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

Gene ID: 1643, updated on 1-Jun-2020

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
109.20200522 current GRCh38.p13 (GCF_000001405.39) 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 MADD antisense RNA 1 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Xeroderma pigmentosum, group E
MedGen: C1848411 OMIM: 278740 GeneReviews: Xeroderma Pigmentosum
Compare labs

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 PubChem

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 IBA
Inferred from Biological aspect of Ancestor
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 
Process Evidence Code Pubs
DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
UV-damage excision repair IDA
Inferred from Direct Assay
more info
PubMed 
global genome nucleotide-excision repair TAS
Traceable Author Statement
more info
 
histone H2A monoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
nucleotide-excision repair TAS
Traceable Author Statement
more info
PubMed 
nucleotide-excision repair, DNA damage recognition TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA duplex unwinding TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA incision TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA incision, 3'-to lesion TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA incision, 5'-to lesion TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex assembly TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex stabilization TAS
Traceable Author Statement
more info
 
post-translational protein modification TAS
Traceable Author Statement
more info
 
protein autoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein polyubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
pyrimidine dimer repair IEA
Inferred from Electronic Annotation
more info
 
response to UV IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to UV 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
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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_000107.3NP_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, 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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 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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