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

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; AllianceGenome:HGNC:2717
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; WHIKERS
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: mouse all
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Genomic context

Location:: 11q12.2

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (61299451..61333105, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (61288439..61322058, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (61066923..61100577, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hepatocyte-specific loss of DDB1 attenuates hepatic steatosis but aggravates liver inflammation and fibrosis in MASH.
Title: Hepatocyte-specific loss of DDB1 attenuates hepatic steatosis but aggravates liver inflammation and fibrosis in MASH.
DDB1 regulates the activation-induced apoptosis of T cells via downregulating the expression of histone methyltransferase SETD7.
Title: DDB1 regulates the activation-induced apoptosis of T cells via downregulating the expression of histone methyltransferase SETD7.
Insight into Viral Hijacking of CRL4 Ubiquitin Ligase through Structural Analysis of the pUL145-DDB1 Complex.
Title: Insight into Viral Hijacking of CRL4 Ubiquitin Ligase through Structural Analysis of the pUL145-DDB1 Complex.
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.
HBx represses WDR77 to enhance HBV replication by DDB1-mediated WDR77 degradation in the liver.
Title: HBx represses WDR77 to enhance HBV replication by DDB1-mediated WDR77 degradation in the liver.
Cul4A-DDB1-mediated monoubiquitination of phosphoglycerate dehydrogenase promotes colorectal cancer metastasis via increased S-adenosylmethionine.
Title: Cul4A-DDB1-mediated monoubiquitination of phosphoglycerate dehydrogenase promotes colorectal cancer metastasis via increased S-adenosylmethionine.
A DNA repair disorder caused by de novo monoallelic DDB1 variants is associated with a neurodevelopmental syndrome.
Title: A DNA repair disorder caused by de novo monoallelic DDB1 variants is associated with a neurodevelopmental syndrome.
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.
CUL4-DDB1-CRBN E3 Ubiquitin Ligase Regulates Proteostasis of ClC-2 Chloride Channels: Implication for Aldosteronism and Leukodystrophy.
Title: CUL4-DDB1-CRBN E3 Ubiquitin Ligase Regulates Proteostasis of ClC-2 Chloride Channels: Implication for Aldosteronism and Leukodystrophy.
Hepatitis B Virus HBx Protein Mediates the Degradation of Host Restriction Factors through the Cullin 4 DDB1 E3 Ubiquitin Ligase Complex.
Title: Hepatitis B Virus HBx Protein Mediates the Degradation of Host Restriction Factors through the Cullin 4 DDB1 E3 Ubiquitin Ligase Complex.

Submit: New GeneRIF Correction See all GeneRIFs (87)

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
White-Kernohan syndrome MedGen: C5543635 OMIM: 619426 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-81421 (e-PCR)
- UniSTS:103178

RH78281 (e-PCR)
- UniSTS:16919

D11S4371 (e-PCR)
- UniSTS:68946

D11S952E (e-PCR)
- UniSTS:147545

D11S952E (e-PCR)
- UniSTS:82265

RH11844 (e-PCR)
- UniSTS:82266

A002C24 (e-PCR)
- UniSTS:10090

MARC_15735-15736:1013528885:1 (e-PCR)
- UniSTS:267887

MARC_15735-15736:1032190398:5 (e-PCR)
- UniSTS:267887

G19976 (e-PCR)
- UniSTS:77472

MARC_21157-21158:1025280537:1 (e-PCR)
- UniSTS:268494

DDB1 (e-PCR), detects polymorphism
- UniSTS:48337

T03687 (e-PCR)
- UniSTS:24536

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables WD40-repeat domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables cullin family protein binding	IDA Inferred from Direct Assay more info	PubMed
enables 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
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin ligase complex scaffold 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	IMP Inferred from Mutant Phenotype 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 Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in biological process involved in interaction with symbiont	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 ectopic germ cell programmed cell death	IEA Inferred from Electronic Annotation more info
involved_in epigenetic programming in the zygotic pronuclei	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of developmental process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of reproductive process	IEA Inferred from Electronic Annotation more info
involved_in nucleotide-excision repair	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation by virus of viral protein levels in host cell	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gluconeogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of viral genome replication	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within proteasomal protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in regulation of mitotic cell cycle phase transition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in spindle assembly involved in female meiosis	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in viral release from host cell	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of Cul4-RING E3 ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed
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 Cul4A-RING E3 ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed
part_of Cul4B-RING E3 ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	HDA more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular space	HDA more info	PubMed
is_active_in nucleolus	IDA Inferred from Direct Assay 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
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in site of double-strand break	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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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)

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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.