Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0006392
UniProt IDP06746
Primary gene name(s)POLB
Synonym gene name(s)unknown
Protein nameDNA polymerase beta
Protein functionRepair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase, dRP lyase activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases. {ECO:0000269|PubMed:11805079, ECO:0000269|PubMed:21362556, ECO:0000269|PubMed:9207062, ECO:0000269|PubMed:9572863}.
Subcellular locationNucleus. Cytoplasm. Note=Cytoplasmic in normal conditions. Translocates to the nucleus following DNA damage.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P06746
Gene Ontology
(Biological Process)
Complete annatation
aging [GO:0007568];
base-excision repair [GO:0006284];
base-excision repair, base-free sugar-phosphate removal [GO:0006286];
base-excision repair, DNA ligation [GO:0006288];
base-excision repair, gap-filling [GO:0006287];
cellular response to DNA damage stimulus [GO:0006974];
DNA-dependent DNA replication [GO:0006261];
DNA repair [GO:0006281];
homeostasis of number of cells [GO:0048872];
immunoglobulin heavy chain V-D-J recombination [GO:0071707];
inflammatory response [GO:0006954];
intrinsic apoptotic signaling pathway in response to DNA damage [GO:0008630];
lymph node development [GO:0048535];
neuron apoptotic process [GO:0051402];
pyrimidine dimer repair [GO:0006290];
response to ethanol [GO:0045471];
response to gamma radiation [GO:0010332];
response to hyperoxia [GO:0055093];
salivary gland morphogenesis [GO:0007435];
somatic hypermutation of immunoglobulin genes [GO:0016446];
spleen development [GO:0048536]
Gene Ontology
(Molecular Function)
Complete annatation
damaged DNA binding [GO:0003684];
DNA-(apurinic or apyrimidinic site lyase activity [GO:0003906];
DNA-directed DNA polymerase activity [GO:0003887];
enzyme binding [GO:0019899];
lyase activity [GO:0016829];
metal ion binding [GO:0046872];
microtubule binding [GO:0008017]
Gene Ontology
(Cellular Component)
Complete annatation
cytoplasm [GO:0005737];
microtubule [GO:0005874];
nucleoplasm [GO:0005654];
nucleus [GO:0005634];
protein complex [GO:0043234];
spindle microtubule [GO:0005876]
Protein-protein interaction111419
Phylogenetic treeP06746
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
      Yes - >6 <7 SD (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. CD30.07746397220409360.8170868442425150.875711648753693
AZA vs. DISU0.1517694611243770.5534843665484440.947615666465684
AZA vs. IL7-0.001835040908835860.9925731007560070.999311006273513
AZA vs. SAHA0.3076935413766840.2178822455910620.585967791750363
DISU vs. CD30.06169043868670120.8677970721046390.910754930370071
DISU vs. IL7-0.1625694458442170.5236028951906260.839357044342693
DISU vs. SAHA0.157566910334420.594106867317640.869949460756231
DMSO vs. AZA-0.1027890388707170.5537881061794631
DMSO vs. CD3-0.1921751682815990.5579787647675370.660741242825259
DMSO vs. DISU-0.2564720551590990.2994733830693880.807887568985919
DMSO vs. IL70.1078673581503220.5594002717437020.901054298323369
DMSO vs. SAHA0.4043180284883770.09339905204565990.358754772286177
HIV vs. Mock in Activation-0.2326040522351710.7574531250972040.999983755607037
HIV vs. Mock in Latency-0.1284037253003280.449171374454180.999834320637052
IL7 vs. CD3-0.07043415546717380.8345371859318260.893179540491112
SAHA vs. CD30.2064629016500790.6072061366843710.703729637763091
SAHA vs. IL70.3070650110784920.2181477140384330.456589647516708
(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 -0.0883438 0.697954
(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
1.025 0.936 0.9 0.94 0.92
(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
DB00987 Cytarabine approved, investigational yes inhibitor
DB03222 2&,39;-Deoxyadenosine 5&,39;-Triphosphate experimental unknown unknown
DB07479 (1S)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL experimental unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1BPX X-ray 2.4Å A=1-335.
1BPY X-ray 2.2Å A=1-335.
1BPZ X-ray 2.6Å A=1-335.
1MQ2 X-ray 3.1Å A=1-335.
1MQ3 X-ray 2.8Å A=1-335.
1TV9 X-ray 2.0Å A=1-335.
1TVA X-ray 2.6Å A=1-335.
1ZJM X-ray 2.1Å A=1-335.
1ZJN X-ray 2.6Å A=1-335.
1ZQA X-ray 3.2Å A=1-335.
1ZQB X-ray 3.2Å A=1-335.
1ZQC X-ray 3.2Å A=1-335.
1ZQD X-ray 3.5Å A=1-335.
1ZQE X-ray 3.7Å A=1-335.
1ZQF X-ray 2.9Å A=1-335.
1ZQG X-ray 3.1Å A=1-335.
1ZQH X-ray 3.1Å A=1-335.
1ZQI X-ray 2.7Å A=1-335.
1ZQJ X-ray 3.3Å A=1-335.
1ZQK X-ray 3.2Å A=1-335.
1ZQL X-ray 3.3Å A=1-335.
1ZQM X-ray 3.2Å A=1-335.
1ZQN X-ray 3.0Å A=1-335.
1ZQO X-ray 3.2Å A=1-335.
1ZQP X-ray 2.8Å A=1-335.
1ZQQ X-ray 3.3Å A=1-335.
1ZQR X-ray 3.7Å A=1-335.
1ZQS X-ray 3.3Å A=1-335.
1ZQT X-ray 3.4Å A=1-335.
2FMP X-ray 1.6Å A=1-335.
2FMQ X-ray 2.2Å A=1-335.
2FMS X-ray 2.0Å A=1-335.
2I9G X-ray 2.1Å A=1-335.
2ISO X-ray 2.1Å A=1-335.
2ISP X-ray 2.2Å A=1-335.
2P66 X-ray 2.5Å A=1-335.
2PXI X-ray 2.1Å A=1-335.
3C2K X-ray 2.4Å A=1-335.
3C2L X-ray 2.6Å A=1-335.
3C2M X-ray 2.1Å A=1-335.
3GDX X-ray 2.2Å A=10-335.
3ISB X-ray 2.0Å A=1-335.
3ISC X-ray 2.0Å A=1-335.
3ISD X-ray 2.6Å A=1-335.
3JPN X-ray 2.1Å A=1-335.
3JPO X-ray 2.0Å A=1-335.
3JPP X-ray 2.1Å A=1-335.
3JPQ X-ray 1.9Å A=1-335.
3JPR X-ray 2.1Å A=1-335.
3JPS X-ray 2.0Å A=1-335.
3JPT X-ray 2.1Å A=1-335.
3LK9 X-ray 2.5Å A=1-335.
3MBY X-ray 2.0Å A=1-335.
3OGU X-ray 1.8Å A=1-335.
3RH4 X-ray 1.9Å A=1-335.
3RH5 X-ray 2.1Å A=1-335.
3RH6 X-ray 2.0Å A=1-335.
3RJE X-ray 2.1Å A=1-335.
3RJF X-ray 2.3Å A=1-335.
3RJG X-ray 2.0Å A=1-335.
3RJH X-ray 2.2Å A=1-335.
3RJI X-ray 2.3Å A=1-335.
3RJJ X-ray 2.0Å A=1-335.
3RJK X-ray 2.1Å A=1-335.
3TFR X-ray 2.0Å A=1-335.
3TFS X-ray 2.0Å A=1-335.
4DO9 X-ray 2.0Å A=1-335.
4DOA X-ray 2.0Å A=1-335.
4DOB X-ray 2.0Å A=1-335.
4DOC X-ray 1.9Å A=1-335.
4F5N X-ray 1.8Å A=1-335.
4F5O X-ray 2.0Å A=1-335.
4F5P X-ray 1.8Å A=1-335.
4F5Q X-ray 2.2Å A=1-335.
4F5R X-ray 2.2Å A/B=1-335.
4GXI X-ray 1.9Å A=1-335.
4GXJ X-ray 2.2Å A=1-335.
4GXK X-ray 2.0Å A=1-335.
4JWM X-ray 2.0Å A=1-335.
4JWN X-ray 2.3Å A=1-335.
4KLD X-ray 1.9Å A=1-335.
4KLE X-ray 1.9Å A=1-335.
4KLF X-ray 1.8Å A=1-335.
4KLG X-ray 1.7Å A=1-335.
4KLH X-ray 1.8Å A=1-335.
4KLI X-ray 1.6Å A=1-335.
4KLJ X-ray 1.8Å A=1-335.
4KLL X-ray 1.8Å A=1-335.
4KLM X-ray 1.7Å A=1-335.
4KLO X-ray 1.8Å A=1-335.
4KLQ X-ray 2.0Å A=1-335.
4KLS X-ray 1.9Å A=1-335.
4KLT X-ray 1.9Å A=1-335.
4KLU X-ray 1.9Å A=1-335.
4LVS X-ray 2.0Å A=1-335.
4M2Y X-ray 2.2Å A=11-335.
4M47 X-ray 2.3Å A=12-335.
4M9G X-ray 2.0Å A=1-335.
4M9H X-ray 2.3Å A=1-335.
4M9J X-ray 2.0Å A=1-335.
4M9L X-ray 2.0Å A=1-335.
4M9N X-ray 2.2Å A=1-335.
4MF2 X-ray 2.4Å A=11-335.
4MF8 X-ray 2.3Å A=7-335.
4MFA X-ray 2.2Å A=11-335.
4MFC X-ray 2.1Å A=11-335.
4MFF X-ray 2.5Å A=11-335.
4NLK X-ray 2.4Å A=7-335.
4NLN X-ray 2.2Å A=7-335.
4NLZ X-ray 2.6Å A=7-335.
4NM1 X-ray 2.4Å A=7-335.
4NM2 X-ray 2.5Å A=7-335.
4NXZ X-ray 2.5Å A=10-335.
4NY8 X-ray 2.2Å A=10-335.
4O5C X-ray 2.3Å A=7-335.
4O5E X-ray 2.5Å A=7-335.
4O5K X-ray 2.0Å A=10-335.
4O9M X-ray 2.3Å A=1-335.
4P2H X-ray 1.9Å A=10-335.
4PGQ X-ray 2.3Å A=7-335.
4PGX X-ray 2.0Å A=10-335.
4PGY X-ray 2.2Å A=7-335.
4PH5 X-ray 2.5Å A=10-335.
4PHA X-ray 2.5Å A=7-335.
4PHD X-ray 2.2Å A=7-335.
4PHE X-ray 2.1Å A=7-335.
4PHP X-ray 2.6Å A=10-335.
4PPX X-ray 2.0Å A=1-335.
4R63 X-ray 1.8Å A=1-335.
4R64 X-ray 2.2Å A=1-335.
4R65 X-ray 1.9Å A=1-335.
4R66 X-ray 2.2Å A=1-335.
4RPX X-ray 1.9Å A=1-335.
4RPY X-ray 1.9Å A=1-335.
4RPZ X-ray 2.1Å A=1-335.
4RQ0 X-ray 2.2Å A=1-335.
4RQ1 X-ray 2.7Å A=1-335.
4RQ2 X-ray 2.2Å A=1-335.
4RQ3 X-ray 2.0Å A=1-335.
4RQ4 X-ray 2.1Å A=1-335.
4RQ5 X-ray 2.3Å A=1-335.
4RQ6 X-ray 2.2Å A=1-335.
4RQ7 X-ray 2.0Å A=1-335.
4RQ8 X-ray 2.0Å A=1-335.
4RT2 X-ray 1.9Å A=1-335.
4RT3 X-ray 1.9Å A=1-335.
4TUP X-ray 1.8Å A=7-335.
4TUQ X-ray 2.3Å A=10-335.
4TUR X-ray 2.1Å A=7-335.
4TUS X-ray 2.4Å A=10-335.
4UAW X-ray 1.9Å A=1-335.
4UAY X-ray 1.9Å A=1-335.
4UAZ X-ray 1.8Å A=1-335.
4UB1 X-ray 2.3Å A=1-335.
4UB2 X-ray 2.5Å A=1-335.
4UB3 X-ray 2.0Å A=1-335.
4UB4 X-ray 1.9Å A=1-335.
4UB5 X-ray 2.1Å A=1-335.
4UBB X-ray 1.9Å A=1-335.
4UBC X-ray 2.0Å A=1-335.
4YMM X-ray 2.2Å A=1-335.
4YMN X-ray 2.5Å A=1-335.
4YMO X-ray 2.1Å A=1-335.
4YN4 X-ray 2.2Å A=1-335.
4Z6C X-ray 2.6Å A=1-335.
4Z6D X-ray 2.5Å A=1-335.
4Z6E X-ray 2.7Å A=1-335.
4Z6F X-ray 2.4Å A=1-335.
5BOL X-ray 1.9Å A=1-335.
5BOM X-ray 2.0Å A=1-335.
5BPC X-ray 2.0Å A=1-335.
5DB6 X-ray 2.8Å A=1-335.
5DB7 X-ray 2.2Å A=1-335.
5DB8 X-ray 2.5Å A=1-335.
5DB9 X-ray 2.4Å A=1-335.
5DBA X-ray 1.9Å A=1-335.
5DBB X-ray 2.2Å A=1-335.
5DBC X-ray 2.4Å A=1-335.
7ICE X-ray 2.8Å A=1-335.
7ICF X-ray 3.1Å A=1-335.
7ICG X-ray 3.0Å A=1-335.
7ICH X-ray 2.9Å A=1-335.
7ICI X-ray 2.8Å A=1-335.
7ICJ X-ray 3.5Å A=1-335.
7ICK X-ray 2.9Å A=1-335.
7ICL X-ray 3.1Å A=1-335.
7ICM X-ray 3.0Å A=1-335.
7ICN X-ray 2.8Å A=1-335.
7ICO X-ray 3.3Å A=1-335.
7ICP X-ray 3.0Å A=1-335.
7ICQ X-ray 2.9Å A=1-335.
7ICR X-ray 3.0Å A=1-335.
7ICS X-ray 2.8Å A=1-335.
7ICT X-ray 2.8Å A=1-335.
7ICU X-ray 3.3Å A=1-335.
7ICV X-ray 2.8Å A=1-335.
8ICA X-ray 3.0Å A=1-335.
8ICB X-ray 3.1Å A=1-335.
8ICC X-ray 2.8Å A=1-335.
8ICE X-ray 3.2Å A=1-335.
8ICF X-ray 2.9Å A=1-335.
8ICG X-ray 3.3Å A=1-335.
8ICH X-ray 3.3Å A=1-335.
8ICI X-ray 2.8Å A=1-335.
8ICJ X-ray 3.2Å A=1-335.
8ICK X-ray 2.7Å A=1-335.
8ICL X-ray 3.1Å A=1-335.
8ICM X-ray 2.9Å A=1-335.
8ICN X-ray 2.8Å A=1-335.
8ICO X-ray 2.7Å A=1-335.
8ICP X-ray 2.9Å A=1-335.
8ICQ X-ray 3.0Å A=1-335.
8ICR X-ray 2.9Å A=1-335.
8ICS X-ray 2.9Å A=1-335.
8ICT X-ray 3.1Å A=1-335.
8ICU X-ray 3.0Å A=1-335.
8ICV X-ray 3.2Å A=1-335.
8ICW X-ray 3.3Å A=1-335.
8ICX X-ray 3.0Å A=1-335.
8ICY X-ray 3.1Å A=1-335.
8ICZ X-ray 3.1Å A=1-335.
9ICA X-ray 3.0Å A=1-335.
9ICB X-ray 3.2Å A=1-335.
9ICC X-ray 3.1Å A=1-335.
9ICE X-ray 3.3Å A=1-335.
9ICF X-ray 3.0Å A=1-335.
9ICG X-ray 3.0Å A=1-335.
9ICH X-ray 2.9Å A=1-335.
9ICI X-ray 3.1Å A=1-335.
9ICJ X-ray 3.1Å A=1-335.
9ICK X-ray 2.7Å A=1-335.
9ICL X-ray 2.8Å A=1-335.
9ICM X-ray 2.9Å A=1-335.
9ICN X-ray 3.0Å A=1-335.
9ICO X-ray 2.9Å A=1-335.
9ICP X-ray 3.1Å A=1-335.
9ICQ X-ray 2.9Å A=1-335.
9ICR X-ray 3.0Å A=1-335.
9ICS X-ray 2.9Å A=1-335.
9ICT X-ray 3.0Å A=1-335.
9ICU X-ray 2.9Å A=1-335.
9ICV X-ray 2.7Å A=1-335.
9ICW X-ray 2.6Å A=1-335.
9ICX X-ray 2.6Å A=1-335.
9ICY X-ray 3.0Å A=1-335.

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

HIV Partner Interaction Type PubMed
Tat upregulates 11242139
HIV-1 virus replication inhibited by expression of human gene 22082156

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa03410 Base excision repair - Homo sapiens (human)
hsa05166 HTLV-I infection - Homo sapiens (human)
hsa05203 Viral carcinogenesis - Homo sapiens (human)