Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000765
UniProt IDQ92466
Primary gene name(s)DDB2
Synonym gene name(s)unknown
Protein nameDNA damage-binding protein 2
Protein functionRequired 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. {ECO:0000269|PubMed:10882109, ECO:0000269|PubMed:11278856, ECO:0000269|PubMed:11705987, ECO:0000269|PubMed:12732143, ECO:0000269|PubMed:12944386, ECO:0000269|PubMed:14751237, ECO:0000269|PubMed:15882621, ECO:0000269|PubMed:16260596, ECO:0000269|PubMed:16473935, ECO:0000269|PubMed:16678110, ECO:0000269|PubMed:18593899, ECO:0000269|PubMed:9892649}.
Subcellular locationNucleus {ECO:0000269|PubMed:10777490, ECO:0000269|PubMed:10777491, ECO:0000269|PubMed:11705987, ECO:0000269|PubMed:12944386, ECO:0000269|PubMed:14751237, ECO:0000269|PubMed:16473935, ECO:0000269|PubMed:16713579, ECO:0000269|PubMed:17635991, ECO:0000269|PubMed:18593899}. Note=Accumulates at sites of DNA damage following UV irradiation.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92466
Gene Ontology
(Biological Process)
Complete annatation
DNA repair [GO:0006281];
global genome nucleotide-excision repair [GO:0070911];
histone H2A monoubiquitination [GO:0035518];
nucleotide-excision repair [GO:0006289];
nucleotide-excision repair, DNA damage recognition [GO:0000715];
nucleotide-excision repair, DNA duplex unwinding [GO:0000717];
nucleotide-excision repair, DNA incision [GO:0033683];
nucleotide-excision repair, DNA incision, 3'-to lesion [GO:0006295];
nucleotide-excision repair, DNA incision, 5'-to lesion [GO:0006296];
nucleotide-excision repair, preincision complex assembly [GO:0006294];
nucleotide-excision repair, preincision complex stabilization [GO:0006293];
protein autoubiquitination [GO:0051865];
protein polyubiquitination [GO:0000209];
pyrimidine dimer repair [GO:0006290];
response to UV [GO:0009411];
UV-damage excision repair [GO:0070914]
Gene Ontology
(Molecular Function)
Complete annatation
damaged DNA binding [GO:0003684];
DNA binding [GO:0003677]
Gene Ontology
(Cellular Component)
Complete annatation
cell junction [GO:0030054];
Cul4B-RING E3 ubiquitin ligase complex [GO:0031465];
nucleoplasm [GO:0005654];
protein complex [GO:0043234]
Protein-protein interaction108010
Phylogenetic treeQ92466
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
      unknown
Brass et al., Science, 2008
      unknown
Smith et al., J. Immunol, 2010
      unknown
Interferon-stimulated
gene status
Lu et al., J. Virol., 2011
      Folds changes 8h: unknown; Folds changes 16h: unknown; Tested: unknown;
Schoggins JW and Rice CM, Curr. Opin. Virol., 2011
      Targeted viruses: unknown
      Viral life cycle: unknown
      Mechanism related to antiviral activity: unknown
Anti-viral restriction factor Liu et al., Retrovirology, 2011
      unknown (Triplicates)

Gene Expression Profile       top

            Up-regulated;            Down-regulated

For brief introduction to each study, please go to the help page.

Gene expression during HIV latency

(1). Mohammadi et al., PLoS Pathog., 2014

Differentially expressed transcripts (Pairwise) during latency and subsequent viral reactivation using several agents - Primary CD4+ T-cell based model


DMSO: Dimethyl suloxyde (negative control) - 0.0033% final
SAHA: Vorinostat (Histone deacetylase inhibitor) - 0.5 μM
CD3: TCR Stimulation by IL-2+ antiCD3/anti-CD28 antibodies
IL7: Interleukin-7 based stimulation
DISU: Disulfiram (alcohol dehydrogenase inhibitor) - 0.5 μM
AZA: 5-azacytidine (AZA; DNA methylation inhibitor) - 1 μM
Experimental Condition Log2 Fold Change P value Adjusted P value
AZA vs. CD3-0.2075613302078760.5786877184482040.686391854289079
AZA vs. DISU0.04393833000926810.8620526093616580.991133096247651
AZA vs. IL7-0.212860498889760.2697373610332110.999311006273513
AZA vs. SAHA-0.8521744329500330.001725279511179510.0300657379786358
DISU vs. CD30.2380659988910420.5192005913222110.641852308502487
DISU vs. IL7-0.26609760461180.2923184046446130.677686348192229
DISU vs. SAHA-0.8939043841483950.00253833132694770.0403110552459734
DMSO vs. AZA-0.3410400373389140.04246548775165861
DMSO vs. CD3-0.1467671538307740.6909795886014370.772455291056741
DMSO vs. DISU-0.387188900318920.1130408800824150.589659419467634
DMSO vs. IL70.1354394634144490.4537972406506470.870758796926069
DMSO vs. SAHA-0.5165315161042920.04683416668741240.242973399706021
HIV vs. Mock in Activation-0.2143789077220390.7996532216018590.999983755607037
HIV vs. Mock in Latency-0.03837656482322550.8168038161546670.999834320637052
IL7 vs. CD30.001717026864705090.9965723648034540.997763882742109
SAHA vs. CD3-0.6691588280644250.1290210813058810.213758541697408
SAHA vs. IL7-0.6420676696371430.03439284623388190.142702384841601
(2). Iglesias-Ussel et al., J. Virol., 2013

Up and Downregulated transcripts during Latency (Latently infected CD4+ T cells vs Uninfected)- Primary CD4+Tcell based model
Log2 Fold Change P Value
0.631 0.02996

Gene expression during HIV infection and replication

(1). Imbeault et al., PloS Pathog., 2012

Transcriptomic profiling of HIV-1 infected CD4+ T cells - Primary CD4+ T cells
Experiment type Log2 Fold Change P Value Adjusted P Value
Infected vs. Mock unknown unknown unknown
Infected vs. Bystander unknown unknown unknown
(2). Lefebvre et al., J. Virol., 2011

Transcriptome analysis of T-cell line (Sup T1)
Log2 Fold Change unknown
(3). Li et al., J. Immunol., 2013

Lymphatic tissue
Acute Fold Change Acute P Value Asymt Fold Change Asypt P Value AIDS Fold Change AIDS P Value
unknown unknown unknown unknown unknown unknown
(4). Chang et al., MBio., 2011

Transcriptome analysis of T-cell line (Sup T1)

Derived from Sherrill-Mix et al., BMC Retrovirol., 2015 cross validation
Up-regulated (True) TRUE
(5). Sherrill-Mix et al., BMC Retrovirol., 2015

Deep RNA-seq analysis of primary human T cell infected with low passage HIV isolate HIV89.6 - Primary CD4+ T cell based
Test Status Log2 Fold Change P Value
OK 0.253147 0.0774612
(6). Rotger et al., PLoS Pathog., 2010

Genome-wide mRNA expression of CD4+ T cells from HIV-infected patient
(Genes differentially expressed (at adjusted p<0.01) according to the empirical Bayes approach)
Log2 Fold Change P Value
unknown unknown

Proteomic/Transcriptomics studies indicating differentially expressed genes mediated by HIV

(1). Greenwood et al., Elife, 2016

Activated (CD3/CD28) Primary human CD4+ T cells infected with pNL4-3-dE-EGFP. The table shows the complete (unfiltered) TMT (tandem mass tag)-based proteomic time course dataset
6 h 24 h 48 h 72 h RTi
1.116 0.972 1.106 1.062 0.808
(2). Navare et al., Virology, 2012

SUP-T1 cell line
FC-4hpi P-value FC-8hpi P-value FC-20hpi P-value Category
unknown unknown unknown unknown unknown unknown unknown
(3). Hyrcza et al., J. Virolo., 2007

Primary human CD4+ and CD8+ T Cells
Affymetrix Prob ID Fold Change In CD8? Category
203409_at 1.75 No upregulated in CD8+ cells

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

not found

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
3EI4 X-ray 3.3Å B/D/F=10-427.
3I7L X-ray 2.8Å B=68-81.
4E54 X-ray 2.8Å B=2-427.
4E5Z X-ray 3.2Å B=2-427.

HIV-1 Interaction       (annotations from NCBI HIV-1 Interaction Database)      top

HIV Partner Interaction Type PubMed
Vpr inhibits 17360488
17855541

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03420 Nucleotide excision repair - Homo sapiens (human)
hsa04115 p53 signaling pathway - Homo sapiens (human)
hsa04120 Ubiquitin mediated proteolysis - Homo sapiens (human)
hsa05161 Hepatitis B - Homo sapiens (human)
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