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DDB2 damage specific DNA binding protein 2 [ Homo sapiens (human) ]

Gene ID: 1643, updated on 23-Apr-2019

Summary

Official Symbol
DDB2provided by HGNC
Official Full Name
damage specific DNA binding protein 2provided by HGNC
Primary source
HGNC:HGNC:2718
See related
Ensembl:ENSG00000134574 MIM:600811
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
XPE; DDBB; UV-DDB2
Summary
This gene encodes a protein that is necessary for the repair of ultraviolet light-damaged DNA. This protein is the smaller subunit of a heterodimeric protein complex that participates in nucleotide excision repair, and this complex mediates the ubiquitylation of histones H3 and H4, which facilitates the cellular response to DNA damage. This subunit appears to be required for DNA binding. Mutations in this gene cause xeroderma pigmentosum complementation group E, a recessive disease that is characterized by an increased sensitivity to UV light and a high predisposition for skin cancer development, in some cases accompanied by neurological abnormalities. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in skin (RPKM 32.0), esophagus (RPKM 13.6) and 24 other tissues See more
Orthologs

Genomic context

See DDB2 in Genome Data Viewer
Location:
11p11.2
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (47214942..47239218)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47236493..47260769)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene protein kinase C and casein kinase substrate in neurons 3 Neighboring gene microRNA 6745 Neighboring gene ribosomal protein S20 pseudogene 26 Neighboring gene acid phosphatase 2, lysosomal Neighboring gene nuclear receptor subfamily 1 group H member 3 Neighboring gene uncharacterized LOC101928943 Neighboring gene MAP kinase activating death domain

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Xeroderma pigmentosum, group E
MedGen: C1848411 OMIM: 278740 GeneReviews: Xeroderma Pigmentosum
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NHGRI GWAS Catalog

Description
Two new susceptibility loci 1q24.2 and 11p11.2 confer risk to severe acne.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr interferes with the interaction of DDB1 and DDB2 in cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cul4-DDB1-DDB2 complex, organism-specific biosystem (from KEGG)
    Cul4-DDB1-DDB2 complex, organism-specific biosystemStructural complex; Genetic information processing; Ubiquitin system
  • Cul4-DDB1-DDB2 complex, conserved biosystem (from KEGG)
    Cul4-DDB1-DDB2 complex, conserved biosystemStructural complex; Genetic information processing; Ubiquitin system
  • DNA Damage Recognition in GG-NER, organism-specific biosystem (from REACTOME)
    DNA Damage Recognition in GG-NER, organism-specific biosystemIn global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DN...
  • DNA Damage Response, organism-specific biosystem (from WikiPathways)
    DNA Damage Response, organism-specific biosystemThis is the first pathway out of two pathways which deals with DNA damage response. It has two central gene products (ATM and ATR) which are connected to the sources of DNA damage (in blue). The two ...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • Dual Incision in GG-NER, organism-specific biosystem (from REACTOME)
    Dual Incision in GG-NER, organism-specific biosystemDouble incision at the damaged DNA strand excises the oligonucleotide that contains the lesion from the open bubble. The excised oligonucleotide is ~27-30 bases long. Incision 5' to the damage site, ...
  • Formation of Incision Complex in GG-NER, organism-specific biosystem (from REACTOME)
    Formation of Incision Complex in GG-NER, organism-specific biosystemAfter the XPC complex and the UV-DDB complex bind damaged DNA, a basal transcription factor TFIIH is recruited to the nucleotide excision repair (NER) site (Volker et al. 2001, Riedl et al. 2003). DN...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
    Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
  • Hepatitis B, organism-specific biosystem (from KEGG)
    Hepatitis B, organism-specific biosystemHepatitis B virus (HBV) is an enveloped virus and contains a partially double-stranded relaxed circular DNA (RC-DNA) genome. After entry into hepatocytes, HBV RC-DNA is transported to the nucleus and...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • Nucleotide excision repair, organism-specific biosystem (from KEGG)
    Nucleotide excision repair, organism-specific biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Nucleotide excision repair, conserved biosystem (from KEGG)
    Nucleotide excision repair, conserved biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • TP53 Regulates Transcription of DNA Repair Genes, organism-specific biosystem (from REACTOME)
    TP53 Regulates Transcription of DNA Repair Genes, organism-specific biosystemSeveral DNA repair genes contain p53 response elements and their transcription is positively regulated by TP53 (p53). TP53-mediated regulation probably ensures increased protein level of DNA repair g...
  • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
    Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...
  • Ubiquitin mediated proteolysis, organism-specific biosystem (from KEGG)
    Ubiquitin mediated proteolysis, organism-specific biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...
  • Ubiquitin mediated proteolysis, conserved biosystem (from KEGG)
    Ubiquitin mediated proteolysis, conserved biosystemProtein ubiquitination plays an important role in eukaryotic cellular processes. It mainly functions as a signal for 26S proteasome dependent protein degradation. The addition of ubiquitin to protein...
  • miRNA Regulation of DNA Damage Response, organism-specific biosystem (from WikiPathways)
    miRNA Regulation of DNA Damage Response, organism-specific biosystemThis is the first out of two pathways which deals with the DNA damage response. It is comprised of two central gene products (ATM and ATR) influenced by different sources of DNA damage (in blue). The...
  • p53 signaling pathway, organism-specific biosystem (from KEGG)
    p53 signaling pathway, organism-specific biosystemp53 activation is induced by a number of stress signals, including DNA damage, oxidative stress and activated oncogenes. The p53 protein is employed as a transcriptional activator of p53-regulated ge...
  • p53 signaling pathway, conserved biosystem (from KEGG)
    p53 signaling pathway, conserved biosystemp53 activation is induced by a number of stress signals, including DNA damage, oxidative stress and activated oncogenes. The p53 protein is employed as a transcriptional activator of p53-regulated ge...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34321

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding TAS
Traceable Author Statement
more info
PubMed 
contributes_to damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
Cul4-RING E3 ubiquitin ligase complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
Cul4B-RING E3 ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 
cell junction IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
DNA damage-binding protein 2
Names
DDB p48 subunit
UV-DDB 2
UV-damaged DNA-binding protein 2
damage-specific DNA binding protein 2, 48kDa
xeroderma pigmentosum group E protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009365.1 RefSeqGene

    Range
    5001..29277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_467

mRNA and Protein(s)

  1. NM_000107.2NP_000098.1  DNA damage-binding protein 2 isoform WT

    See identical proteins and their annotated locations for NP_000098.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (WT) represents the longer transcript and encodes the longer isoform (WT).
    Source sequence(s)
    AA278953, DB053816, U18300
    Consensus CDS
    CCDS7927.1
    UniProtKB/Swiss-Prot
    Q92466
    Related
    ENSP00000256996.3, ENST00000256996.8
    Conserved Domains (2) summary
    sd00039
    Location:115154
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:115419
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_001300734.1NP_001287663.1  DNA damage-binding protein 2 isoform D1

    See identical proteins and their annotated locations for NP_001287663.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (D1) lacks four consecutive alternate exons compared to variant WT, without a reading frame change. The resulting isoform (D1) has the same N- and C-termini but is shorter compared to isoform WT.
    Source sequence(s)
    AA278953, AB107037, DB053816
    Consensus CDS
    CCDS73284.1
    UniProtKB/Swiss-Prot
    Q92466
    Related
    ENSP00000367863.3, ENST00000378600.7
    Conserved Domains (2) summary
    COG2319
    Location:115230
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:114151
    7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    47214942..47239218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_242780.4 RNA Sequence

    Related
    ENST00000378601.7
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