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Protein

UV excision repair protein RAD23 homolog B

Gene

Rad23b

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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 (By similarity).By similarity
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).By similarity
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:Rad22b induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1 (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, Ubl conjugation pathway

Enzyme and pathway databases

ReactomeiR-RNO-5696394. DNA Damage Recognition in GG-NER.
R-RNO-5696395. Formation of Incision Complex in GG-NER.

Names & Taxonomyi

Protein namesi
Recommended name:
UV excision repair protein RAD23 homolog B
Gene namesi
Name:Rad23b
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi1562958. Rad23b.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Proteasome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 415415UV excision repair protein RAD23 homolog BPRO_0000287582Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei155 – 1551PhosphothreonineCombined sources
Modified residuei160 – 1601PhosphoserineCombined sources
Modified residuei174 – 1741PhosphoserineCombined sources
Modified residuei186 – 1861PhosphothreonineCombined sources
Modified residuei199 – 1991PhosphoserineCombined sources
Modified residuei202 – 2021PhosphotyrosineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ4KMA2.
PRIDEiQ4KMA2.

PTM databases

iPTMnetiQ4KMA2.
PhosphoSiteiQ4KMA2.

Expressioni

Gene expression databases

GenevisibleiQ4KMA2. RN.

Interactioni

Subunit structurei

Component of the XPC complex composed of XPC, RAD23B and CETN2. Interacts with NGLY1 and PSMC1. Interacts with ATXN3. Interacts with AMFR. Interacts with VCP; the interaction is indirect and mediated by NGLY1 (By similarity).By similarity

Protein-protein interaction databases

BioGridi255730. 63 interactions.
IntActiQ4KMA2. 53 interactions.
STRINGi10116.ENSRNOP00000021629.

Structurei

3D structure databases

ProteinModelPortaliQ4KMA2.
SMRiQ4KMA2. Positions 1-82, 184-231, 273-332, 371-415.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7979Ubiquitin-likePROSITE-ProRule annotationAdd
BLAST
Domaini188 – 22841UBA 1PROSITE-ProRule annotationAdd
BLAST
Domaini274 – 31744STI1Add
BLAST
Domaini370 – 41041UBA 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi255 – 2617Poly-Ala
Compositional biasi262 – 2709Poly-Thr
Compositional biasi336 – 35419Poly-GlyAdd
BLAST

Sequence similaritiesi

Belongs to the RAD23 family.Curated
Contains 1 STI1 domain.Curated
Contains 2 UBA domains.PROSITE-ProRule annotation
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0011. Eukaryota.
COG5272. LUCA.
GeneTreeiENSGT00390000012078.
HOGENOMiHOG000172162.
HOVERGENiHBG055042.
InParanoidiQ4KMA2.
KOiK10839.
OMAiIEAFIAC.
OrthoDBiEOG72C51D.
PhylomeDBiQ4KMA2.
TreeFamiTF101216.

Family and domain databases

Gene3Di1.10.10.540. 1 hit.
InterProiIPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR015940. UBA.
IPR009060. UBA-like.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
IPR015360. XPC-bd.
[Graphical view]
PfamiPF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view]
PRINTSiPR01839. RAD23PROTEIN.
SMARTiSM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF101238. SSF101238. 1 hit.
SSF46934. SSF46934. 2 hits.
SSF54236. SSF54236. 1 hit.
TIGRFAMsiTIGR00601. rad23. 1 hit.
PROSITEiPS50030. UBA. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q4KMA2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG
60 70 80 90 100
KILSDDTALK EYKIDEKNFV VVMVTKPKAV TSAVPATTQQ SSSPSTTTVS
110 120 130 140 150
SSPAAAVAQA PAPTPALAPT STPASTTPAS TTASSEPAPT GATQPEKPAE
160 170 180 190 200
KPAQTPVLTS PAPADSTPGD SSRSNLFEDA TSALVTGQSY ENMVTEIMSM
210 220 230 240 250
GYEREQVIAA LRASFNNPDR AVEYLLMGIP GDRESQAVVD PPPQAVSTGT
260 270 280 290 300
PQSPAVAAAA ATTTATTTTT SGGHPLEFLR NQPQFQQMRQ IIQQNPSLLP
310 320 330 340 350
ALLQQIGREN PQLLQQISQH QEHFIQMLNE PVQEAGGQGG GGGGGGGGGG
360 370 380 390 400
GGGGIAEAGS GHMNYIQVTP QEKEAIERLK ALGFPEGLVI QAYFACEKNE
410
NLAANFLLQQ NFDED
Length:415
Mass (Da):43,497
Last modified:August 2, 2005 - v1
Checksum:i221022C803418390
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC070960 mRNA. Translation: AAH70960.1.
BC090351 mRNA. Translation: AAH90351.1.
BC098674 mRNA. Translation: AAH98674.1.
BC111406 mRNA. Translation: AAI11407.1.
RefSeqiNP_001020446.1. NM_001025275.1.
UniGeneiRn.67042.

Genome annotation databases

EnsembliENSRNOT00000021629; ENSRNOP00000021629; ENSRNOG00000016137.
GeneIDi298012.
KEGGirno:298012.
UCSCiRGD:1562958. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC070960 mRNA. Translation: AAH70960.1.
BC090351 mRNA. Translation: AAH90351.1.
BC098674 mRNA. Translation: AAH98674.1.
BC111406 mRNA. Translation: AAI11407.1.
RefSeqiNP_001020446.1. NM_001025275.1.
UniGeneiRn.67042.

3D structure databases

ProteinModelPortaliQ4KMA2.
SMRiQ4KMA2. Positions 1-82, 184-231, 273-332, 371-415.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi255730. 63 interactions.
IntActiQ4KMA2. 53 interactions.
STRINGi10116.ENSRNOP00000021629.

PTM databases

iPTMnetiQ4KMA2.
PhosphoSiteiQ4KMA2.

Proteomic databases

PaxDbiQ4KMA2.
PRIDEiQ4KMA2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000021629; ENSRNOP00000021629; ENSRNOG00000016137.
GeneIDi298012.
KEGGirno:298012.
UCSCiRGD:1562958. rat.

Organism-specific databases

CTDi5887.
RGDi1562958. Rad23b.

Phylogenomic databases

eggNOGiKOG0011. Eukaryota.
COG5272. LUCA.
GeneTreeiENSGT00390000012078.
HOGENOMiHOG000172162.
HOVERGENiHBG055042.
InParanoidiQ4KMA2.
KOiK10839.
OMAiIEAFIAC.
OrthoDBiEOG72C51D.
PhylomeDBiQ4KMA2.
TreeFamiTF101216.

Enzyme and pathway databases

ReactomeiR-RNO-5696394. DNA Damage Recognition in GG-NER.
R-RNO-5696395. Formation of Incision Complex in GG-NER.

Miscellaneous databases

NextBioi642963.
PROiQ4KMA2.

Gene expression databases

GenevisibleiQ4KMA2. RN.

Family and domain databases

Gene3Di1.10.10.540. 1 hit.
InterProiIPR004806. Rad23.
IPR006636. STI1_HS-bd.
IPR015940. UBA.
IPR009060. UBA-like.
IPR029071. Ubiquitin-rel_dom.
IPR000626. Ubiquitin_dom.
IPR015360. XPC-bd.
[Graphical view]
PfamiPF00627. UBA. 2 hits.
PF00240. ubiquitin. 1 hit.
PF09280. XPC-binding. 1 hit.
[Graphical view]
PRINTSiPR01839. RAD23PROTEIN.
SMARTiSM00727. STI1. 1 hit.
SM00165. UBA. 2 hits.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF101238. SSF101238. 1 hit.
SSF46934. SSF46934. 2 hits.
SSF54236. SSF54236. 1 hit.
TIGRFAMsiTIGR00601. rad23. 1 hit.
PROSITEiPS50030. UBA. 2 hits.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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].
    Tissue: Brain, Heart, Lung and Placenta.
  2. Lubec G., Chen W.-Q., Kang S.U., Lubec S.
    Submitted (SEP-2007) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 7-14; 37-45; 52-60 AND 205-212, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: Sprague-Dawley.
    Tissue: Brain and Hippocampus.
  3. "Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites."
    Hoffert J.D., Pisitkun T., Wang G., Shen R.-F., Knepper M.A.
    Proc. Natl. Acad. Sci. U.S.A. 103:7159-7164(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174; THR-186; SER-199 AND TYR-202, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  4. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-155 AND SER-160, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRD23B_RAT
AccessioniPrimary (citable) accession number: Q4KMA2
Secondary accession number(s): Q0D2G8, Q5CZZ8, Q6IRD5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2007
Last sequence update: August 2, 2005
Last modified: May 11, 2016
This is version 93 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.