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DDB1 damage specific DNA binding protein 1 [ Homo sapiens (human) ]

Gene ID: 1642, updated on 5-Jul-2020

Summary

Official Symbol
DDB1provided by HGNC
Official Full Name
damage specific DNA binding protein 1provided by HGNC
Primary source
HGNC:HGNC:2717
See related
Ensembl:ENSG00000167986 MIM:600045
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; DDBA; XAP1; XPCE; XPE-BF; UV-DDB1
Summary
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]
Expression
Ubiquitous expression in adrenal (RPKM 89.2), placenta (RPKM 76.1) and 25 other tissues See more
Orthologs

Genomic context

See DDB1 in Genome Data Viewer
Location:
11q12.2
Exon count:
27
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (61299451..61333105, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61066919..61100691, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene pepsinogen A5 Neighboring gene von Willebrand factor C and EGF domains Neighboring gene triokinase and FMN cyclase Neighboring gene cytochrome b561 family member A3 Neighboring gene transmembrane protein 138

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, DNA damage-binding protein 1 (DDB1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with DDB1 is increased by RRE PubMed
Vif vif HIV-1 Vif interacts with DDB1; interaction predicted to be relevant to proteolysis PubMed
Vpr vpr DDB1-specific shRNA silencing demonstrates that DDB1 enhances TNF-alpha secretion from wild type HIV-1(NL43) infected AND delta-vpr HIV-infected MT4C5 cells suggesting that DDB1 enhances TNF-alpha release from HIV-1-infected cells independently of Vpr PubMed
vpr HIV-1 Vpr binds a ternary complex composed of DDB1, DDA1, and VprBP, and modulates the interaction between the DDB1-DDA1-VprBP complex and other factors PubMed
vpr Upregulation of NKG2D ligands is dependent on HIV-1 Vpr-mediated activation of the TAR DNA damage/stress pathway, which requires the recruitment of the Cul4/DDB1/DCAF1 E3 ubiquitin ligase complex PubMed
vpr HIV-1 Vpr-mediated UNG2 degradation and constitutive UNG2 turnover are dependent on DCAF1 or DDB1 but not on CUL4a or CUL4B in the cullin4 (CUL4)-containing ubiquitin ligase complex in HEK293T cells PubMed
vpr The minimal domain (residues 1041-1393) of DCAF1, which contains the motifs required for proper recruitment of both Vpr and DDB1, is not sufficient to support Vpr-mediated G2 arrest activity PubMed
vpr The two WD-40 motifs (residues 1041-1393) in the C-terminal region of DCAF1 form a complex with HIV-1 Vpr and DDB1. The double mutant DCAF1 R1247/1283A completely abolishes its ability to bind both Vpr and DDB1 PubMed
vpr Co-immunoprecipitation and glycerol-gradient sedimentation demonstrate that HIV-1 Vpr, VPRBP, DDB1, SLX4, MUS81, EME1, ERCC1, and ERCC4 form a complex PubMed
vpr Mutation of Trp18, Gln65, and His71 residues in HIV-1 Vpr abrogates DDB1-DCAF1 binding and Vpr-induced cell cycle arrest PubMed
vpr The interaction of Vpr with DDB1 facilitates the formation of complexes containing Cul4A-Roc1 E3 ubiquitin ligase. The association of Vpr with DDB1-containing E3 ligase mediates the degradation of UNG2 and SMUG1 PubMed
vpr The interaction between Vpr and the Cul4A-DDB1-VprBP complex is required for the induction of G2 arrest PubMed
vpr HIV-1 Vpr-induced downregulation of Dicer is not dependent on G2 cell cycle arrest but on the Cul4A-DCAF1-DDB1 ubiquitin ligase complex PubMed
vpr HIV-1 Vpr-mediated upregulation of PVR (CD155) requires the interaction of Vpr with the DDB1-Cul4A E3 ligase and induction of ATR-mediated DNA damage repair and G2 arrest PubMed
vpr The interaction of HIV-1 Vpr with the EDVP E3 ligase complex (EDD, DDB1, and VPRBP) promotes Vpr-mediated downregulation of TERT protein PubMed
vpr HIV-1 Vpr co-localizes with the Cul4A ubiquitin ligase complex (Cul4A, DCAF1, and DDB1) in the cellular chromatin compartment PubMed
vpr HIV-1 Vpr significantly downregulates expression level of MFN2 in the mitochondria via VprBP-DDB1-CUL4A ubiquitin ligase in a proteasome-dependent manner PubMed
vpr HIV-1 Vpr binds the Cul4A-DDB1-VprBP complex and increases the levels of neddylated Cul4A in that complex only PubMed
vpr DDB1 overexpression enables G2 cell cycle arrest by both HIV-1 Vpr and its carboxy-terminally truncated form C81 PubMed
vpr HIV-1 Vpr(Q65R) mutant, which is defective in Cul4A-DDB1 (DCAF1) binding, undergoes proteasome-mediated degradation at a higher rate than wild-type Vpr. DCAF1 overexpression stabilizes wild-type Vpr and leads to its cytoplasmic accumulation PubMed
vpr DCAF1 interacts with DDB1 as well as the Vpr-UNG2 complex, which leads to polyubiquitination of UNG2 via Vpr PubMed
vpr HIV-1 Vpr interferes with the interaction of DDB1 and DDB2 in cells PubMed
vpr HIV-1 Vpr interacts with damage-specific DNA-binding protein 1 (DDB1) in cells. L64P mutation in DDB1 fails to interact efficiently with Vpr 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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding TAS
Traceable Author Statement
more info
PubMed 
WD40-repeat domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
cullin family protein binding IPI
Inferred from Physical Interaction
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 binding, bridging IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA damage response, detection of DNA damage TAS
Traceable Author Statement
more info
 
DNA repair TAS
Traceable Author Statement
more info
PubMed 
UV-damage excision repair IDA
Inferred from Direct Assay
more info
PubMed 
Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
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 
interaction with symbiont IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
nucleotide-excision repair IBA
Inferred from Biological aspect of Ancestor
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
 
positive regulation by virus of viral protein levels in host cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gluconeogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of viral genome replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of viral release from host cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-translational protein modification TAS
Traceable Author Statement
more info
 
proteasomal protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of circadian rhythm IEA
Inferred from Electronic Annotation
more info
 
regulation of mitotic cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-dependent protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Cul4-RING E3 ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 
Cul4-RING E3 ubiquitin ligase complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
Cul4A-RING E3 ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 
Cul4B-RING E3 ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 
cullin-RING ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
extracellular space HDA PubMed 
nuclear chromosome, telomeric region HDA PubMed 
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 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
DNA damage-binding protein 1
Names
DDB p127 subunit
DNA damage-binding protein a
HBV X-associated protein 1
UV-DDB 1
UV-damaged DNA-binding factor
UV-damaged DNA-binding protein 1
XAP-1
XPE-binding factor
damage-specific DNA binding protein 1, 127kDa
xeroderma pigmentosum group E-complementing 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_032697.2 RefSeqGene

    Range
    14385..48150
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_474

mRNA and Protein(s)

  1. NM_001923.5NP_001914.3  DNA damage-binding protein 1

    See identical proteins and their annotated locations for NP_001914.3

    Status: REVIEWED

    Source sequence(s)
    AA665872, BC050530
    Consensus CDS
    CCDS31576.1
    UniProtKB/Swiss-Prot
    Q16531
    Related
    ENSP00000301764.7, ENST00000301764.12
    Conserved Domains (2) summary
    pfam03178
    Location:7911099
    CPSF_A; CPSF A subunit region
    pfam10433
    Location:75543
    MMS1_N; Mono-functional DNA-alkylating methyl methanesulfonate N-term

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
    61299451..61333105 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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