Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0000119
UniProt IDQ9UBZ4
Primary gene name(s)APEX2
Synonym gene name(s)APE2, APEXL2, XTH2
Protein nameDNA-(apurinic or apyrimidinic site lyase 2
Protein functionFunction as a weak apurinic/apyrimidinic, AP endodeoxyribonuclease in the DNA base excision repair, BER pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Displays also double-stranded DNA 3'-5' exonuclease, 3'-phosphodiesterase activities. Shows robust 3'-5' exonuclease activity on 3'-recessed heteroduplex DNA and is able to remove mismatched nucleotides preferentially. Shows fairly strong 3'-phosphodiesterase activity involved in the removal of 3'-damaged termini formed in DNA by oxidative agents. In the nucleus functions in the PCNA-dependent BER pathway. Required for somatic hypermutation, SHM and DNA cleavage step of class switch recombination, CSR of immunoglobulin genes. Required for proper cell cycle progression during proliferation of peripheral lymphocytes. {ECO:0000269|PubMed:11376153, ECO:0000269|PubMed:16687656, ECO:0000269|PubMed:19443450}.
Subcellular locationNucleus. Cytoplasm. Mitochondrion {ECO:0000305}. Note=Together with PCNA, is redistributed in discrete nuclear foci in presence of oxidative DNA damaging agents.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q9UBZ4
Gene Ontology
(Biological Process)
Complete annatation
base-excision repair [GO:0006284];
cell cycle [GO:0007049];
DNA recombination [GO:0006310]
Gene Ontology
(Molecular Function)
Complete annatation
DNA-(apurinic or apyrimidinic site lyase activity [GO:0003906];
DNA binding [GO:0003677];
double-stranded DNA 3'-5' exodeoxyribonuclease activity [GO:0008311];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
intracellular membrane-bounded organelle [GO:0043231];
mitochondrion [GO:0005739];
nucleolus [GO:0005730];
nucleus [GO:0005634]
Protein-protein interaction118124
Phylogenetic treeQ9UBZ4
HIV replication factor status Zhou et al., Cell. Host. Microbe., 2008
Brass et al., Science, 2008
Smith et al., J. Immunol, 2010
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. CD30.4619266125517360.1614792578800750.257901385479335
AZA vs. DISU-0.2910055710492520.2533570287238150.834412027743672
AZA vs. IL7-0.09274373968624410.6514515880222370.999311006273513
AZA vs. SAHA-0.04746297146927990.8466681983282440.963550011990275
DISU vs. CD3-0.7651448485290540.03744752712150010.0856316783721925
DISU vs. IL70.1882104355058030.4584006305745720.800985500845827
DISU vs. SAHA0.2466273792501990.3996668722164020.760071021924645
DMSO vs. AZA0.05882391281556150.7497928541908881
DMSO vs. CD3-0.414083126867390.1982021175360350.297105960266703
DMSO vs. DISU0.348195906985440.1565904818502240.660089108107097
DMSO vs. IL7-0.1441557486210410.4277465877926950.856781521896319
DMSO vs. SAHA-0.1106238885363390.6408124120617540.884160382878577
HIV vs. Mock in Activation0.1167555239500210.8514597583352850.999983755607037
HIV vs. Mock in Latency0.1164672741402120.4890345525470920.999834320637052
IL7 vs. CD3-0.5502084246338220.08874125260526210.172704570757794
SAHA vs. CD3-0.5319316101982190.135349052118820.221876451150943
SAHA vs. IL70.04404004230144830.8573703075297080.94031369111162
(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 0.279153 0.0385494
(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
unknown unknown unknown unknown unknown
(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

not found

Protein Secondary Structure       (annotations from PDB)      top

not found

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

not found

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03410 Base excision repair - Homo sapiens (human)