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Ligase PDB id
1bbw
Jmol
Contents
Protein chain
469 a.a. *
Waters ×114
* Residue conservation analysis
PDB id:
1bbw
Name: Ligase
Title: Lysyl-tRNA synthetase (lyss)
Structure: Protein (lysyl-tRNA synthetase). Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cellular_location: cytoplasmic. Gene: lyss. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.252     R-free:   0.308
Authors: S.Onesti,G.Desogus,A.Brevet,J.Chen,P.Plateau,S.Blanquet,P.Br
Key ref:
S.Onesti et al. (2000). Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding. Biochemistry, 39, 12853-12861. PubMed id: 11041850 DOI: 10.1021/bi001487r
Date:
24-Apr-98     Release date:   10-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A8N3  (SYK1_ECOLI) -  Lysyl-tRNA synthetase
Seq:
Struc: 		505 a.a.
469 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.6  - Lysine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys)
ATP
 + L-lysine
 + tRNA(Lys)
 = AMP
 + diphosphate
 + L-lysyl-tRNA(Lys)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi001487r Biochemistry 39:12853-12861 (2000)
PubMed id: 11041850  
 
 
Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
S.Onesti, G.Desogus, A.Brevet, J.Chen, P.Plateau, S.Blanquet, P.Brick.
 
  ABSTRACT  
 
Lysyl-tRNA synthetase is a member of the class II aminoacyl-tRNA synthetases and catalyses the specific aminoacylation of tRNA(Lys). The crystal structure of the constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli has been determined to 2.7 A resolution in the unliganded form and in a complex with the lysine substrate. A comparison between the unliganded and lysine-bound structures reveals major conformational changes upon lysine binding. The lysine substrate is involved in a network of hydrogen bonds. Two of these interactions, one between the alpha-amino group and the carbonyl oxygen of Gly 216 and the other between the carboxylate group and the side chain of Arg 262, trigger a subtle and complicated reorganization of the active site, involving the ordering of two loops (residues 215-217 and 444-455), a change in conformation of residues 393-409, and a rotation of a 4-helix bundle domain (located between motif 2 and 3) by 10 degrees. The result of these changes is a closing up of the active site upon lysine binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20571084 R.A.Hughes, and A.D.Ellington (2010).
Rational design of an orthogonal tryptophanyl nonsense suppressor tRNA.
  Nucleic Acids Res, 38, 6813-6830.  
19174549 H.Sakurama, T.Takita, B.Mikami, T.Itoh, K.Yasukawa, and K.Inouye (2009).
Two crystal structures of lysyl-tRNA synthetase from Bacillus stearothermophilus in complex with lysyladenylate-like compounds: insights into the irreversible formation of the enzyme-bound adenylate of L-lysine hydroxamate.
  J Biochem, 145, 555-563.
PDB codes: 3e9h 3e9i
18076053 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2008).
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.
  Proteins, 71, 1450-1460.  
18272479 M.Guo, M.Ignatov, K.Musier-Forsyth, P.Schimmel, and X.L.Yang (2008).
Crystal structure of tetrameric form of human lysyl-tRNA synthetase: Implications for multisynthetase complex formation.
  Proc Natl Acad Sci U S A, 105, 2331-2336.
PDB code: 3bju
18180246 N.Shen, M.Zhou, B.Yang, Y.Yu, X.Dong, and J.Ding (2008).
Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states.
  Nucleic Acids Res, 36, 1288-1299.
PDB codes: 2quh 2qui 2quj 2quk
18628952 S.I.Choi, K.S.Han, C.W.Kim, K.S.Ryu, B.H.Kim, K.H.Kim, S.I.Kim, T.H.Kang, H.C.Shin, K.H.Lim, H.K.Kim, J.M.Hyun, and B.L.Seong (2008).
Protein solubility and folding enhancement by interaction with RNA.
  PLoS ONE, 3, e2677.  
17384228 C.W.Kim, K.S.Han, K.S.Ryu, B.H.Kim, K.H.Kim, S.I.Choi, and B.L.Seong (2007).
N-terminal domains of native multidomain proteins have the potential to assist de novo folding of their downstream domains in vivo by acting as solubility enhancers.
  Protein Sci, 16, 635-643.  
17690095 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2007).
Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase.
  J Biol Chem, 282, 30856-30868.  
17560369 P.Kamenski, O.Kolesnikova, V.Jubenot, N.Entelis, I.A.Krasheninnikov, R.P.Martin, and I.Tarassov (2007).
Evidence for an adaptation mechanism of mitochondrial translation via tRNA import from the cytosol.
  Mol Cell, 26, 625-637.  
  18154269 S.F.Ataide, S.N.Wilson, S.Dang, T.E.Rogers, B.Roy, R.Banerjee, T.M.Henkin, and M.Ibba (2007).
Mechanisms of resistance to an amino acid antibiotic that targets translation.
  ACS Chem Biol, 2, 819-827.  
16317719 S.J.Hughes, J.A.Tanner, A.D.Miller, and I.R.Gould (2006).
Molecular dynamics simulations of LysRS: an asymmetric state.
  Proteins, 62, 649-662.  
16533047 S.Wang, M.Praetorius-Ibba, S.F.Ataide, H.Roy, and M.Ibba (2006).
Discrimination of cognate and noncognate substrates at the active site of class I lysyl-tRNA synthetase.
  Biochemistry, 45, 3646-3652.  
14747465 J.Levengood, S.F.Ataide, H.Roy, and M.Ibba (2004).
Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases.
  J Biol Chem, 279, 17707-17714.  
12660169 C.Charron, H.Roy, M.Blaise, R.Giegé, and D.Kern (2003).
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain.
  EMBO J, 22, 1632-1643.
PDB code: 1n9w
12417586 M.Francin, and M.Mirande (2003).
Functional dissection of the eukaryotic-specific tRNA-interacting factor of lysyl-tRNA synthetase.
  J Biol Chem, 278, 1472-1479.  
14690420 M.L.Bovee, M.A.Pierce, and C.S.Francklyn (2003).
Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
  Biochemistry, 42, 15102-15113.  
12787471 S.J.Hughes, J.A.Tanner, A.D.Hindley, A.D.Miller, and I.R.Gould (2003).
Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment.
  BMC Struct Biol, 3, 5.  
12458790 C.Francklyn, J.J.Perona, J.Puetz, and Y.M.Hou (2002).
Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.
  RNA, 8, 1363-1372.  
12019264 T.Takita, and K.Inouye (2002).
Transition state stabilization by the N-terminal anticodon-binding domain of lysyl-tRNA synthetase.
  J Biol Chem, 277, 29275-29282.  
11887185 T.Terada, O.Nureki, R.Ishitani, A.Ambrogelly, M.Ibba, D.Söll, and S.Yokoyama (2002).
Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.
  Nat Struct Biol, 9, 257-262.
PDB code: 1irx
11483577 L.Aravind, and E.V.Koonin (2001).
Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system.
  Genome Res, 11, 1365-1374.  
11551911 N.S.Entelis, O.A.Kolesnikova, S.Dogan, R.P.Martin, and I.A.Tarassov (2001).
5 S rRNA and tRNA import into human mitochondria. Comparison of in vitro requirements.
  J Biol Chem, 276, 45642-45653.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.