Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001258
UniProt IDQ92769
Primary gene name(s)HDAC2
Synonym gene name(s)unknown
Protein nameHistone deacetylase 2
Protein functionResponsible for the deacetylation of lysine residues on the N-terminal part of the core histones, H2A, H2B, H3 and H4. Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Forms transcriptional repressor complexes by associating with MAD, SIN3, YY1 and N-COR. Interacts in the late S-phase of DNA-replication with DNMT1 in the other transcriptional repressor complex composed of DNMT1, DMAP1, PCNA, CAF1. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase, HDAC recruitment, a number of genes implicated in multilineage blood cell development. May be involved in the transcriptional repression of circadian target genes, such as PER1, mediated by CRY1 through histone deacetylation. Involved in MTA1-mediated transcriptional corepression of TFF1 and CDKN1A. {ECO:0000269|PubMed:19343227, ECO:0000269|PubMed:21965678}.
Subcellular locationNucleus {ECO:0000269|PubMed:24970816}. Cytoplasm {ECO:0000269|PubMed:24970816}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q92769
Gene Ontology
(Biological Process)
Complete annatation
ATP-dependent chromatin remodeling [GO:0043044];
behavioral response to ethanol [GO:0048149];
blood coagulation [GO:0007596];
cardiac muscle hypertrophy [GO:0003300];
cellular response to dopamine [GO:1903351];
cellular response to heat [GO:0034605];
cellular response to hydrogen peroxide [GO:0070301];
cellular response to retinoic acid [GO:0071300];
cellular response to transforming growth factor beta stimulus [GO:0071560];
chromatin remodeling [GO:0006338];
circadian regulation of gene expression [GO:0032922];
dendrite development [GO:0016358];
embryonic digit morphogenesis [GO:0042733];
epidermal cell differentiation [GO:0009913];
eyelid development in camera-type eye [GO:0061029];
fungiform papilla formation [GO:0061198];
hair follicle placode formation [GO:0060789];
histone deacetylation [GO:0016575];
histone H3 deacetylation [GO:0070932];
histone H4 deacetylation [GO:0070933];
maintenance of chromatin silencing [GO:0006344];
negative regulation of apoptotic process [GO:0043066];
negative regulation of dendritic spine development [GO:0061000];
negative regulation of DNA binding [GO:0043392];
negative regulation of MHC class II biosynthetic process [GO:0045347];
negative regulation of neuron projection development [GO:0010977];
negative regulation of peptidyl-lysine acetylation [GO:2000757];
negative regulation of sequence-specific DNA binding transcription factor activity [GO:0043433];
negative regulation of transcription, DNA-templated [GO:0045892];
negative regulation of transcription from RNA polymerase II promoter [GO:0000122];
odontogenesis of dentin-containing tooth [GO:0042475];
positive regulation of cell proliferation [GO:0008284];
positive regulation of collagen biosynthetic process [GO:0032967];
positive regulation of epithelial to mesenchymal transition [GO:0010718];
positive regulation of interleukin-1 production [GO:0032732];
positive regulation of oligodendrocyte differentiation [GO:0048714];
positive regulation of proteolysis [GO:0045862];
positive regulation of receptor biosynthetic process [GO:0010870];
positive regulation of transcription, DNA-templated [GO:0045893];
positive regulation of transcription from RNA polymerase II promoter [GO:0045944];
positive regulation of tumor necrosis factor production [GO:0032760];
positive regulation of tyrosine phosphorylation of Stat3 protein [GO:0042517];
regulation of signal transduction by p53 class mediator [GO:1901796];
response to amphetamine [GO:0001975];
response to caffeine [GO:0031000];
response to cocaine [GO:0042220];
response to drug [GO:0042493];
response to hyperoxia [GO:0055093];
response to lipopolysaccharide [GO:0032496];
response to nicotine [GO:0035094];
transcription, DNA-templated [GO:0006351]
Gene Ontology
(Molecular Function)
Complete annatation
chromatin binding [GO:0003682];
core promoter binding [GO:0001047];
deacetylase activity [GO:0019213];
enzyme binding [GO:0019899];
histone deacetylase activity [GO:0004407];
NAD-dependent histone deacetylase activity, H3-K14 specific [GO:0032041];
NF-kappaB binding [GO:0051059];
poly(A RNA binding [GO:0044822];
protein deacetylase activity [GO:0033558];
RNA polymerase II repressing transcription factor binding [GO:0001103];
sequence-specific DNA binding [GO:0043565];
transcription factor binding [GO:0008134]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
ESC/E(Z complex [GO:0035098];
nuclear chromatin [GO:0000790];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
NuRD complex [GO:0016581];
protein complex [GO:0043234];
Sin3 complex [GO:0016580]
Protein-protein interaction109316
Phylogenetic treeQ92769
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. CD31.540881457658894.06054200141615e-062.74441654911857e-05
AZA vs. DISU-0.172497442842330.4955024247828250.934608728211275
AZA vs. IL70.2833295722705150.1409520722039010.90605511616137
AZA vs. SAHA0.09034559553575330.7115632144545730.918972149307812
DISU vs. CD3-1.725540738055583.54308605077236e-062.95728012897799e-05
DISU vs. IL70.4471023526083540.07674067459615750.368137278547681
DISU vs. SAHA0.2628062564761220.3690906066286620.740391924996747
DMSO vs. AZA-0.1499103295446650.371721033684831
DMSO vs. CD3-1.7019139175862.15428495486947e-071.76403211452764e-06
DMSO vs. DISU0.02067374942620470.9325659800227540.991044421109467
DMSO vs. IL70.440594598366870.01447883663450230.252079537207989
DMSO vs. SAHA0.2324126746812070.3247196044129210.678194173795334
HIV vs. Mock in Activation-0.129103051448740.8354027445430840.999983755607037
HIV vs. Mock in Latency-0.1120332141456230.4979187243172360.999834320637052
IL7 vs. CD3-1.248326848920870.0001264199284001230.000715825537481239
SAHA vs. CD3-1.476396351899674.30261390799158e-050.000228472133873972
SAHA vs. IL7-0.1974559702829680.4177250277252160.661820548905035
(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
unknown unknown

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) FALSE
(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 0.0980452 0.580402
(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
0.953 1.036 0.928 0.945 1.018
(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
unknown unknown unknown unknown

Protein Overview       top

Drug-protein Interaction       (annotations from DrugBank)      top

Drugbank ID Drug Name Drug Status Pharmacological Action Drug Action
DB02546 Vorinostat approved, investigational yes inhibitor
DB05223 SB939 investigational unknown unknown
DB05651 MGCD-0103 investigational unknown unknown
DB00227 Lovastatin approved, investigational unknown other
DB01303 Oxtriphylline approved yes activator
DB00277 Theophylline approved yes activator
DB01223 Aminophylline approved yes activator
DB00313 Valproic Acid approved, investigational unknown unknown
DB06176 Romidepsin approved, investigational yes antagonist
DB05015 Belinostat approved, investigational yes inhibitor
DB06603 Panobinostat approved, investigational yes inhibitor

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
3MAX X-ray 2.0Å A/B/C=9-374.
4LXZ X-ray 1.8Å A/B/C=8-376.
4LY1 X-ray 1.5Å A/B/C=8-376.
5IWG X-ray 1.6Å A/B/C=8-375.
5IX0 X-ray 1.7Å A/B/C=7-375.

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

HIV Partner Interaction Type PubMed
Vpr cooperates with 19581932
Tat upregulates 21315782
Tat interacts with 19454010
20471948

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa04110 Cell cycle - Homo sapiens (human)
hsa04213 Longevity regulating pathway - multiple species - Homo sapiens (human)
hsa04330 Notch signaling pathway - Homo sapiens (human)
hsa04919 Thyroid hormone signaling pathway - Homo sapiens (human)
hsa05016 Huntington's disease - Homo sapiens (human)
hsa05034 Alcoholism - Homo sapiens (human)
hsa05169 Epstein-Barr virus infection - Homo sapiens (human)
hsa05200 Pathways in cancer - Homo sapiens (human)
hsa05202 Transcriptional misregulation in cancer - Homo sapiens (human)
hsa05203 Viral carcinogenesis - Homo sapiens (human)
hsa05220 Chronic myeloid leukemia - Homo sapiens (human)
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