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0SYK_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NameKARS
DescriptionLysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0005737 cytoplasm (TAS)
0005625 soluble fraction (TAS)
0004824 lysine-tRNA ligase activity (TAS)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
The aminoacyl-tRNA synthetases () catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state.nd have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes. and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold and are mostly monomeric .hile class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet formation.lanked byalpha-helices .nd are mostly dimeric or multimeric. In reactions catalysed by the class I aminoacyl-tRNA synthetases.he aminoacyl group is coupled to the 2-hydroxyl of the tRNA.hile.nclass II reactions.he 3-hydroxyl site is preferred. The synthetases specific for arginine.ysteine.lutamic acid.lutamine.soleucine.eucine.ethionine.yrosine.ryptophan and valine belong to class I synthetases.The synthetases specific for alanine.sparagine.spartic acid.lycine.istidine.ysine.henylalanine.roline.erine.nd threonine belong to class-II synthetases .The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold.hich is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses.. and c.ccording to sequence homology. tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases.Class-II tRNA synthetases do not share a high degree of similarity.owever at least three conserved regions are present . This entry includes the asparagine.spartic acid and lysine tRNA synthetases.
  IPR004364:tRNA synthetase, class II (D, K and N)
The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this fold-related binding face to.ariously.ind oligosaccharides.ligonucleotides.roteins.etal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids . It includes the anti-codon binding domain of lysyl.spartyl.nd asparaginyl-tRNA synthetases (See ). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule (EC 6.1.1.-) This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex.hat contains a subunit in this family . This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.
  IPR004365:nucleic acid binding, OB-fold, tRNA/helicase-type
The aminoacyl-tRNA synthetases () catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state.nd have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes. and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold and are mostly monomeric .hile class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet formation.lanked byalpha-helices .nd are mostly dimeric or multimeric. In reactions catalysed by the class I aminoacyl-tRNA synthetases.he aminoacyl group is coupled to the 2-hydroxyl of the tRNA.hile.nclass II reactions.he 3-hydroxyl site is preferred. The synthetases specific for arginine.ysteine.lutamic acid.lutamine.soleucine.eucine.ethionine.yrosine.ryptophan and valine belong to class I synthetases.The synthetases specific for alanine.sparagine.spartic acid.lycine.istidine.ysine.henylalanine.roline.erine.nd threonine belong to class-II synthetases .The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold.hich is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses.. and c.ccording to sequence homology. tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases.Class-II tRNA synthetases do not share a high degree of similarity.owever at least three conserved regions are present . Aspartyl tRNA synthetase is an alpha2 dimer that belongs to class IIb. Structural analysis combined with mutagenesis and enzymology data on the yeast enzyme point to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module .
  IPR002312:Aspartyl-tRNA synthetase, class IIb
The aminoacyl-tRNA synthetases () catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state.nd have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes. and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold and are mostly monomeric .hile class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet formation.lanked byalpha-helices .nd are mostly dimeric or multimeric. In reactions catalysed by the class I aminoacyl-tRNA synthetases.he aminoacyl group is coupled to the 2-hydroxyl of the tRNA.hile.nclass II reactions.he 3-hydroxyl site is preferred. The synthetases specific for arginine.ysteine.lutamic acid.lutamine.soleucine.eucine.ethionine.yrosine.ryptophan and valine belong to class I synthetases.The synthetases specific for alanine.sparagine.spartic acid.lycine.istidine.ysine.henylalanine.roline.erine.nd threonine belong to class-II synthetases .The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold.hich is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses.. and c.ccording to sequence homology. tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases.Class-II tRNA synthetases do not share a high degree of similarity.owever at least three conserved regions are present . Lysyl-tRNA synthetase () is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong toclass II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and some eubacteria . Moreover in some eubacteria there is a gene X.hich is similar to a part of lysyl-tRNA synthetase from class II. Lysyl-tRNA synthetase is duplicated in some species with.or example in E. coli.s aconstitutive gene (lysS) and an induced one (lysU). No residues are directly involved in catalysis.ut a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. Lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis.ut a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket.isordered in the lysine-bound structure.ecomes ordered upon adenine binding .
  IPR002313:Lysyl-tRNA synthetase, class-2
A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease andaspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1).nd has been termed the oligonucleotide/oligosaccharide binding motif.r OB fold. five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands . Two ribosomal proteins.17 and S1.re members of this class.nd have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case .There are many nucleic acid-binding proteins that contain domains with this OB-fold structure.ncluding anticodon-binding tRNA synthetases.NA helicases RecG and RuvA.sDNA-binding proteins (BRCA2.DC13.elomere-end binding proteins).hage ssDNA-binding proteins (gp32.p2.5.pV).old shock proteins.NA ligases.NA-capping enzymes.NA replication initiators and RNA polymerase subunit RBP8 .Please be aware that some of the protein hits may be false positives.
  IPR008994:Nucleic acid-binding, OB-fold
A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease andaspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1).nd has been termed the oligonucleotide/oligosaccharide binding motif.r OB fold. five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands . Two ribosomal proteins.17 and S1.re members of this class.nd have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case .This entry differs from Nucleic acid-binding OB-fold in the classification of the fold: both the NAD+-dependent DNA ligases.NA helicase RecG.nd the phage ssDNA-binding protein gp32 are absent from this classification.ut are found in the Nucleic acid-binding OB-fold.
  IPR012340:Nucleic acid-binding, OB-fold, subgroup
IPR004364:tRNA-synt_2 
Evalue:-128.657577514648 
Location:222-575IPR004365:tRNA_anti 
Evalue:-15.6020603179932 
Location:126-206IPR002312:TRNASYNTHASP 
Evalue:0 
Location:0-0
SequencesProtein: SYK_HUMAN (597 aa)
mRNA: AF285758 NM_005548
Local Annotation
Synapse Ontology
Calcium release from RyR (Ryanodine Receptor) in the SR (Sarcoplasmic Reticulum) is activated by the calcium induced-calcium-release
sdb:0325 RyR-CICR  (Evidence:keywords)
KO assignmentK04567
  Level 3 annotation:
    lysyl-tRNA synthetase, class II
  Level 2 annotation:
    Lysine biosynthesis
    Aminoacyl-tRNA biosynthesis
    Amyotrophic lateral sclerosis (ALS)
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 88 residues, 74219131-74219392Exon2: 50 residues, 74219967-74220111Exon3: 44 residues, 74220813-74220940Exon4: 30 residues, 74221821-74221907Exon5: 30 residues, 74222566-74222652Exon6: 60 residues, 74222814-74222988Exon7: 56 residues, 74223091-74223254Exon8: 42 residues, 74225571-74225691Exon9: 44 residues, 74227078-74227204Exon10: 64 residues, 74227310-74227497Exon11: 33 residues, 74227852-74227946Exon12: 57 residues, 74231582-74231748Exon13: 55 residues, 74232962-74233122Exon14: 36 residues, 74238976-74239078Exon15: 2 residues, -Jump to SYK_HUMANExon1: 34 residues, 74219293-74219392Exon2: 50 residues, 74219967-74220111Exon3: 44 residues, 74220813-74220940Exon4: 30 residues, 74221821-74221907Exon5: 30 residues, 74222566-74222652Exon6: 60 residues, 74222814-74222988Exon7: 56 residues, 74223091-74223254Exon8: 42 residues, 74225571-74225691Exon9: 44 residues, 74227078-74227204Exon10: 64 residues, 74227310-74227497Exon11: 33 residues, 74227852-74227946Exon12: 57 residues, 74231582-74231748Exon13: 55 residues, 74232962-74233122Exon14: 62 residues, 74235681-74235861Exon15: 31 residues, 74238976-74239064Exon16: 2 residues, -Jump to SYK_HUMAN  
Tune and view alternative isoforms
Loci Cluster (Details)Loci: 4236 74119930-74136827 ~-17K 14534(CHST5)(-)Loci: 2952 74157749-74169279 ~-12K 14538(GABARAPL2)(+)Loci: 4237 74219131-74239078 ~-20K 14541(KARS)(-)Loci: 4235 74070013-74073246 ~-3K 14533(CHST6)(-)Link out to UCSC