ECO:0000250|UniProtKB:Q4KMA2}.
MOD_RES 186 186 Phosphothreonine.
{ECO:0000250|UniProtKB:Q4KMA2}.
MOD_RES 199 199 Phosphoserine.
{ECO:0000250|UniProtKB:Q4KMA2}.
MOD_RES 202 202 Phosphotyrosine.
{ECO:0000250|UniProtKB:Q4KMA2}.
CONFLICT 98 98 A -> T (in Ref. 1; CAA63146 and 4;
AAH27747). {ECO:0000305}.
CONFLICT 118 118 P -> A (in Ref. 1; CAA63146 and 4;
AAH27747). {ECO:0000305}.
CONFLICT 127 127 A -> T (in Ref. 1; CAA63146 and 4;
AAH27747). {ECO:0000305}.
CONFLICT 337 337 S -> G (in Ref. 1; CAA63146 and 4;
AAH27747). {ECO:0000305}.
HELIX 275 279 {ECO:0000244|PDB:2F4M}.
HELIX 283 294 {ECO:0000244|PDB:2F4M}.
HELIX 296 298 {ECO:0000244|PDB:2F4M}.
HELIX 299 309 {ECO:0000244|PDB:2F4M}.
HELIX 311 319 {ECO:0000244|PDB:2F4M}.
HELIX 321 328 {ECO:0000244|PDB:2F4M}.
SEQUENCE 416 AA; 43513 MW; 7440E6A9C8ADF454 CRC64;
MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILSDDTALK
EYKIDEKNFV VVMVTKPKAV TTAVPATTQP SSTPSPTAVS SSPAVAAAQA PAPTPALPPT
STPASTAPAS TTASSEPAPA GATQPEKPAE KPAQTPVLTS PAPADSTPGD SSRSNLFEDA
TSALVTGQSY ENMVTEIMSM GYEREQVIAA LRASFNNPDR AVEYLLMGIP GDRESQAVVD
PPPQAVSTGT PQSPAVAAAA ATTTATTTTT SGGHPLEFLR NQPQFQQMRQ IIQQNPSLLP
ALLQQIGREN PQLLQQISQH QEHFIQMLNE PVQEAGSQGG GGGGGGGGGG GGGGGIAEAG
SGHMNYIQVT PQEKEAIERL KALGFPEGLV IQAYFACEKN ENLAANFLLQ QNFDED


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