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PDBsum entry 1wnz

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Ligase PDB id
1wnz
Jmol
Contents
Protein chain
180 a.a. *
Ligands
2VA
Waters ×183
* Residue conservation analysis
PDB id:
1wnz
Name: Ligase
Title: Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, val-2aa
Structure: Isoleucyl-tRNA synthetase. Chain: a. Fragment: cp1 domain. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.210     R-free:   0.257
Authors: R.Fukunaga,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Fukunaga and S.Yokoyama (2006). Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase. J Mol Biol, 359, 901-912. PubMed id: 16697013 DOI: 10.1016/j.jmb.2006.04.025
Date:
11-Aug-04     Release date:   25-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56690  (SYI_THET8) -  Isoleucine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1043 a.a.
180 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.5  - Isoleucine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl- tRNA(Ile)
ATP
+ L-isoleucine
+ tRNA(Ile)
=
AMP
Bound ligand (Het Group name = 2VA)
matches with 58.00% similarity
+ diphosphate
+ L-isoleucyl- tRNA(Ile)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     tRNA aminoacylation for protein translation   1 term 
  Biochemical function     aminoacyl-tRNA editing activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.04.025 J Mol Biol 359:901-912 (2006)
PubMed id: 16697013  
 
 
Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase.
R.Fukunaga, S.Yokoyama.
 
  ABSTRACT  
 
In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In the present study, we determined the crystal structures of the Thermus thermophilus IleRS editing domain complexed with the substrate analogues in the pre and post-transfer modes, both at 1.7 A resolution. The active site accommodates the two analogues differently, with the valine side-chain rotated by about 120 degrees and the adenosine moiety oriented upside down. The substrate-binding pocket adjusts to the adenosine-monophosphate and adenosine moieties in the pre and post-transfer modes, respectively, by flipping the Trp227 side-chain by about 180 degrees . The substrate recognition mechanisms of IleRS are characterized by the active-site rearrangement between the two editing modes, and therefore differ from those of the homologous valyl and leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer mode is predominant. Both modes of editing activities were reduced by replacements of Trp227 with Ala, Val, Leu, and His, but not by those with Phe and Tyr, indicating that the aromatic ring of Trp227 is important for the substrate recognition. In both editing modes, Thr233 and His319 recognize the substrate valine side-chain, regardless of the valine side-chain rotation, and reject the isoleucine side-chain. The T233A and H319A mutants have detectable editing activities against the cognate isoleucine.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Editing activities of the wild-type and mutant IleRSs. (a) Post-transfer editing activity against Val-tRNA^Ile. (b) Total editing activity against valine. (c) Val-tRNA^Ile mis-formation activity. Figure 5. Editing activities of the wild-type and mutant IleRSs. (a) Post-transfer editing activity against Val-tRNA^Ile. (b) Total editing activity against valine. (c) Val-tRNA^Ile mis-formation activity.
Figure 6.
Figure 6. Recognition manners of the valine side-chain. (a) Stereo view of the superposition of the valyl moieties. The free valine, Val-2AA, and Val-AMS are shown in yellow, cyan, and magenta, respectively. (b) Post-transfer editing activity against the cognate Ile-tRNA^Ile. (c) Total editing activity against the cognate isoleucine (sum of the pre and post-transfer editing activities, measured by ATP consumption). Figure 6. Recognition manners of the valine side-chain. (a) Stereo view of the superposition of the valyl moieties. The free valine, Val-2AA, and Val-AMS are shown in yellow, cyan, and magenta, respectively. (b) Post-transfer editing activity against the cognate Ile-tRNA^Ile. (c) Total editing activity against the cognate isoleucine (sum of the pre and post-transfer editing activities, measured by ATP consumption).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 359, 901-912) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19941860 S.A.Martinis, and M.T.Boniecki (2010).
The balance between pre- and post-transfer editing in tRNA synthetases.
  FEBS Lett, 584, 455-459.  
21098258 T.Hussain, V.Kamarthapu, S.P.Kruparani, M.V.Deshmukh, and R.Sankaranarayanan (2010).
Mechanistic insights into cognate substrate discrimination during proofreading in translation.
  Proc Natl Acad Sci U S A, 107, 22117-22121.
PDB codes: 3pd2 3pd3 3pd4 3pd5
19379069 J.Ling, N.Reynolds, and M.Ibba (2009).
Aminoacyl-tRNA synthesis and translational quality control.
  Annu Rev Microbiol, 63, 61-78.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
17327676 R.Fukunaga, and S.Yokoyama (2007).
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 63, 390-400.
PDB code: 2e1b
17890314 V.A.Karkhanis, A.P.Mascarenhas, and S.A.Martinis (2007).
Amino acid toxicities of Escherichia coli that are prevented by leucyl-tRNA synthetase amino acid editing.
  J Bacteriol, 189, 8765-8768.  
17501926 W.Paulander, S.Maisnier-Patin, and D.I.Andersson (2007).
Multiple mechanisms to ameliorate the fitness burden of mupirocin resistance in Salmonella typhimurium.
  Mol Microbiol, 64, 1038-1048.  
16864571 S.Hati, B.Ziervogel, J.Sternjohn, F.C.Wong, M.C.Nagan, A.E.Rosen, P.G.Siliciano, J.W.Chihade, and K.Musier-Forsyth (2006).
Pre-transfer editing by class II prolyl-tRNA synthetase: role of aminoacylation active site in "selective release" of noncognate amino acids.
  J Biol Chem, 281, 27862-27872.  
17027500 T.Crepin, A.Yaremchuk, M.Tukalo, and S.Cusack (2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
  Structure, 14, 1511-1525.
PDB codes: 2i4l 2i4m 2i4n 2i4o 2j3l 2j3m
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.