Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0006394
UniProt IDP49005
Primary gene name(s)POLD2
Synonym gene name(s)unknown
Protein nameDNA polymerase delta subunit 2
Protein functionAs a component of the trimeric and tetrameric DNA polymerase delta complexes, Pol-delta3 and Pol-delta4, respectively, plays a role in high fidelity genome replication, including in lagging strand synthesis, and repair, PubMed:12403614, PubMed:16510448, PubMed:19074196, PubMed:20334433, PubMed:24035200. Pol-delta3 and Pol-delta4 are characterized by the absence or the presence of POLD4. They exhibit differences in catalytic activity. Most notably, Pol-delta3 shows higher proofreading activity than Pol-delta4, PubMed:19074196, PubMed:20334433. Although both Pol-delta3 and Pol-delta4 process Okazaki fragments in vitro, Pol-delta3 may also be better suited to fulfill this task, exhibiting near-absence of strand displacement activity compared to Pol-delta4 and stalling on encounter with the 5'-blocking oligonucleotides. Pol-delta3 idling process may avoid the formation of a gap, while maintaining a nick that can be readily ligated, PubMed:24035200. Along with DNA polymerase kappa, DNA polymerase delta carries out approximately half of nucleotide excision repair, NER synthesis following UV irradiation, PubMed:20227374. Under conditions of DNA replication stress, required for the repair of broken replication forks through break-induced replication, BIR, PubMed:24310611. Involved in the translesion synthesis, TLS of templates carrying O6-methylguanine or abasic sites performed by Pol-delta4, independently of DNA polymerase zeta, REV3L or eta, POLH. Facilitates abasic site bypass by DNA polymerase delta by promoting extension from the nucleotide inserted opposite the lesion. Also involved in TLS as a component of the POLZ complex. Along with POLD3, dramatically increases the efficiency and processivity of DNA synthesis of the minimal DNA polymerase zeta complex, consisting of only REV3L and REV7, PubMed:24449906. {ECO:0000269|PubMed:12403614, ECO:0000269|PubMed:16510448, ECO:0000269|PubMed:19074196, ECO:0000269|PubMed:20227374, ECO:0000269|PubMed:20334433, ECO:0000269|PubMed:24035200, ECO:0000269|PubMed:24310611, ECO:0000269|PubMed:24449906}.
Subcellular locationNucleus {ECO:0000269|PubMed:22801543}. Note=Recruited to DNA damage sites within 2 hours following UV irradiation. {ECO:0000269|PubMed:22801543}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P49005
Gene Ontology
(Biological Process)
Complete annatation
DNA damage response, detection of DNA damage [GO:0042769];
DNA replication [GO:0006260];
DNA strand elongation involved in DNA replication [GO:0006271];
mismatch repair [GO:0006298];
nucleotide-excision repair, DNA gap filling [GO:0006297];
nucleotide-excision repair, DNA incision [GO:0033683];
nucleotide-excision repair, DNA incision, 5'-to lesion [GO:0006296];
telomere maintenance [GO:0000723];
telomere maintenance via recombination [GO:0000722];
transcription-coupled nucleotide-excision repair [GO:0006283];
translesion synthesis [GO:0019985]
Gene Ontology
(Molecular Function)
Complete annatation
DNA binding [GO:0003677];
DNA-directed DNA polymerase activity [GO:0003887]
Gene Ontology
(Cellular Component)
Complete annatation
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction111421
Phylogenetic treeP49005
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. CD32.047448906248521.73776226741751e-092.38105026313788e-08
AZA vs. DISU-0.6492329155959620.01452857150130430.294870316543206
AZA vs. IL70.4581742822241510.01782228850719790.436597117879048
AZA vs. SAHA-0.09712450914739470.6920877762073570.912333287149077
DISU vs. CD3-2.708723773907052.193245585147e-127.44616755642023e-11
DISU vs. IL71.097989551300081.80274249568235e-050.00137950980316809
DISU vs. SAHA0.554269940573310.06031308805172620.309811443512653
DMSO vs. AZA0.1291025707803410.4443172321131511
DMSO vs. CD3-1.932249468385435.50246004316080e-096.19078122107673e-08
DMSO vs. DISU0.7758273091279460.001688927538243350.0834496327912368
DMSO vs. IL70.3368678557331110.06215424403271130.477974995702589
DMSO vs. SAHA-0.2307419500370980.3293618415696460.683438291931177
HIV vs. Mock in Activation0.003085584771988190.9960502654739710.999983755607037
HIV vs. Mock in Latency-0.1220534890651080.4646308276136030.999834320637052
IL7 vs. CD3-1.583007914338121.51541658810483e-061.42494536696844e-05
SAHA vs. CD3-2.167531654710234.61959714925797e-096.61761682883247e-08
SAHA vs. IL7-0.5573618925806470.02282888361616920.109593182047814
(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) unknown
(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 0.378109 0.00551063
(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
1.006 1.034 0.941 0.732 0.893
(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

PDB Accession Method Resolution Chain Structure Preview
3E0J X-ray 3.0Å A/C/E/G=1-469.

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
hsa00230 Purine metabolism - Homo sapiens (human)
hsa00240 Pyrimidine metabolism - Homo sapiens (human)
hsa01100 Metabolic pathways - Homo sapiens (human)
hsa03030 DNA replication - Homo sapiens (human)
hsa03410 Base excision repair - Homo sapiens (human)
hsa03420 Nucleotide excision repair - Homo sapiens (human)
hsa03430 Mismatch repair - Homo sapiens (human)
hsa03440 Homologous recombination - Homo sapiens (human)
hsa05166 HTLV-I infection - Homo sapiens (human)
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