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

    Gene ID: 3735, updated on 14-Jan-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
    Location:
    16q23.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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 RNA, 7SL, cytoplasmic 520, pseudogene

    • 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 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p7 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)

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      77074018..77093985 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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