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KARS lysyl-tRNA synthetase [ Homo sapiens (human) ]

Gene ID: 3735, updated on 3-Jun-2018
Official Symbol
KARSprovided by HGNC
Official Full Name
lysyl-tRNA synthetaseprovided by HGNC
Primary source
HGNC:HGNC:6215
See related
Ensembl:ENSG00000065427 MIM:601421; Vega:OTTHUMG00000137609
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KRS; KARS1; KARS2; CMTRIB; DFNB89
Summary
Aminoacyl-tRNA synthetases are a class of enzymes that charge tRNAs with their cognate amino acids. Lysyl-tRNA synthetase is a homodimer localized to the cytoplasm which belongs to the class II family of tRNA synthetases. It has been shown to be a target of autoantibodies in the human autoimmune diseases, polymyositis or dermatomyositis. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 57.5), lymph node (RPKM 40.9) and 25 other tissues See more
Orthologs
See KARS in Genome Data Viewer
Location:
16q23.1
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (75627724..75647687, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75661622..75681585, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene GABA type A receptor associated protein like 2 Neighboring gene adenosine deaminase, tRNA specific 1 Neighboring gene TERF2 interacting protein Neighboring gene uncharacterized LOC112268164

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Charcot-Marie-Tooth disease, recessive intermediate B
MedGen: C3150897 OMIM: 613641 GeneReviews: Not available
Compare labs
Deafness, autosomal recessive 89
MedGen: C3151351 OMIM: 613916 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
NHGRI GWA Catalog

Replication interactions

Interaction Pubs
Knockdown of lysyl-tRNA synthetase (KARS) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Gag-Pol gag-pol The Pol domain of HIV-1 Gag-Pol associates specifically with Lysyl-tRNA synthetase PubMed
Pol gag-pol HIV-1 Pol interacts with lysyl-tRNA synthetase (LysRS). Sequences in Pol binding to LysRS are found within connection domain/RNaseH domain of RT PubMed
gag-pol The p6 and Integrase (IN) domains of HIV-1 Pol act synergistically to build a strong and stable anchoring platform for its binding to LysRS. The catalytic domain (amino acids 237-597) of LysRS is involved in its interaction with Pol PubMed
Pr55(Gag) gag Homodimeric lysyl-tRNA synthetase dissociates into a monomer that bridges between HIV-1 Gag and tRNA(Lys3) PubMed
gag LysRS double mutants at positions I246D/R247A, I250D/I251D, and I254D/R255A in the helix 7 dimerization domain reduce its binding to HIV-1 Gag/delta p6 and CA-CTD PubMed
gag A peptide containing 10 amino acid residues from helix4 of C-terminal domain of HIV-1 CA (CA-CTD) can form a helical structure upon binding to LysRS through strong hydrogen bond interactions between R247-Q219 and R241-E212 PubMed
gag The interaction of Lysyl-tRNA synthetase with HIV-1 Gag is dependent upon Gag amino acids 310-363 (last 54 amino acids of the capsid domain) and amino acids 208-259 of Lysyl-tRNA synthetase PubMed
gag Lysyl-tRNA synthetase is incorporated into HIV-1 virions through an interaction with HIV-1 Gag PubMed
Vpr vpr Mitochondrial localization of lysyl-tRNA synthetase (LysRS) is altered in the presence of HIV-1 Vpr in HeLa cells PubMed
vpr HIV-1 Vpr binds to Lysyl-tRNA synthetase (LysRS) and inhibits LysRS-mediated aminoacylation of tRNA-Lys, an effect that may influence the initiation of HIV-1 reverse transcription PubMed
capsid gag LysRS double mutants at positions I246D/R247A, I250D/I251D, and I254D/R255A in the helix 7 dimerization domain reduce its binding to HIV-1 Gag/delta p6 and CA-CTD PubMed
gag The Capsid domain of HIV-1 Gag is sufficient for the interaction of Gag with lysyl-tRNA synthetase in an in vitro pull-down assay PubMed
gag Cyclic peptides inhibit the interaction of HIV-1 CA with lysyl-tRNA synthetase by binding to the helix 4 motif of the C-terminal domain of CA PubMed
gag Peptides derived from the helix-4 of HIV-1 capsid C-terminal domain significantly bind to LysRS PubMed
matrix gag HIV-1 MA is identified to have a physical interaction with lysyl-tRNA synthetase (KARS) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
retropepsin gag-pol Using a bioluminescence resonance energy transfer assay to directly measure HIV-1 protease activity in vivo indicates that the overexpression of lysyl tRNA synthetase (LysRS) in the cell reduces viral protease activity PubMed
reverse transcriptase gag-pol HIV-1 Pol interacts with lysyl-tRNA synthetase (LysRS). Sequences in Pol binding to LysRS are found within connection domain/RNaseH domain of RT PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0070

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP adenylyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
ATP binding IEA
Inferred from Electronic Annotation
more info
 
amino acid binding IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
lysine-tRNA ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
lysine-tRNA ligase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
tRNA binding NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
ERK1 and ERK2 cascade IGI
Inferred from Genetic Interaction
more info
PubMed 
activation of MAPK activity IDA
Inferred from Direct Assay
more info
PubMed 
basophil activation involved in immune response IGI
Inferred from Genetic Interaction
more info
PubMed 
diadenosine tetraphosphate biosynthetic process IDA
Inferred from Direct Assay
more info
PubMed 
diadenosine tetraphosphate biosynthetic process IGI
Inferred from Genetic Interaction
more info
PubMed 
lysyl-tRNA aminoacylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cytokine production involved in inflammatory response IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cytokine secretion involved in immune response IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of macrophage activation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of macrophage chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of metallopeptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of p38MAPK cascade IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IGI
Inferred from Genetic Interaction
more info
PubMed 
response to X-ray IEA
Inferred from Electronic Annotation
more info
 
tRNA aminoacylation for protein translation TAS
Traceable Author Statement
more info
 
tRNA processing NAS
Non-traceable Author Statement
more info
PubMed 
tumor necrosis factor-mediated signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
aminoacyl-tRNA synthetase multienzyme complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
lysine--tRNA ligase
Names
lysRS
lysine tRNA ligase
NP_001123561.1
NP_005539.1
XP_016878706.1

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_028025.1 RefSeqGene

    Range
    5001..24964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_366

mRNA and Protein(s)

  1. NM_001130089.1NP_001123561.1  lysine--tRNA ligase isoform 1

    See identical proteins and their annotated locations for NP_001123561.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AA503390, AF285758, AK315687, BM781594
    Consensus CDS
    CCDS45532.1
    UniProtKB/Swiss-Prot
    Q15046
    Related
    ENSP00000325448.5, OTTHUMP00000174949, ENST00000319410.9, OTTHUMT00000269024
    Conserved Domains (3) summary
    PLN02502
    Location:48605
    PLN02502; lysyl-tRNA synthetase
    cd00775
    Location:265603
    LysRS_core; Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three ...
    cd04322
    Location:153262
    LysRS_N; LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. ...
  2. NM_005548.2NP_005539.1  lysine--tRNA ligase isoform 2

    See identical proteins and their annotated locations for NP_005539.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an internal exon in the 5' region, which results in an upstream AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AA503390, AF285758, AK315687
    Consensus CDS
    CCDS10923.1
    UniProtKB/Swiss-Prot
    Q15046
    Related
    ENSP00000303043.3, OTTHUMP00000174948, ENST00000302445.7, OTTHUMT00000269023
    Conserved Domains (1) summary
    PLN02502
    Location:12577
    PLN02502; lysyl-tRNA synthetase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    75627724..75647687 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023217.1XP_016878706.1  lysine--tRNA ligase isoform X1

    Conserved Domains (3) summary
    cd00775
    Location:81419
    LysRS_core; Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three ...
    cd04322
    Location:178
    LysRS_N; LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. ...
    pfam00152
    Location:66418
    tRNA-synt_2; tRNA synthetases class II (D, K and N)
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