Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001631
UniProt IDP49916
Primary gene name(s)LIG3
Synonym gene name(s)unknown
Protein nameDNA ligase 3
Protein functionIsoform 3 functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair, PubMed:10207110, PubMed:24674627. {ECO:0000269|PubMed:10207110, ECO:0000269|PubMed:24674627}.
Subcellular locationIsoform 1: Mitochondrion {ECO:0000269|PubMed:10207110, ECO:0000269|PubMed:24674627}. Note=Contains an N-terminal mitochondrial transit peptide. {ECO:0000269|PubMed:10207110}.;
SUBCELLULAR LOCATION: Isoform 2: Mitochondrion {ECO:0000305|PubMed:10207110}. Note=Contains an N-terminal mitochondrial transit peptide. {ECO:0000305|PubMed:10207110}.;
SUBCELLULAR LOCATION: Isoform 3: Nucleus {ECO:0000269|PubMed:10207110}. Note=Lacks the N-terminal mitochondrial transit peptide. {ECO:0000269|PubMed:10207110}.;
SUBCELLULAR LOCATION: Isoform 4: Nucleus {ECO:0000305|PubMed:10207110}. Note=Lacks the N-terminal mitochondrial transit peptide. {ECO:0000305|PubMed:10207110}.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: P49916
Gene Ontology
(Biological Process)
Complete annatation
base-excision repair, DNA ligation [GO:0006288];
cell cycle [GO:0007049];
cell division [GO:0051301];
DNA biosynthetic process [GO:0071897];
DNA ligation [GO:0006266];
DNA replication [GO:0006260];
double-strand break repair [GO:0006302];
double-strand break repair via alternative nonhomologous end joining [GO:0097681];
double-strand break repair via homologous recombination [GO:0000724];
mitochondrial DNA repair [GO:0043504];
mitochondrion organization [GO:0007005];
negative regulation of mitochondrial DNA replication [GO:0090298];
nucleotide-excision repair, DNA gap filling [GO:0006297];
transcription-coupled nucleotide-excision repair [GO:0006283]
Gene Ontology
(Molecular Function)
Complete annatation
ATP binding [GO:0005524];
DNA binding [GO:0003677];
DNA ligase, ATP activity [GO:0003910];
DNA ligase activity [GO:0003909];
zinc ion binding [GO:0008270]
Gene Ontology
(Cellular Component)
Complete annatation
DNA ligase III-XRCC1 complex [GO:0070421];
mitochondrion [GO:0005739];
nucleoplasm [GO:0005654];
nucleus [GO:0005634]
Protein-protein interaction110168
Phylogenetic treeP49916
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. CD30.8050785428997720.01483253134180380.036433492891732
AZA vs. DISU0.05301845994319340.8351233073375250.986167923867511
AZA vs. IL70.1181939637657010.5432300706098120.999311006273513
AZA vs. SAHA-0.1983195686039680.4222605080204860.775576324832559
DISU vs. CD3-0.765591705690880.03576747641027320.0825032807051964
DISU vs. IL70.05596667154074810.8251707436010920.963018774091083
DISU vs. SAHA-0.2494604674366840.3997404605705970.760071021924645
DMSO vs. AZA0.05848421117028810.7311355106080171
DMSO vs. CD3-0.7594391518679090.01855555097835950.0420423184672861
DMSO vs. DISU0.003114103740810430.9898889362915040.99806609310612
DMSO vs. IL70.06737978186505080.7109915683853190.941316067698277
DMSO vs. SAHA-0.2626241340549290.270892760283340.620295739730931
HIV vs. Mock in Activation0.2725289545274540.6616737510621780.999983755607037
HIV vs. Mock in Latency-0.0876486313588110.6013337213708340.999834320637052
IL7 vs. CD3-0.6802469308934430.03545288280844430.0832369630173957
SAHA vs. CD3-1.028120504828720.004429605689941660.0128844157011042
SAHA vs. IL7-0.3199747950988540.1946255199280710.426112576237581
(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 1.67646 0.000305467
(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
1.034 0.942 0.884 0.886 1.004
(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
DB00290 Bleomycin approved unknown inhibitor

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
1IMO NMR - A=924-1009.
1IN1 NMR - A=924-1009.
1UW0 NMR - A=88-204.
3L2P X-ray 3.0Å A=257-833.
3PC7 X-ray 1.6Å A/B=924-1009.
3PC8 X-ray 2.3Å C/D=924-1008.
3QVG X-ray 2.2Å A/C=924-1008.

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

HIV Partner Interaction Type PubMed
Rev interacts with 22174317
Tat downregulates 22632162

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

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