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

Gene ID: 1643, updated on 3-Apr-2024

Summary

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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; AllianceGenome:HGNC:2718
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
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Genomic context

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See DDB2 in Genome Data Viewer
Location:
11p11.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47214454..47239217)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47371205..47395960)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47236005..47260768)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:47207755-47208641 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 ReSE screen-validated silencer GRCh37_chr11:47231264-47231443 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47235129-47235965 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:47236089-47237288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4694 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47270641-47270808 Neighboring gene acid phosphatase 2, lysosomal Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47280987-47281555 Neighboring gene nuclear receptor subfamily 1 group H member 3 Neighboring gene Sharpr-MPRA regulatory region 2100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3325 Neighboring gene Sharpr-MPRA regulatory region 9889 Neighboring gene MADD antisense RNA 1 Neighboring gene MAP kinase activating death domain

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients. Wang X, et al. Genes (Basel), 2022 Dec 23. PMID 36672781, Free PMC Article
  2. Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E. Karagün E, et al. Int J Dermatol, 2020 Aug. PMID 32530099
  3. Identification of a novel DDB2 mutation in a Chinese Han family with Xeroderma pigmentosum group E:a case report and literature review. Yang R, et al. BMC Med Genet, 2020 Mar 30. PMID 32228487, Free PMC Article
  4. Association between Single-Nucleotide Polymorphism in MicroRNA Target Site of DDB2 and Risk of Hepatocellular Carcinoma in a Southern Chinese Population. Qiu M, et al. Biomed Res Int, 2020. PMID 32090112, Free PMC Article
  5. Expression of DDB2 Protein in the Initiation, Progression, and Prognosis of Colorectal Cancer. Yang H, et al. Dig Dis Sci, 2018 Nov. PMID 30054844

See all (194) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Brazilian XP-E siblings carrying a novel DDB2 variant developed early-onset melanoma: a case report.
    Title: Brazilian XP-E siblings carrying a novel DDB2 variant developed early-onset melanoma: a case report.
  2. Four Genes Predictive for the Severity of Hematological Damage Reveal a Similar Response after X Irradiation and Chemotherapy.
    Title: Four Genes Predictive for the Severity of Hematological Damage Reveal a Similar Response after X Irradiation and Chemotherapy.
  3. The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients.
    Title: The Role of Alternative Splicing Factors, DDB2-Related Ageing and DNA Damage Repair in the Progression and Prognosis of Stomach Adenocarcinoma Patients.
  4. Histone demethylase JHDM2A participates in the repair of arsenic-induced DNA damage in L-02 cells by regulating DDB2.
    Title: Histone demethylase JHDM2A participates in the repair of arsenic-induced DNA damage in L-02 cells by regulating DDB2.
  5. Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins.
    Title: Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins.
  6. Proteomic Analysis of Nuclear Hepatitis B Virus Relaxed Circular DNA-Associated Proteins Identifies UV-Damaged DNA Binding Protein as a Host Factor Involved in Covalently Closed Circular DNA Formation.
    Title: Proteomic Analysis of Nuclear Hepatitis B Virus Relaxed Circular DNA-Associated Proteins Identifies UV-Damaged DNA Binding Protein as a Host Factor Involved in Covalently Closed Circular DNA Formation.
  7. Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E.
    Title: Novel mutation identified in the DDB2 gene in patients with xeroderma pigmentosum group-E.
  8. Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer.
    Title: Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer.
  9. Functional impacts of the ubiquitin-proteasome system on DNA damage recognition in global genome nucleotide excision repair.
    Title: Functional impacts of the ubiquitin-proteasome system on DNA damage recognition in global genome nucleotide excision repair.
  10. Knockdown of Ubiquitin-Specific Protease 53 Enhances the Radiosensitivity of Human Cervical Squamous Cell Carcinoma by Regulating DNA Damage-Binding Protein 2.
    Title: Knockdown of Ubiquitin-Specific Protease 53 Enhances the Radiosensitivity of Human Cervical Squamous Cell Carcinoma by Regulating DNA Damage-Binding Protein 2.
Submit: New GeneRIF Correction See all GeneRIFs (99)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

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

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ34321

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
contributes_to damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to damaged DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables 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
involved_in DNA damage response EXP
Inferred from Experiment
more info
 PubMed 
involved_in DNA damage response ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in UV-damage excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to UV EXP
Inferred from Experiment
more info
 PubMed 
involved_in cellular response to UV ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nucleotide-excision repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nucleotide-excision repair ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in protein autoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein polyubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in pyrimidine dimer repair IEA
Inferred from Electronic Annotation
more info
  
involved_in response to UV IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to UV IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of Cul4-RING E3 ubiquitin ligase complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of Cul4A-RING E3 ubiquitin ligase complex EXP
Inferred from Experiment
more info
 PubMed 
part_of Cul4B-RING E3 ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cell junction IDA
Inferred from Direct Assay
more info
  
part_of chromatin ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in site of DNA damage IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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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_000107.3 → NP_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
    B2R875, Q76E54, Q76E55, Q76E56, Q76E57, Q92466
    Related
    ENSP00000256996.4, ENST00000256996.9
    Conserved Domains (2) summary
    sd00039
    Location:115 → 154
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:115 → 419
    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_001300734.2 → NP_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:115 → 230
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:114 → 151
    7WD40; WD40 repeat [structural motif]

  3. NM_001399874.1 → NP_001386803.1  DNA damage-binding protein 2 isoform WT

    Status: REVIEWED

    Source sequence(s)
    AC018410, AC090589, KF459540
    Consensus CDS
    CCDS7927.1
    UniProtKB/Swiss-Prot
    B2R875, Q76E54, Q76E55, Q76E56, Q76E57, Q92466

  4. NM_001399875.1 → NP_001386804.1  DNA damage-binding protein 2 isoform WT

    Status: REVIEWED

    Source sequence(s)
    AC018410, AC090589, KF459540
    Consensus CDS
    CCDS7927.1
    UniProtKB/Swiss-Prot
    B2R875, Q76E54, Q76E55, Q76E56, Q76E57, Q92466

  5. NM_001399876.1 → NP_001386805.1  DNA damage-binding protein 2 isoform D1

    Status: REVIEWED

    Source sequence(s)
    AC018410, AC090589, KF459540
    Consensus CDS
    CCDS73284.1

  6. NM_001399878.1 → NP_001386807.1  DNA damage-binding protein 2 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC018410, AC090589
    Consensus CDS
    CCDS91469.1
    Related
    ENSP00000367866.3, ENST00000378603.7

RNA

  1. NR_174610.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC018410, AC090589, KF459540

  2. NR_174611.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC018410, AC090589, KF459540

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    47214454..47239217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426487.1 → XP_047282443.1  DNA damage-binding protein 2 isoform X1

    Related
    ENSP00000367864.3, ENST00000378601.7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    47371205..47395960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367876.1 → XP_054223851.1  DNA damage-binding protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92466.1 GenPept UniProtKB/Swiss-Prot:Q92466

Gene LinkOut

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Chemical Information
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