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

Gene ID: 3735, updated on 27-Sep-2014
Official Symbol
KARSprovided by HGNC
Official Full Name
lysyl-tRNA synthetaseprovided by HGNC
Primary source
HGNC:HGNC:6215
See related
Ensembl:ENSG00000065427; HPRD:03249; 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]
See KARS in Epigenomics, MapViewer
Location:
16q23.1
Exon count:
15
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 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(A) receptor-associated protein-like 2 Neighboring gene adenosine deaminase, tRNA-specific 1 Neighboring gene telomeric repeat binding factor 2, interacting protein Neighboring gene ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1 pseudogene 7

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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 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 Homodimeric lysyl-tRNA synthetase dissociates into a monomer that bridges between HIV-1 Gag and tRNA(Lys3) 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 binding IEA
Inferred from Electronic Annotation
more info
 
amino acid binding IEA
Inferred from Electronic Annotation
more info
 
lysine-tRNA ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
lysine-tRNA ligase activity TAS
Traceable Author Statement
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
tRNA binding NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell death IEA
Inferred from Electronic Annotation
more info
 
diadenosine tetraphosphate biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
gene expression TAS
Traceable Author Statement
more info
 
lysyl-tRNA aminoacylation IDA
Inferred from Direct Assay
more info
PubMed 
tRNA aminoacylation for protein translation TAS
Traceable Author Statement
more info
 
tRNA processing NAS
Non-traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
aminoacyl-tRNA synthetase multienzyme complex IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
lysine--tRNA ligase
Names
lysine--tRNA ligase
lysRS
lysine tRNA ligase
NP_001123561.1
NP_005539.1

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 

    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 proteins identical to 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, OTTHUMP00000174949, ENST00000319410, 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 proteins identical to 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, OTTHUMP00000174948, ENST00000302445, OTTHUMT00000269023
    Conserved Domains (4) summary
    PLN02502
    Location:12577
    PLN02502; lysyl-tRNA synthetase
    cd00775
    Location:237575
    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:125234
    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. ...
    pfam15437
    Location:1550
    PGBA_C; Plasminogen-binding protein pgbA C-terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000016.10 

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

Alternate HuRef

Genomic

  1. AC_000148.1 

    Range
    61415299..61435262
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 

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