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UniProtKB - Q01831 (XPC_HUMAN)

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Protein

DNA repair protein complementing XP-C cells

Gene

XPC

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in global genome nucleotide excision repair (GG-NER) by acting as damage sensing and DNA-binding factor component of the XPC complex. Has only a low DNA repair activity by itself which is stimulated by RAD23B and RAD23A. Has a preference to bind DNA containing a short single-stranded segment but not to damaged oligonucleotides. This feature is proposed to be related to a dynamic sensor function: XPC can rapidly screen duplex DNA for non-hydrogen-bonded bases by forming a transient nucleoprotein intermediate complex which matures into a stable recognition complex through an intrinsic single-stranded DNA-binding activity.
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:RAD23B induces a bend in DNA upon binding. XPC:RAD23B stimulates the activity of DNA glycosylases TDG and SMUG1.

GO - Molecular functioni

  • bubble DNA binding Source: UniProtKB
  • damaged DNA binding Source: UniProtKB
  • heteroduplex DNA loop binding Source: UniProtKB
  • single-stranded DNA binding Source: UniProtKB
View the complete GO annotation on QuickGO ...

GO - Biological processi

  • DNA repair Source: ProtInc
  • global genome nucleotide-excision repair Source: Reactome
  • intra-S DNA damage checkpoint Source: Ensembl
  • mismatch repair Source: GO_Central
  • nucleotide-excision repair Source: UniProtKB
  • nucleotide-excision repair, DNA damage recognition Source: UniProtKB
  • nucleotide-excision repair, preincision complex assembly Source: Reactome
  • regulation of mitotic cell cycle phase transition Source: UniProtKB
  • response to auditory stimulus Source: Ensembl
  • response to drug Source: Ensembl
  • response to UV-B Source: Ensembl
  • UV-damage excision repair Source: CACAO
View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionDNA-binding
Biological processDNA damage, DNA repair

Enzyme and pathway databases

ReactomeiR-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-5696394 DNA Damage Recognition in GG-NER
R-HSA-5696395 Formation of Incision Complex in GG-NER
SIGNORiQ01831

Names & Taxonomyi

Protein namesi
Recommended name:
DNA repair protein complementing XP-C cells
Alternative name(s):
Xeroderma pigmentosum group C-complementing protein
p125
Gene namesi
Name:XPC
Synonyms:XPCC
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000154767.14
HGNCiHGNC:12816 XPC
MIMi613208 gene
neXtProtiNX_Q01831

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Xeroderma pigmentosum complementation group C (XP-C)6 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive pigmentary skin disorder characterized by solar hypersensitivity of the skin, high predisposition for developing cancers on areas exposed to sunlight and, in some cases, neurological abnormalities. The skin develops marked freckling and other pigmentation abnormalities.
See also OMIM:278720
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_005846334P → H in XP-C; severe. 1 PublicationCorresponds to variant dbSNP:rs74737358EnsemblClinVar.1
Natural variantiVAR_064039690W → S in XP-C; diminishes repair activity and impairs DNA binding. 4 Publications1
Natural variantiVAR_005847697V → VV in XP-C; mild. 1 Publication1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi531W → A: Slightly diminishes repair activity and sligtly impairs DNA binding. 1 Publication1
Mutagenesisi542W → A: Slightly diminishes repair activity and sligtly impairs DNA binding. 1 Publication1
Mutagenesisi733F → A: Diminishes repair activity and impairs DNA binding. 2 Publications1
Mutagenesisi754N → A: Reduces DNA repair activity; abolishes single-stranded DNA binding; reduces binding to homoduplex DNA; reduces localization at DNA damaged foci. 1 Publication1
Mutagenesisi755E → K: Reduces nuclear mobility and impairs repair activity. 1 Publication1
Mutagenesisi756F → A: Reduces DNA repair activity; abolishes single-stranded DNA binding; reduces binding to homoduplex DNA; reduces localization at DNA damaged foci. 1 Publication1
Mutagenesisi797F → A: Reduces DNA repair activity; abolishes single-stranded DNA binding; reduces binding to homoduplex DNA; reduces localization at DNA damaged foci; decreases recruitment of TFIIH complex to lesion sites. 1 Publication1
Mutagenesisi799F → A: Reduces DNA repair activity; abolishes single-stranded DNA binding; reduces binding to homoduplex DNA; greatly reduces localization at DNA damaged foci; decreases recruitment of TFIIH complex to lesion sites. 1 Publication1
Mutagenesisi848W → A: Reduces NER activity and abolishes interaction with CETN2; when associated with A-851 and A-855. 1 Publication1
Mutagenesisi851L → A: Reduces NER activity and abolishes interaction with CETN2; when associated with A-848 and A-855. 1 Publication1
Mutagenesisi855L → A: Reduces NER activity and abolishes interaction with CETN2; when associated with A-848 and A-851. 1 Publication1

Keywords - Diseasei

Disease mutation, Xeroderma pigmentosum

Organism-specific databases

DisGeNETi7508
GeneReviewsiXPC
MalaCardsiXPC
MIMi278720 phenotype
OpenTargetsiENSG00000154767
Orphaneti276255 Xeroderma pigmentosum complementation group C
PharmGKBiPA37413

Polymorphism and mutation databases

BioMutaiXPC
DMDMi296453081

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00002182932 – 940DNA repair protein complementing XP-C cellsAdd BLAST939

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki41Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki81Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki89Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei94PhosphoserineCombined sources1
Modified residuei129PhosphoserineCombined sources1
Modified residuei140PhosphoserineCombined sources1
Cross-linki161Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei169PhosphothreonineCombined sources1
Modified residuei397PhosphoserineCombined sources1
Modified residuei398PhosphoserineCombined sources1
Modified residuei399PhosphoserineCombined sources1
Modified residuei453PhosphoserineCombined sources1
Modified residuei460PhosphoserineCombined sources1
Modified residuei876PhosphothreonineCombined sources1
Modified residuei883PhosphoserineCombined sources1
Modified residuei884PhosphoserineCombined sources1
Modified residuei891PhosphoserineCombined sources1
Modified residuei903PhosphoserineCombined sources1

Post-translational modificationi

Ubiquitinated upon UV irradiation; the ubiquitination requires the UV-DDB complex, appears to be reversible and does not serve as a signal for degradation (PubMed:15882621, PubMed:23751493). Ubiquitinated by RNF11 via 'Lys-63'-linked ubiquitination (PubMed:23751493). Ubiquitination by RNF111 is polysumoylation-dependent and promotes nucleotide excision repair (PubMed:23751493).2 Publications
Sumoylated; sumoylation promotes ubiquitination by RNF111.1 Publication

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ01831
PaxDbiQ01831
PeptideAtlasiQ01831
PRIDEiQ01831
ProteomicsDBi58003

PTM databases

iPTMnetiQ01831
PhosphoSitePlusiQ01831
SwissPalmiQ01831

Expressioni

Gene expression databases

BgeeiENSG00000154767
CleanExiHS_XPC
ExpressionAtlasiQ01831 baseline and differential
GenevisibleiQ01831 HS

Organism-specific databases

HPAiCAB009932
HPA035707
HPA069673

Interactioni

Subunit structurei

Component of the XPC complex composed of XPC, RAD23B and CETN2. Interacts with RAD23A; the interaction is suggesting the existence of a functional equivalent variant XPC complex. Interacts with TDG; the interaction is demonstrated using the XPC:RAD23B dimer. Interacts with SMUG1; the interaction is demonstrated using the XPC:RAD23B dimer. Interacts with DDB2. Interacts with CCNH, GTF2H1 and ERCC3.12 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi113345, 79 interactors
DIPiDIP-31225N
IntActiQ01831, 26 interactors
MINTiQ01831
STRINGi9606.ENSP00000285021

Structurei

Secondary structure

1940
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni120 – 123Combined sources4
Beta strandi124 – 126Combined sources3
Beta strandi134 – 137Combined sources4
Helixi150 – 153Combined sources4
Helixi848 – 861Combined sources14

3D structure databases

ProteinModelPortaliQ01831
SMRiQ01831
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ01831

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni496 – 734Interaction with RAD23BAdd BLAST239
Regioni607 – 766Minimal sensor domain involved in damage recognitionAdd BLAST160
Regioni607 – 741DNA-binding; preference for heteroduplex DNAAdd BLAST135
Regioni767 – 831DNA-binding; preference for single stranded DNA; required for formation of stable nucleoprotein complexAdd BLAST65
Regioni816 – 940Interaction with ERCC2 and GTF2H11 PublicationAdd BLAST125
Regioni847 – 866Interaction with CETN2Add BLAST20

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi390 – 395Nuclear localization signalSequence analysis6

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi30 – 177Glu-rich (acidic)Add BLAST148
Compositional biasi30 – 34Poly-Glu5
Compositional biasi124 – 130Poly-Glu7
Compositional biasi359 – 395Lys-rich (basic)Add BLAST37
Compositional biasi408 – 431Arg/Lys-rich (basic)Add BLAST24
Compositional biasi432 – 461Asp/Glu-rich (acidic)Add BLAST30
Compositional biasi466 – 493Arg/Lys-rich (basic)Add BLAST28
Compositional biasi501 – 507Poly-Ser7

Sequence similaritiesi

Belongs to the XPC family.Curated

Phylogenomic databases

eggNOGiKOG2179 Eukaryota
COG5535 LUCA
GeneTreeiENSGT00390000005194
HOGENOMiHOG000124671
HOVERGENiHBG000407
InParanoidiQ01831
KOiK10838
OMAiEDTHKVH
OrthoDBiEOG091G0HLY
PhylomeDBiQ01831
TreeFamiTF101242

Family and domain databases

Gene3Di3.90.260.10, 1 hit
InterProiView protein in InterPro
IPR018327 BHD_2
IPR004583 DNA_repair_Rad4
IPR018026 DNA_repair_Rad4_subgr
IPR038765 Papain_like_cys_pep_sf
IPR018325 Rad4/PNGase_transGLS-fold
IPR018326 Rad4_beta-hairpin_dom1
IPR018328 Rad4_beta-hairpin_dom3
IPR036985 Transglutaminase-like_sf
PANTHERiPTHR12135 PTHR12135, 1 hit
PfamiView protein in Pfam
PF10403 BHD_1, 1 hit
PF10404 BHD_2, 1 hit
PF10405 BHD_3, 1 hit
PF03835 Rad4, 1 hit
SMARTiView protein in SMART
SM01030 BHD_1, 1 hit
SM01031 BHD_2, 1 hit
SM01032 BHD_3, 1 hit
SUPFAMiSSF54001 SSF54001, 2 hits
TIGRFAMsiTIGR00605 rad4, 1 hit

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q01831-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MARKRAAGGE PRGRELRSQK SKAKSKARRE EEEEDAFEDE KPPKKSLLSK 
        60         70         80         90        100
VSQGKRKRGC SHPGGSADGP AKKKVAKVTV KSENLKVIKD EALSDGDDLR 
       110        120        130        140        150
DFPSDLKKAH HLKRGATMNE DSNEEEEESE NDWEEVEELS EPVLGDVRES 
       160        170        180        190        200
TAFSRSLLPV KPVEIEIETP EQAKTRERSE KIKLEFETYL RRAMKRFNKG 
       210        220        230        240        250
VHEDTHKVHL LCLLANGFYR NNICSQPDLH AIGLSIIPAR FTRVLPRDVD 
       260        270        280        290        300
TYYLSNLVKW FIGTFTVNAE LSASEQDNLQ TTLERRFAIY SARDDEELVH 
       310        320        330        340        350
IFLLILRALQ LLTRLVLSLQ PIPLKSATAK GKKPSKERLT ADPGGSSETS 
       360        370        380        390        400
SQVLENHTKP KTSKGTKQEE TFAKGTCRPS AKGKRNKGGR KKRSKPSSSE 
       410        420        430        440        450
EDEGPGDKQE KATQRRPHGR ERRVASRVSY KEESGSDEAG SGSDFELSSG 
       460        470        480        490        500
EASDPSDEDS EPGPPKQRKA PAPQRTKAGS KSASRTHRGS HRKDPSLPAA 
       510        520        530        540        550
SSSSSSSKRG KKMCSDGEKA EKRSIAGIDQ WLEVFCEQEE KWVCVDCVHG 
       560        570        580        590        600
VVGQPLTCYK YATKPMTYVV GIDSDGWVRD VTQRYDPVWM TVTRKCRVDA 
       610        620        630        640        650
EWWAETLRPY QSPFMDREKK EDLEFQAKHM DQPLPTAIGL YKNHPLYALK 
       660        670        680        690        700
RHLLKYEAIY PETAAILGYC RGEAVYSRDC VHTLHSRDTW LKKARVVRLG 
       710        720        730        740        750
EVPYKMVKGF SNRARKARLA EPQLREENDL GLFGYWQTEE YQPPVAVDGK 
       760        770        780        790        800
VPRNEFGNVY LFLPSMMPIG CVQLNLPNLH RVARKLDIDC VQAITGFDFH 
       810        820        830        840        850
GGYSHPVTDG YIVCEEFKDV LLTAWENEQA VIERKEKEKK EKRALGNWKL 
       860        870        880        890        900
LAKGLLIRER LKRRYGPKSE AAAPHTDAGG GLSSDEEEGT SSQAEAARIL 
       910        920        930        940
AASWPQNRED EEKQKLKGGP KKTKREKKAA ASHLFPFEQL
Length:940
Mass (Da):105,953
Last modified:May 18, 2010 - v4
Checksum:i2F8C80D43FAA1256
GO
Isoform 2 (identifier: Q01831-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     136-172: Missing.

Note: No experimental confirmation available.
Show »
Length:903
Mass (Da):101,847
Checksum:iAF2F96DDCC4DB78E
GO
Isoform 3 (identifier: Q01831-3) [UniParc]FASTAAdd to basket
Also known as: B

The sequence of this isoform differs from the canonical sequence as follows:
     138-140: ELS → VKR
     141-940: Missing.

Show »
Length:140
Mass (Da):15,712
Checksum:iCA721AA7474B6D20
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti135E → Q in BAG58555 (PubMed:14702039).Curated1
Sequence conflicti489G → E in BAG58555 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01889416L → V1 PublicationCorresponds to variant dbSNP:rs1870134EnsemblClinVar.1
Natural variantiVAR_01889548L → F1 PublicationCorresponds to variant dbSNP:rs2229089EnsemblClinVar.1
Natural variantiVAR_01889686K → R1 PublicationCorresponds to variant dbSNP:rs3731063Ensembl.1
Natural variantiVAR_057475287F → C. Corresponds to variant dbSNP:rs35629274EnsemblClinVar.1
Natural variantiVAR_018897314R → Q1 PublicationCorresponds to variant dbSNP:rs3731126Ensembl.1
Natural variantiVAR_005846334P → H in XP-C; severe. 1 PublicationCorresponds to variant dbSNP:rs74737358EnsemblClinVar.1
Natural variantiVAR_018898492R → H1 PublicationCorresponds to variant dbSNP:rs2227999EnsemblClinVar.1
Natural variantiVAR_018899499A → V3 PublicationsCorresponds to variant dbSNP:rs2228000EnsemblClinVar.1
Natural variantiVAR_059963511K → Q. Corresponds to variant dbSNP:rs6413541Ensembl.1
Natural variantiVAR_018900513M → I1 PublicationCorresponds to variant dbSNP:rs3731130EnsemblClinVar.1
Natural variantiVAR_057476514C → S. Corresponds to variant dbSNP:rs3731130EnsemblClinVar.1
Natural variantiVAR_018901632Q → E1 PublicationCorresponds to variant dbSNP:rs3731139Ensembl.1
Natural variantiVAR_018902671R → H1 PublicationCorresponds to variant dbSNP:rs3731140Ensembl.1
Natural variantiVAR_018903689T → M1 PublicationCorresponds to variant dbSNP:rs3731152EnsemblClinVar.1
Natural variantiVAR_064039690W → S in XP-C; diminishes repair activity and impairs DNA binding. 4 Publications1
Natural variantiVAR_005847697V → VV in XP-C; mild. 1 Publication1
Natural variantiVAR_018904928K → Q1 PublicationCorresponds to variant dbSNP:rs3731177EnsemblClinVar.1
Natural variantiVAR_005848939Q → K3 PublicationsCorresponds to variant dbSNP:rs2228001EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_046344136 – 172Missing in isoform 2. 1 PublicationAdd BLAST37
Alternative sequenceiVSP_055890138 – 140ELS → VKR in isoform 3. 1 Publication3
Alternative sequenceiVSP_055891141 – 940Missing in isoform 3. 1 PublicationAdd BLAST800

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D21089 mRNA Translation: BAA04651.1
AF261901
, AF261892, AF261893, AF261894, AF261895, AF261896, AF261897, AF261898, AF261899, AF261900 Genomic DNA Translation: AAF87574.1
KJ535085 mRNA Translation: AHW56724.1
AY131066 Genomic DNA Translation: AAM77801.1
AK295711 mRNA Translation: BAG58555.1
AC093495 Genomic DNA No translation available.
FJ695191 Genomic DNA No translation available.
FJ695192 Genomic DNA No translation available.
BC016620 mRNA Translation: AAH16620.1
AK222844 mRNA Translation: BAD96564.1
X65024 mRNA Translation: CAA46158.1
CCDSiCCDS46763.1 [Q01831-1]
PIRiS44345
RefSeqiNP_004619.3, NM_004628.4 [Q01831-1]
UniGeneiHs.475538
Hs.739296

Genome annotation databases

EnsembliENST00000285021; ENSP00000285021; ENSG00000154767 [Q01831-1]
ENST00000476581; ENSP00000424548; ENSG00000154767 [Q01831-3]
GeneIDi7508
KEGGihsa:7508
UCSCiuc062gzd.1 human [Q01831-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiXPC_HUMAN
AccessioniPrimary (citable) accession number: Q01831
Secondary accession number(s): B4DIP3
, E9PB96, E9PH69, Q53GT7, Q96AX0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: May 18, 2010
Last modified: July 18, 2018
This is version 188 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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