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Aliases for DDB1 Gene

Aliases for DDB1 Gene

  • Damage Specific DNA Binding Protein 1 2 3
  • Xeroderma Pigmentosum Group E-Complementing Protein 3 4
  • UV-Damaged DNA-Binding Protein 1 3 4
  • UV-Damaged DNA-Binding Factor 3 4
  • DNA Damage-Binding Protein A 3 4
  • HBV X-Associated Protein 1 3 4
  • XPE-Binding Factor 3 4
  • DDB P127 Subunit 3 4
  • UV-DDB 1 3 4
  • XPE-BF 3 4
  • XAP-1 3 4
  • DDBA 3 4
  • XPCE 3 4
  • XAP1 3 4
  • Damage-Specific DNA Binding Protein 1 (127kD) 2
  • Damage-Specific DNA Binding Protein 1, 127kDa 3
  • Damage-Specific DNA-Binding Protein 1 4
  • Damage-Specific DNA Binding Protein 1 5
  • UV-DDB1 3
  • XPE 3

External Ids for DDB1 Gene

Previous GeneCards Identifiers for DDB1 Gene

  • GC11P063499
  • GC11M062579
  • GC11M060842
  • GC11M060823
  • GC11M061066
  • GC11M057394

Summaries for DDB1 Gene

Entrez Gene Summary for DDB1 Gene

  • The protein encoded by this gene is the large subunit (p127) of the heterodimeric DNA damage-binding (DDB) complex while another protein (p48) forms the small subunit. This protein complex functions in nucleotide-excision repair and binds to DNA following UV damage. Defective activity of this complex causes the repair defect in patients with xeroderma pigmentosum complementation group E (XPE) - an autosomal recessive disorder characterized by photosensitivity and early onset of carcinomas. However, it remains for mutation analysis to demonstrate whether the defect in XPE patients is in this gene or the gene encoding the small subunit. In addition, Best vitelliform mascular dystrophy is mapped to the same region as this gene on 11q, but no sequence alternations of this gene are demonstrated in Best disease patients. The protein encoded by this gene also functions as an adaptor molecule for the cullin 4 (CUL4) ubiquitin E3 ligase complex by facilitating the binding of substrates to this complex and the ubiquitination of proteins. [provided by RefSeq, May 2012]

GeneCards Summary for DDB1 Gene

DDB1 (Damage Specific DNA Binding Protein 1) is a Protein Coding gene. Diseases associated with DDB1 include hepatitis b and xeroderma pigmentosum, group e, ddb-negative subtype. Among its related pathways are DNA Double-Strand Break Repair and Transcription-Coupled Nucleotide Excision Repair (TC-NER). GO annotations related to this gene include nucleic acid binding and damaged DNA binding. An important paralog of this gene is SF3B3.

UniProtKB/Swiss-Prot for DDB1 Gene

  • Required for DNA repair. Binds to DDB2 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 a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) 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. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.

Gene Wiki entry for DDB1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDB1 Gene

Genomics for DDB1 Gene

Regulatory Elements for DDB1 Gene

Genomic Location for DDB1 Gene

Chromosome:
11
Start:
61,299,447 bp from pter
End:
61,342,596 bp from pter
Size:
43,150 bases
Orientation:
Minus strand

Genomic View for DDB1 Gene

Genes around DDB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDB1 Gene

Proteins for DDB1 Gene

  • Protein details for DDB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q16531-DDB1_HUMAN
    Recommended name:
    DNA damage-binding protein 1
    Protein Accession:
    Q16531
    Secondary Accessions:
    • A6NG77
    • B2R648
    • B4DG00
    • O15176
    • Q13289
    • Q58F96

    Protein attributes for DDB1 Gene

    Size:
    1140 amino acids
    Molecular mass:
    126968 Da
    Quaternary structure:
    • Component of the UV-DDB complex which includes DDB1 and DDB2; the heterodimer dimerizes to give rise to a heterotetramer when bound to damaged DNA (PubMed:22822215). The UV-DDB complex interacts with monoubiquitinated histone H2A and binds to XPC via the DDB2 subunit. Component of numerous DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which consist of a core of DDB1, CUL4A or CUL4B and RBX1. DDB1 may recruit specific substrate targeting subunits to the DCX complex. These substrate targeting subunits are generally known as DCAF (DDB1- and CUL4-associated factor) or CDW (CUL4-DDB1-associated WD40-repeat) proteins. Interacts with AMBRA1, ATG16L1, BTRC, CRBN, DCAF1, DCAF4, DCAF5, DCAF6, DCAF7, DCAF8, DCAF9, DCAF10, DCAF11, DCAF12, DCAF15, DCAF16, DCAF17, DDA1, DET1, DTL, ERCC8, FBXW5, FBXW8, GRWD1, KATNB1, NLE1, NUP43, PAFAH1B1, PHIP, PWP1, RBBP4, RBBP5, RBBP7, RFWD2, SNRNP40, VPRBP, WDR5, WDR5B, WDR12, WDR26, WDR39, WDR42, WDR53, WDR59, WDR61, WSB1, WSB2, LRWD1 and WDTC1. DCX complexes may associate with the COP9 signalosome, and this inhibits the E3 ubiquitin-protein ligase activity of the complex. Interacts with NF2, TSC1 and TSC2. Interacts with Simian virus 5 protein V. Interacts with the hepatitis B virus protein HBX, the woodchuck hepatitis virus X protein WHX and the paramyxovirus protein SV5-V; these viral proteins contain a short helical motif that competes for the same binding site as the N-terminal helical motif found in endogenous DCAF proteins (PubMed:19966799). Interaction with SV5 protein V may prevent the recruitment of DCAF proteins to DCX complexes. Interacts with AGO1 and AGO2. Associates with the E3 ligase complex containing DYRK2, EDD/UBR5, DDB1 and VPRBP proteins (EDVP complex). Interacts directly with DYRK2. DCX(DTL) complex interacts with FBXO11; does not ubiquitinate and degradate FBXO11. Interacts with TRPC4AP (PubMed:19966799).

    Three dimensional structures from OCA and Proteopedia for DDB1 Gene

    Alternative splice isoforms for DDB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDB1 Gene

Proteomics data for DDB1 Gene at MOPED

Post-translational modifications for DDB1 Gene

  • Phosphorylated by ABL1.
  • Ubiquitinated by CUL4A. Subsequently degraded by ubiquitin-dependent proteolysis.
  • Ubiquitination at Lys 92, Lys 141, Lys 153, Lys 191, Lys 298, Lys 383, Lys 408, Lys 484, Lys 570, Lys 579, Lys 723, Lys 823, Lys 857, Lys 897, Lys 917, Lys 936, Lys 1067, Lys 1081, Lys 1121, and Lys 1131
  • Modification sites at PhosphoSitePlus

Other Protein References for DDB1 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for DDB1 (DDB1)

No data available for DME Specific Peptides for DDB1 Gene

Domains & Families for DDB1 Gene

Graphical View of Domain Structure for InterPro Entry

Q16531

UniProtKB/Swiss-Prot:

DDB1_HUMAN :
  • The core of the protein consists of three WD40 beta-propeller domains.
  • Belongs to the DDB1 family.
Domain:
  • The core of the protein consists of three WD40 beta-propeller domains.
Family:
  • Belongs to the DDB1 family.
genes like me logo Genes that share domains with DDB1: view

No data available for Gene Families for DDB1 Gene

Function for DDB1 Gene

Molecular function for DDB1 Gene

GENATLAS Biochemistry:
damage specific DNA binding protein 1,p127 subunit,absent from cell strains from a minority of individuals with XP-E,possibly involved in nucleotide excision repair
UniProtKB/Swiss-Prot Function:
Required for DNA repair. Binds to DDB2 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 a component of numerous distinct DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The functional specificity of the DCX E3 ubiquitin-protein ligase complex is determined by the variable substrate recognition component recruited by DDB1. DCX(DDB2) (also known as DDB1-CUL4-ROC1, CUL4-DDB-ROC1 and CUL4-DDB-RBX1) 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. DCX(DDB2) also ubiquitinates XPC, which may enhance DNA-binding by XPC and promote NER. DCX(DTL) plays a role in PCNA-dependent polyubiquitination of CDT1 and MDM2-dependent ubiquitination of TP53 in response to radiation-induced DNA damage and during DNA replication. DCX(ERCC8) (the CSA complex) plays a role in transcription-coupled repair (TCR). May also play a role in ubiquitination of CDKN1B/p27kip when associated with CUL4 and SKP2.
genes like me logo Genes that share phenotypes with DDB1: view

Human Phenotype Ontology for DDB1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for DDB1 Gene

MGI Knock Outs for DDB1:

Animal Model Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for DDB1 Gene

Localization for DDB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDB1 Gene

Cytoplasm. Nucleus. Note=Primarily cytoplasmic. Translocates to the nucleus following UV irradiation and subsequently accumulates at sites of DNA damage.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DDB1 Gene COMPARTMENTS Subcellular localization image for DDB1 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 3
mitochondrion 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for DDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with DDB1: view

Pathways & Interactions for DDB1 Gene

genes like me logo Genes that share pathways with DDB1: view

UniProtKB/Swiss-Prot Q16531-DDB1_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for DDB1 Gene

Activates:

Gene Ontology (GO) - Biological Process for DDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006283 transcription-coupled nucleotide-excision repair TAS --
GO:0006289 nucleotide-excision repair TAS 8407967
GO:0006294 nucleotide-excision repair, preincision complex assembly TAS --
GO:0006295 nucleotide-excision repair, DNA incision, 3-to lesion TAS --
GO:0016032 viral process IEA --
genes like me logo Genes that share ontologies with DDB1: view

Drugs & Compounds for DDB1 Gene

(3) Drugs for DDB1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for DDB1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Pyrimidine
  • 1,3-Diazabenzene
  • 1,3-Diazine
  • M-Diazine
  • Metadiazine
  • Miazine
25247-63-6
genes like me logo Genes that share compounds with DDB1: view

Transcripts for DDB1 Gene

Unigene Clusters for DDB1 Gene

Damage-specific DNA binding protein 1, 127kDa:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDB1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: - -
SP2: -
SP3: - - - - -
SP4: - - -
SP5: - - - -
SP6:
SP7:
SP8:
SP9:

ExUns: 23 ^ 24 ^ 25a · 25b ^ 26a · 26b · 26c · 26d ^ 27a · 27b · 27c · 27d · 27e ^ 28 ^ 29a · 29b
SP1: - -
SP2:
SP3: - - - - - -
SP4:
SP5:
SP6: - - -
SP7: -
SP8:
SP9:

Relevant External Links for DDB1 Gene

GeneLoc Exon Structure for
DDB1
ECgene alternative splicing isoforms for
DDB1

Expression for DDB1 Gene

mRNA expression in normal human tissues for DDB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDB1 Gene

This gene is overexpressed in Lymph node (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDB1 Gene



SOURCE GeneReport for Unigene cluster for DDB1 Gene Hs.290758

genes like me logo Genes that share expression patterns with DDB1: view

Protein tissue co-expression partners for DDB1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for DDB1 Gene

Orthologs for DDB1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDB1 35
  • 99.66 (n)
  • 99.82 (a)
DDB1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DDB1 36
  • 100 (a)
OneToOne
DDB1 35
  • 92.31 (n)
  • 99.74 (a)
dog
(Canis familiaris)
Mammalia DDB1 35
  • 92.43 (n)
  • 99.91 (a)
DDB1 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddb1 36
  • 100 (a)
OneToOne
Ddb1 16
Ddb1 35
  • 90.7 (n)
  • 99.65 (a)
oppossum
(Monodelphis domestica)
Mammalia DDB1 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDB1 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ddb1 35
  • 90.41 (n)
  • 99.74 (a)
chicken
(Gallus gallus)
Aves DDB1 36
  • 97 (a)
OneToOne
DDB1 35
  • 83.77 (n)
  • 97.11 (a)
lizard
(Anolis carolinensis)
Reptilia DDB1 36
  • 97 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia MGC68476 35
tropical clawed frog
(Silurana tropicalis)
Amphibia ddb1 35
  • 77.46 (n)
  • 93.25 (a)
Str.4452 35
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.752 35
zebrafish
(Danio rerio)
Actinopterygii ddb1 36
  • 92 (a)
OneToMany
ddb1 36
  • 92 (a)
OneToMany
ddb1 35
  • 78.37 (n)
  • 90.64 (a)
zgc63840 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002472 35
  • 64.06 (n)
  • 66.23 (a)
fruit fly
(Drosophila melanogaster)
Insecta DDB1 37
  • 60 (a)
pic 36
  • 60 (a)
OneToOne
pic 35
  • 60.42 (n)
  • 61.27 (a)
worm
(Caenorhabditis elegans)
Secernentea M18.5 37
  • 37 (a)
ddb-1 36
  • 37 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RSE1 36
  • 14 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons DDB1A 35
  • 55.67 (n)
  • 55.89 (a)
barley
(Hordeum vulgare)
Liliopsida Hv.5462 35
rice
(Oryza sativa)
Liliopsida Os.419 35
Os05g0592400 35
  • 56.98 (n)
  • 56.39 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.14606 35
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8274 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 60 (a)
OneToOne
Species with no ortholog for DDB1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for DDB1 Gene

ENSEMBL:
Gene Tree for DDB1 (if available)
TreeFam:
Gene Tree for DDB1 (if available)

Paralogs for DDB1 Gene

Paralogs for DDB1 Gene

genes like me logo Genes that share paralogs with DDB1: view

Variants for DDB1 Gene

Sequence variations from dbSNP and Humsavar for DDB1 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs28720299 - 61,316,514(-) TGGTG(C/T)TCTCT reference, missense
rs1053908 -- 61,310,329(-) GTGCA(C/T)AACCT reference, synonymous-codon
rs2230357 -- 61,313,669(-) GGCAC(C/T)CAGCC reference, synonymous-codon
rs2230358 -- 61,309,037(-) GGGGC(C/T)GTGTA reference, synonymous-codon
rs3815103 -- 61,323,871(+) TGTTG(A/T)TAGGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DDB1 Gene

Variant ID Type Subtype PubMed ID
nsv428259 CNV Gain+Loss 18775914
dgv390e1 CNV Complex 17122850
nsv832177 CNV Loss 17160897
nsv509415 CNV Insertion 20534489

Variation tolerance for DDB1 Gene

Residual Variation Intolerance Score: 1.33% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.70; 14.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DDB1 Gene

HapMap Linkage Disequilibrium report
DDB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDB1 Gene

Disorders for DDB1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for DDB1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hepatitis b
  • chronic hepatitis b
xeroderma pigmentosum, group e, ddb-negative subtype
  • xeroderma pigmentosum, type 5
cockayne syndrome
  • cockayne's syndrome
best vitelliform macular dystrophy
  • vitelliform macular dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search DDB1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for DDB1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DDB1
genes like me logo Genes that share disorders with DDB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDB1 Gene

Publications for DDB1 Gene

  1. Chromosomal localization and cDNA cloning of the genes (DDB1 and DDB2) for the p127 and p48 subunits of a human damage-specific DNA binding protein. (PMID: 8530102) Dualan R. … Linn S. (Genomics 1995) 2 3 4 67
  2. Identification of a primary target of thalidomide teratogenicity. (PMID: 20223979) Ito T. … Handa H. (Science 2010) 3 23
  3. Damaged DNA-binding protein 1 (DDB1) interacts with Cdh1 and modulates the function of APC/CCdh1. (PMID: 20395298) Lv X.B. … Kang T. (J. Biol. Chem. 2010) 3 23
  4. DDB1-CUL4 and MLL1 mediate oncogene-induced p16INK4a activation. (PMID: 19208841) Kotake Y. … Xiong Y. (Cancer Res. 2009) 3 23
  5. DDB1 targets Chk1 to the Cul4 E3 ligase complex in normal cycling cells and in cells experiencing replication stress. (PMID: 19276361) Leung-Pineda V. … Piwnica-Worms H. (Cancer Res. 2009) 3 23

Products for DDB1 Gene

Sources for DDB1 Gene

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