Detailed entry information

Protein Information (annotations from UniProt)

Database IDHIV0001491
UniProt IDQ15046
Primary gene name(s)KARS
Synonym gene name(s)KIAA0070
Protein nameLysine--tRNA ligase
Protein functionCatalyzes the specific attachment of an amino acid to its cognate tRNA in a 2 step reaction: the amino acid, AA is first activated by ATP to form AA-AMP and then transferred to the acceptor end of the tRNA. When secreted, acts as a signaling molecule that induces immune response through the activation of monocyte/macrophages. Catalyzes the synthesis of diadenosine oligophosphate, Ap4A, a signaling molecule involved in the activation of MITF transcriptional activity. Interacts with HIV-1 virus GAG protein, facilitating the selective packaging of tRNA(3(Lys, the primer for reverse transcription initiation. {ECO:0000269|PubMed:15851690, ECO:0000269|PubMed:5338216}.
Subcellular locationIsoform Cytoplasmic: Cytoplasm. Nucleus. Cell membrane;
Peripheral membrane protein. Secreted. Note=Secretion is induced by TNF-alpha.;
SUBCELLULAR LOCATION: Isoform Mitochondrial: Mitochondrion.
ECO codeClick here for more information.
Amino acid sequence
FASTA format: Q15046
Gene Ontology
(Biological Process)
Complete annatation
diadenosine tetraphosphate biosynthetic process [GO:0015966];
lysyl-tRNA aminoacylation [GO:0006430];
tRNA aminoacylation for protein translation [GO:0006418];
tRNA processing [GO:0008033];
viral process [GO:0016032]
Gene Ontology
(Molecular Function)
Complete annatation
amino acid binding [GO:0016597];
ATP binding [GO:0005524];
lysine-tRNA ligase activity [GO:0004824];
metal ion binding [GO:0046872];
tRNA binding [GO:0000049]
Gene Ontology
(Cellular Component)
Complete annatation
aminoacyl-tRNA synthetase multienzyme complex [GO:0017101];
cytoplasm [GO:0005737];
cytosol [GO:0005829];
extracellular region [GO:0005576];
microtubule cytoskeleton [GO:0015630];
mitochondrial matrix [GO:0005759];
mitochondrion [GO:0005739];
nucleus [GO:0005634];
plasma membrane [GO:0005886]
Protein-protein interaction109938
Phylogenetic treeQ15046
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. CD31.343173832036765.36622346275495e-050.000277555662424992
AZA vs. DISU-0.1310412019681350.6039915541699470.955158276076142
AZA vs. IL70.4442622216475490.02083084119042990.464059243345433
AZA vs. SAHA-0.1295768669923420.5951070979858140.867158208964865
DISU vs. CD3-1.486512143303095.72666967491031e-050.000347100195736221
DISU vs. IL70.5661997716819130.02489696233964590.20113703497865
DISU vs. SAHA0.003042005854286730.9916597206452580.999572425883731
DMSO vs. AZA0.01980901772917440.9056815151790421
DMSO vs. CD3-1.335854358161383.88428400504015e-050.000193571745074197
DMSO vs. DISU0.1487269148923080.5416622655665840.921635859189505
DMSO vs. IL70.4318607944813610.01628341535109750.266280809624951
DMSO vs. SAHA-0.1553454226892190.5097105269862740.819244134430115
HIV vs. Mock in Activation-0.09371406790019880.8800883445813780.999983755607037
HIV vs. Mock in Latency-0.07232842332976450.661128467608060.999834320637052
IL7 vs. CD3-0.8913652968799770.005835527981303490.0191007412078583
SAHA vs. CD3-1.496845647837483.25947000412441e-050.000178683932201364
SAHA vs. IL7-0.576534579422070.01829881627017430.0948217107104183
(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
-0.3242 0.04091

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 0.219287 0.452384
(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
1.008 0.921 0.902 0.89 0.877
(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
DB00123 L-Lysine approved, nutraceutical unknown unknown

Protein Secondary Structure       (annotations from PDB)      top

PDB Accession Method Resolution Chain Structure Preview
3BJU X-ray 2.3Å A/B/C/D=70-582.
4DPG X-ray 2.8Å A/B/C/D/E/F/G/H=70-581.
4YCU X-ray 2.1Å A/B=70-581.
4YCW X-ray 2.9Å A/B/E/F=70-581.

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

HIV Partner Interaction Type PubMed
Pr55(Gag) incorporates 11333884
Gag-Pol associates with 21763493
Pol interacts with 18708237
HIV-1 virus replication enhanced by expression of human gene 18854154
Pr55(Gag) interacts with 12756246
Vpr relocalizes 17560997
capsid interacts with 16702215
Pr55(Gag) binds 21093454
capsid binds 17724017
Pol binds 21763493
reverse transcriptase interacts with 18708237
retropepsin inhibited by 15888436
matrix interacts with 22190034
Vpr inhibits 9525626

Metabolic/Signalling Pathway       (annotations from KEGG database)      top

Pathway Accession Number Description
hsa00970 Aminoacyl-tRNA biosynthesis - Homo sapiens (human)