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Aliases for DDB1 Gene

Aliases for DDB1 Gene

  • Damage-Specific DNA Binding Protein 1, 127kDa 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 4
  • DNA Damage-Binding Protein 1 3
  • UV-DDB1 3
  • XPE 3

External Ids for DDB1 Gene

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, 127kDa) is a Protein Coding gene. Diseases associated with DDB1 include vitelliform macular dystrophy. Among its related pathways are Protein Stability and Cell Cycle / Checkpoint Control. GO annotations related to this gene include 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

Genomic Location for DDB1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDB1 Gene

Regulatory Elements 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.
  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys92, Lys141, Lys153, Lys191, Lys298, Lys383, Lys408, Lys484, Lys570, Lys579, Lys723, Lys823, Lys857, Lys897, Lys917, Lys936, Lys1067, Lys1081, Lys1121, and Lys1131

No data available for DME Specific Peptides for DDB1 Gene

Domains for DDB1 Gene

Graphical View of Domain Structure for InterPro Entry

Q16531

UniProtKB/Swiss-Prot:

DDB1_HUMAN
Domain:
  • The core of the protein consists of three WD40 beta-propeller domains.:
    • Q16531
Family:
  • Belongs to the DDB1 family.:
    • Q16531
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.

Gene Ontology (GO) - Molecular Function for DDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0003677 DNA binding TAS 8798680
GO:0003684 contributes_to damaged DNA binding IDA 22334663
GO:0003824 catalytic activity --
GO:0005515 protein binding IPI 12732143
genes like me logo Genes that share ontologies with DDB1: view
genes like me logo Genes that share phenotypes with DDB1: view

Animal Models for DDB1 Gene

MGI Knock Outs for DDB1:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting 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
nucleus 5
cytosol 2
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for DDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005615 extracellular space IDA 22664934
GO:0005634 nucleus IDA 18593899
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA 18593899
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex IDA 12732143
genes like me logo Genes that share ontologies with DDB1: view

Pathways 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.

Gene Ontology (GO) - Biological Process for DDB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000718 nucleotide-excision repair, DNA damage removal TAS --
GO:0006281 DNA repair TAS --
GO:0006289 nucleotide-excision repair TAS --
GO:0016032 viral process IEA --
GO:0016055 Wnt signaling pathway IEA --
genes like me logo Genes that share ontologies with DDB1: view

Compounds for DDB1 Gene

(1) HMDB Compounds for DDB1 Gene

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

(3) Novoseek inferred chemical compound relationships for DDB1 Gene

Compound -log(P) Hits PubMed IDs
cisplatin 18.8 5
zinc 0 1
cysteine 0 2
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:

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

Integrated Proteomics: protein expression 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 expressions with DDB1: view

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 35
  • 92.31 (n)
  • 99.74 (a)
DDB1 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDB1 35
  • 92.43 (n)
  • 99.91 (a)
DDB1 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddb1 35
  • 90.7 (n)
  • 99.65 (a)
Ddb1 16
Ddb1 36
  • 100 (a)
OneToOne
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 35
  • 83.77 (n)
  • 97.11 (a)
DDB1 36
  • 97 (a)
OneToOne
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 35
  • 78.37 (n)
  • 90.64 (a)
ddb1 36
  • 92 (a)
OneToMany
ddb1 36
  • 92 (a)
OneToMany
zgc63840 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002472 35
  • 64.06 (n)
  • 66.23 (a)
fruit fly
(Drosophila melanogaster)
Insecta pic 35
  • 60.42 (n)
  • 61.27 (a)
pic 36
  • 60 (a)
OneToOne
DDB1 37
  • 60 (a)
worm
(Caenorhabditis elegans)
Secernentea ddb-1 36
  • 37 (a)
OneToOne
M18.5 37
  • 37 (a)
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 MAF
rs1053100 -- 61,310,334(-) TGGAG(A/G)TGCAC reference, missense
rs1053908 -- 61,310,329(-) GTGCA(C/T)AACCT reference, synonymous-codon
rs1132797 -- 61,299,782(-) TGTGT(A/G)TGTGT utr-variant-3-prime
rs1132827 -- 61,299,707(-) GGGAA(A/G)AGGGT utr-variant-3-prime
rs1132943 -- 61,299,557(-) ACGCC(A/C)CAGCC utr-variant-3-prime

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

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

(3) University of Copenhagen DISEASES for DDB1 Gene

(7) Novoseek inferred disease relationships for DDB1 Gene

Disease -log(P) Hits PubMed IDs
xeroderma pigmentosum, complementation group e 95.4 4
xeroderma pigmentosum 87 6
macular dystrophy, vitelliform 63.9 1
parainfluenza 44.8 1
hepatitis b 22.6 3
genes like me logo Genes that share disorders with DDB1: view

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

Publications for DDB1 Gene

  1. Hepatitis B virus X protein interacts with a probable cellular DNA repair protein. (PMID: 7815490) Lee T.H. … Butel J.S. (J. Virol. 1995) 3 4 23
  2. Isolation of a cDNA encoding a UV-damaged DNA binding factor defective in xeroderma pigmentosum group E cells. (PMID: 8538642) Hwang B.J. … Chu G. (Mutat. Res. 1996) 3 4 23
  3. The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage. (PMID: 12732143) Groisman R. … Nakatani Y. (Cell 2003) 3 4 23
  4. Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. (PMID: 14739464) Wertz I.E. … Dixit V.M. (Science 2004) 3 4 23
  5. Targeted ubiquitination of CDT1 by the DDB1-CUL4A-ROC1 ligase in response to DNA damage. (PMID: 15448697) Hu J. … Xiong Y. (Nat. Cell Biol. 2004) 3 4 23

Products for DDB1 Gene

  • Addgene plasmids for DDB1

Sources for DDB1 Gene

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