P54728 (RD23B_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
UV excision repair protein RAD23 homolog B
Short name=HR23B
Short name=mHR23B

Alternative name(s):
XP-C repair-complementing complex 58 kDa protein
Short name=p58

Gene names

Name:	Rad23b
Synonyms:	Mhr23b

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	416 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

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. Ref.7 Ref.8 Ref.12 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. Ref.7 Ref.8 Ref.12 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. Ref.7 Ref.8 Ref.12
Subunit structure	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. Ref.5 Ref.9 Ref.10 Ref.12
Subcellular location	Nucleus. Cytoplasm Ref.8.
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 Ref.6 no change in NER activity is found and according Ref.8 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. Ref.6 Ref.7 Ref.8
Sequence similarities	Belongs to the RAD23 family. Contains 1 STI1 domain. Contains 2 UBA domains. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair Ubl conjugation pathway
Cellular component	Cytoplasm Nucleus Proteasome
Domain	Repeat
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	nucleotide-excision repair, DNA damage recognition Inferred from electronic annotation. Source: Compara proteasomal ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: InterPro regulation of proteasomal ubiquitin-dependent protein catabolic process Inferred from electronic annotation. Source: Compara response to DNA damage stimulus Inferred from direct assay Ref.7. Source: MGI spermatogenesis Inferred from mutant phenotype Ref.6. Source: MGI
Cellular_component	XPC complex Inferred from sequence or structural similarity. Source: UniProtKB cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell proteasome complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	damaged DNA binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 416

416

UV excision repair protein RAD23 homolog B

PRO_0000114907

Regions

Domain

1 – 79

79

Ubiquitin-like

Domain

188 – 228

41

UBA 1

Domain

274 – 317

44

STI1

Domain

371 – 411

41

UBA 2

Compositional bias

255 – 261

7

Poly-Ala

Compositional bias

262 – 270

9

Poly-Thr

Compositional bias

336 – 355

20

Poly-Gly

Amino acid modifications

Modified residue

155

1

Phosphothreonine By similarity

Modified residue

160

1

Phosphoserine By similarity

Experimental info

Sequence conflict

98

1

A → T in CAA63146. Ref.1

Sequence conflict

98

1

A → T in AAH27747. Ref.4

Sequence conflict

118

1

P → A in CAA63146. Ref.1

Sequence conflict

118

1

P → A in AAH27747. Ref.4

Sequence conflict

127

1

A → T in CAA63146. Ref.1

Sequence conflict

127

1

A → T in AAH27747. Ref.4

Sequence conflict

337

1

S → G in CAA63146. Ref.1

Sequence conflict

337

1

S → G in AAH27747. Ref.4

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

416

Helix Strand Turn

Details...

Helix

275 – 279

5

Helix

283 – 294

12

Helix

296 – 298

3

Helix

299 – 309

11

Helix

311 – 319

9

Helix

321 – 328

8

Sequences

	Sequence		Length	Mass (Da)
	P54728 [UniParc]. Last modified July 27, 2011. Version 2. Checksum: 7440E6A9C8ADF454	FASTA	416	43,513
	10 20 30 40 50 60 MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILSDDTALK 70 80 90 100 110 120 EYKIDEKNFV VVMVTKPKAV TTAVPATTQP SSTPSPTAVS SSPAVAAAQA PAPTPALPPT 130 140 150 160 170 180 STPASTAPAS TTASSEPAPA GATQPEKPAE KPAQTPVLTS PAPADSTPGD SSRSNLFEDA 190 200 210 220 230 240 TSALVTGQSY ENMVTEIMSM GYEREQVIAA LRASFNNPDR AVEYLLMGIP GDRESQAVVD 250 260 270 280 290 300 PPPQAVSTGT PQSPAVAAAA ATTTATTTTT SGGHPLEFLR NQPQFQQMRQ IIQQNPSLLP 310 320 330 340 350 360 ALLQQIGREN PQLLQQISQH QEHFIQMLNE PVQEAGSQGG GGGGGGGGGG GGGGGIAEAG 370 380 390 400 410 SGHMNYIQVT PQEKEAIERL KALGFPEGLV IQAYFACEKN ENLAANFLLQ QNFDED

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning, comparative mapping, and RNA expression of the mouse homologues of the Saccharomyces cerevisiae nucleotide excision repair gene RAD23." van der Spek P.J., Visser C.E., Hanaoka F., Smit B., Hagemeijer A., Bootsma D., Hoeijmakers J.H.J. Genomics 31:20-27(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: BALB/c. Tissue: Testis.
[2]	"The transcriptional landscape of the mammalian genome." 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. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6J. Tissue: Bone marrow, Embryo and Head.
[3]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." 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. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: FVB/N. Tissue: Mammary gland.
[5]	"Identification of proteins that interact with mammalian peptide:N-glycanase and implicate this hydrolase in the proteasome-dependent pathway for protein degradation." Park H., Suzuki T., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 98:11163-11168(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NGLY1.
[6]	"Developmental defects and male sterility in mice lacking the ubiquitin-like DNA repair gene mHR23B." 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. Mol. Cell. Biol. 22:1233-1245(2002) [PubMed] [Europe PMC] [Abstract] Cited for: DISRUPTION PHENOTYPE.
[7]	"A novel regulation mechanism of DNA repair by damage-induced and RAD23-dependent stabilization of xeroderma pigmentosum group C protein." Ng J.M., Vermeulen W., van der Horst G.T., Bergink S., Sugasawa K., Vrieling H., Hoeijmakers J.H. Genes Dev. 17:1630-1645(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[8]	"Relative levels of the two mammalian Rad23 homologs determine composition and stability of the xeroderma pigmentosum group C protein complex." Okuda Y., Nishi R., Ng J.M., Vermeulen W., van der Horst G.T., Mori T., Hoeijmakers J.H., Hanaoka F., Sugasawa K. DNA Repair 3:1285-1295(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
[9]	"A complex between peptide:N-glycanase and two proteasome-linked proteins suggests a mechanism for the degradation of misfolded glycoproteins." Katiyar S., Li G., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 101:13774-13779(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NGLY1.
[10]	"Multiple modes of interaction of the deglycosylation enzyme, mouse peptide N-glycanase, with the proteasome." Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 102:15809-15814(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH NGLY1.
[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]	"The AAA ATPase p97 links peptide N-glycanase to the endoplasmic reticulum-associated E3 ligase autocrine motility factor receptor." Li G., Zhao G., Zhou X., Schindelin H., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 103:8348-8353(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN ERAD, INTERACTION WITH AMFR; NGLY1 AND DEGLYCOSYLATED PROTEINS.
[13]	"Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways." Zhao G., Zhou X., Wang L., Li G., Kisker C., Lennarz W.J., Schindelin H. J. Biol. Chem. 281:13751-13761(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 273-332 IN COMPLEX WITH NGLY1.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X92411 mRNA. Translation: CAA63146.1.
AK150089 mRNA. Translation: BAE29298.1.
AK160880 mRNA. Translation: BAE36067.1.
AK160890 mRNA. Translation: BAE36071.1.
AK160973 mRNA. Translation: BAE36124.1.
AL683890 Genomic DNA. Translation: CAM13976.1.
BC027747 mRNA. Translation: AAH27747.1.

IPI

IPI00108774.

RefSeq

NP_033037.2. NM_009011.4.

UniGene

Mm.196846.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2F4M	X-ray	1.85	B	273-332	[»]
2F4O	X-ray	2.26	B	273-332	[»]

ProteinModelPortal

P54728.

SMR

P54728. Positions 1-416.

ModBase

Search...

Protein-protein interaction databases

IntAct

P54728. 6 interactions.

PTM databases

PhosphoSite

P54728.

Proteomic databases

PaxDb

P54728.

PRIDE

P54728.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000030134; ENSMUSP00000030134; ENSMUSG00000028426.

GeneID

19359.

KEGG

mmu:19359.

Organism-specific databases

CTD

5887.

MGI

MGI:105128. Rad23b.

Phylogenomic databases

eggNOG

COG5272.

GeneTree

ENSGT00390000012078.

HOGENOM

HOG000172162.

HOVERGEN

HBG055042.

InParanoid

Q3TUA4.

KO

K10839.

OMA

EKGFIVC.

OrthoDB

EOG4M399F.

Gene expression databases

ArrayExpress

P54728.

Bgee

P54728.

CleanEx

MM_RAD23B.

Genevestigator

P54728.

GermOnline

ENSMUSG00000028426. Mus musculus.

Family and domain databases

Gene3D

1.10.10.540. 1 hit.

InterPro

IPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR009060. UBA-like.
IPR000449. UBA/transl_elong_EF1B_N.
IPR015940. UBA/transl_elong_EF1B_N_euk.
IPR000626. Ubiquitin.
IPR019955. Ubiquitin_supergroup.
IPR015360. XPC-bd.
[Graphical view]

Pfam

PF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view]

PRINTS

PR01839. RAD23PROTEIN.

SMART

SM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]

SUPFAM

SSF46934. UBA_like. 2 hits.
SSF101238. XPC-bd. 1 hit.

TIGRFAMs

TIGR00601. rad23. 1 hit.

PROSITE

PS50030. UBA. 2 hits.
PS00299. UBIQUITIN_1. False negative.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

RAD23B. mouse.

EvolutionaryTrace

P54728.

NextBio

296413.

SOURCE

Search...

Entry information

Entry name

RD23B_MOUSE

Accession

Primary (citable) accession number: P54728
Secondary accession number(s): Q3TUA4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	July 27, 2011
Last modified:	May 1, 2013
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program