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Aliases for DDB2 Gene

Aliases for DDB2 Gene

  • Damage-Specific DNA Binding Protein 2, 48kDa 2 3
  • UV-Damaged DNA-Binding Protein 2 2 3 4
  • DDB P48 Subunit 2 3 4
  • Xeroderma Pigmentosum Group E Protein 2 3
  • Damage-Specific DNA-Binding Protein 2 3 4
  • UV-DDB 2 3 4
  • DDBB 3 4
  • Damage-Specific DNA Binding Protein 2 (48kD) 2
  • DNA Damage-Binding Protein 2 3
  • UV-DDB2 3

External Ids for DDB2 Gene

Previous GeneCards Identifiers for DDB2 Gene

  • GC11P049176
  • GC11P048114
  • GC11P047268
  • GC11P047200
  • GC11P047193
  • GC11P046935

Summaries for DDB2 Gene

Entrez Gene Summary for DDB2 Gene

  • 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]

GeneCards Summary for DDB2 Gene

DDB2 (Damage-Specific DNA Binding Protein 2, 48kDa) is a Protein Coding gene. Diseases associated with DDB2 include xeroderma pigmentosum, group e, ddb-negative subtype and ddb2-related xeroderma pigmentosum. Among its related pathways are Protein Stability and Direct p53 effectors. GO annotations related to this gene include ubiquitin-protein transferase activity and damaged DNA binding.

UniProtKB/Swiss-Prot for DDB2 Gene

  • Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.

Gene Wiki entry for DDB2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDB2 Gene

Genomics for DDB2 Gene

Regulatory Elements for DDB2 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for DDB2 Gene

Start:
47,214,465 bp from pter
End:
47,239,240 bp from pter
Size:
24,776 bases
Orientation:
Plus strand

Genomic View for DDB2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDB2 Gene

Proteins for DDB2 Gene

  • Protein details for DDB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92466-DDB2_HUMAN
    Recommended name:
    DNA damage-binding protein 2
    Protein Accession:
    Q92466
    Secondary Accessions:
    • B2R875
    • Q76E54
    • Q76E55
    • Q76E56
    • Q76E57

    Protein attributes for DDB2 Gene

    Size:
    427 amino acids
    Molecular mass:
    47864 Da
    Quaternary structure:
    • Component of the UV-DDB complex which includes DDB1 and DDB2. The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit. Component of the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1), which includes CUL4A or CUL4B, DDB1, DDB2 and RBX1. DDB2 may function as the substrate recognition module within this complex. The DDB1-CUL4-ROC1 complex may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex. A large number of other DCX complexes may also exist in which an alternate substrate targeting subunit replaces DDB2. These targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins. Isoform D1 and isoform D2 do not interact with DDB1.

    Three dimensional structures from OCA and Proteopedia for DDB2 Gene

    Alternative splice isoforms for DDB2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDB2 Gene

Proteomics data for DDB2 Gene at MOPED

Post-translational modifications for DDB2 Gene

  • Phosphorylation by ABL1 negatively regulate UV-DDB activity.
  • Ubiquitinated by CUL4A in response to UV irradiation. Ubiquitination appears to both impair DNA-binding and promotes ubiquitin-dependent proteolysis. Degradation of DDB2 at sites of DNA damage may be a prerequisite for their recognition by XPC and subsequent repair. CUL4A-mediated degradation appears to be promoted by ABL1.
  • Ubiquitinated, leading to proteasomal degradation, and deubiquitinated by USP24.
  • Ubiquitination at Lys151, Lys187, Lys278, and Lys362
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for DDB2 Gene

Domains for DDB2 Gene

Gene Families for DDB2 Gene

HGNC:
  • WDR :WD repeat domain containing

Protein Domains for DDB2 Gene

Suggested Antigen Peptide Sequences for DDB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92466

UniProtKB/Swiss-Prot:

DDB2_HUMAN :
  • Q92466
Domain:
  • The DWD box is required for interaction with DDB1.
  • Interblade loops of the WD repeat region mediate most of the interaction with DNA. A hairpin between blades 5 and 6 inserts into DNA minor groove and mediates recognition of lesions and separation of the damaged and undamaged strands.
Family:
  • Belongs to the WD repeat DDB2/WDR76 family.
Similarity:
  • Contains 7 WD repeats.
genes like me logo Genes that share domains with DDB2: view

Function for DDB2 Gene

Molecular function for DDB2 Gene

GENATLAS Biochemistry: damage specific DNA binding protein 2,p48 subunit,absent from cell strains from individuals with XP-E,possibly involved in nucleotide excision repair
UniProtKB/Swiss-Prot Function: Required for DNA repair. Binds to DDB1 to form the UV-damaged DNA-binding protein complex (the UV-DDB complex). The UV-DDB complex may recognize UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also appears to function as the substrate recognition module for the DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB1-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and CUL4-DDB-RBX1). The DDB1-CUL4-ROC1 complex may ubiquitinate histone H2A, histone H3 and histone H4 at sites of UV-induced DNA damage. The ubiquitination of histones may facilitate their removal from the nucleosome and promote subsequent DNA repair. The DDB1-CUL4-ROC1 complex also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. Isoform D1 and isoform D2 inhibit UV-damaged DNA repair.
UniProtKB/Swiss-Prot Induction: Expression is induced in response to treatment with IR or UV and this requires p53/TP53 activity.

Gene Ontology (GO) - Molecular Function for DDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding TAS 8798680
GO:0003684 contributes_to damaged DNA binding IDA 22334663
GO:0003824 catalytic activity --
GO:0004842 contributes_to ubiquitin-protein transferase activity IDA 12732143
GO:0005515 protein binding IPI 12732143
genes like me logo Genes that share ontologies with DDB2: view
genes like me logo Genes that share phenotypes with DDB2: view

Animal Models for DDB2 Gene

MGI Knock Outs for DDB2:

Animal Model Products

CRISPR Products

miRNA for DDB2 Gene

miRTarBase miRNAs that target DDB2

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDB2

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for DDB2 Gene

Localization for DDB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDB2 Gene

Nucleus. Note=Accumulates at sites of DNA damage following UV irradiation.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DDB2 Gene COMPARTMENTS Subcellular localization image for DDB2 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for DDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0030054 cell junction IDA --
GO:0031465 Cul4B-RING E3 ubiquitin ligase complex IDA 22334663
GO:0043234 protein complex IDA 12732143
genes like me logo Genes that share ontologies with DDB2: view

Pathways for DDB2 Gene

genes like me logo Genes that share pathways with DDB2: view

Pathways by source for DDB2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

UniProtKB/Swiss-Prot Q92466-DDB2_HUMAN

  • Pathway: Protein modification; protein ubiquitination

Gene Ontology (GO) - Biological Process for DDB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IDA 12732143
GO:0000718 nucleotide-excision repair, DNA damage removal TAS --
GO:0006281 DNA repair TAS --
GO:0006289 nucleotide-excision repair TAS --
GO:0006290 pyrimidine dimer repair IEA --
genes like me logo Genes that share ontologies with DDB2: view

Compounds for DDB2 Gene

(1) HMDB Compounds for DDB2 Gene

Compound Synonyms Cas Number PubMed IDs
Pyrimidine
  • 1,3-Diazabenzene
25247-63-6

(2) Novoseek inferred chemical compound relationships for DDB2 Gene

Compound -log(P) Hits PubMed IDs
cpds 70.6 1
cisplatin 0 3
genes like me logo Genes that share compounds with DDB2: view

Transcripts for DDB2 Gene

Unigene Clusters for DDB2 Gene

Damage-specific DNA binding protein 2, 48kDa:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDB2

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDB2 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e · 2f · 2g ^ 3a · 3b · 3c · 3d · 3e · 3f ^ 4a · 4b · 4c · 4d ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9a ·
SP1: - - - - -
SP2: - - - - - - - - -
SP3: - - - - - -
SP4: - - - - - - - -
SP5: - - -
SP6: - - - - - - - -
SP7: - - - - - - - - - - -
SP8: -
SP9:
SP10: - - - - - - - -
SP11: - - -
SP12: - - -
SP13: - -
SP14: - -
SP15: - - - - - - -
SP16: - - - - - -
SP17: - -
SP18: - - - -
SP19:
SP20: -

ExUns: 9b · 9c ^ 10a · 10b ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b
SP1: - -
SP2: - -
SP3: - - -
SP4: - - -
SP5: - -
SP6:
SP7: - - - - -
SP8: -
SP9: - - -
SP10: - - - - -
SP11: - - - - -
SP12: - - - - -
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:
SP19:
SP20:

Relevant External Links for DDB2 Gene

GeneLoc Exon Structure for
DDB2
ECgene alternative splicing isoforms for
DDB2

Expression for DDB2 Gene

mRNA expression in normal human tissues for DDB2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDB2 Gene

SOURCE GeneReport for Unigene cluster for DDB2 Gene Hs.700338

mRNA Expression by UniProt/SwissProt for DDB2 Gene

Q92466-DDB2_HUMAN
Tissue specificity: Ubiquitously expressed; with highest levels in corneal endothelium and lowest levels in brain. Isoform D1 is highly expressed in brain and heart. Isoform D2, isoform D3 and isoform D4 are weakly expressed.
genes like me logo Genes that share expressions with DDB2: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for DDB2 Gene

Orthologs for DDB2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDB2 35
  • 99.92 (n)
  • 100 (a)
DDB2 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DDB2 35
  • 88.97 (n)
  • 84.98 (a)
DDB2 36
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDB2 35
  • 90.06 (n)
  • 86.85 (a)
DDB2 36
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddb2 35
  • 82.98 (n)
  • 78.45 (a)
Ddb2 16
Ddb2 36
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 65 (a)
OneToMany
-- 36
  • 68 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia DDB2 36
  • 71 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ddb2 35
  • 83.25 (n)
  • 78.91 (a)
chicken
(Gallus gallus)
Aves DDB2 35
  • 66.2 (n)
  • 61.67 (a)
DDB2 36
  • 46 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDB2 36
  • 42 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddb2 35
  • 65.04 (n)
  • 64.37 (a)
zebrafish
(Danio rerio)
Actinopterygii ddb2 35
  • 54.28 (n)
  • 46.45 (a)
ddb2 36
  • 37 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons DDB2 35
  • 45.62 (n)
  • 34.47 (a)
rice
(Oryza sativa)
Liliopsida Os01g0141700 35
  • 43.89 (n)
  • 32.67 (a)
Species with no ortholog for DDB2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for DDB2 Gene

ENSEMBL:
Gene Tree for DDB2 (if available)
TreeFam:
Gene Tree for DDB2 (if available)

Paralogs for DDB2 Gene

Pseudogenes.org Pseudogenes for DDB2 Gene

genes like me logo Genes that share paralogs with DDB2: view

No data available for Paralogs for DDB2 Gene

Variants for DDB2 Gene

Sequence variations from dbSNP and Humsavar for DDB2 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs326211 -- 47,217,114(-) acagg(C/T)gcgaa intron-variant
rs326212 -- 47,216,971(-) GCCAC(A/C/G)GTGCT reference, synonymous-codon, nc-transcript-variant
rs326222 -- 47,238,117(+) TCATG(C/T)TGACA intron-variant
rs326223 -- 47,234,352(-) GGTTA(C/T)GGCTG intron-variant
rs326224 -- 47,234,047(-) CTAGG(A/G)GGGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DDB2 Gene

Variant ID Type Subtype PubMed ID
nsv897323 CNV Loss 21882294

Relevant External Links for DDB2 Gene

HapMap Linkage Disequilibrium report
DDB2
Human Gene Mutation Database (HGMD)
DDB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDB2 Gene

Disorders for DDB2 Gene

(1) OMIM Diseases for DDB2 Gene (600811)

UniProtKB/Swiss-Prot

DDB2_HUMAN
  • Xeroderma pigmentosum complementation group E (XP-E) [MIM:278740]: An 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. XP-E patients show a mild phenotype with minimal or no neurologic features. {ECO:0000269 PubMed:8798680}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(3) University of Copenhagen DISEASES for DDB2 Gene

(9) Novoseek inferred disease relationships for DDB2 Gene

Disease -log(P) Hits PubMed IDs
xeroderma pigmentosum, complementation group e 95.2 5
xeroderma pigmentosum 87.9 18
skin cancer 54.2 3
tumors 26.5 7
cancer 13.4 3

Relevant External Links for DDB2

GeneTests
DDB2
GeneReviews
DDB2
Genetic Association Database (GAD)
DDB2
Human Genome Epidemiology (HuGE) Navigator
DDB2
genes like me logo Genes that share disorders with DDB2: view

Publications for DDB2 Gene

  1. In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product. (PMID: 12944386) Fitch M.E. … Ford J.M. (J. Biol. Chem. 2003) 3 4 23
  2. DDB1-DDB2 (xeroderma pigmentosum group E) protein complex recognizes a cyclobutane pyrimidine dimer, mismatches, apurinic/apyrimidinic sites, and compound lesions in DNA. (PMID: 16223728) Wittschieben B.O. … Wood R.D. (J. Biol. Chem. 2005) 3 4 23
  3. Xeroderma pigmentosum complementation group E protein (XPE/DDB2): purification of various complexes of XPE and analyses of their damaged DNA binding and putative DNA repair properties. (PMID: 16260596) Kulaksiz G. … Sancar A. (Mol. Cell. Biol. 2005) 3 4 23
  4. The DDB1-CUL4ADDB2 ubiquitin ligase is deficient in xeroderma pigmentosum group E and targets histone H2A at UV-damaged DNA sites. (PMID: 16473935) Kapetanaki M.G. … Levine A.S. (Proc. Natl. Acad. Sci. U.S.A. 2006) 3 4 23
  5. Polymorphisms in DNA damage binding protein 2 (DDB2) and susceptibility of primary lung cancer in the Chinese: a case-control study. (PMID: 16522664) Hu Z. … Shen H. (Carcinogenesis 2006) 3 23 48

Products for DDB2 Gene

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