PDBsum entry 1udz

Go to PDB code: 
protein links
Ligase PDB id
Protein chains
179 a.a. *
Waters ×251
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Isoleucyl-tRNA synthetase editing domain
Structure: Isoleucyl-tRNA synthetase. Chain: a, b. Fragment: cp1 domain. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: iles. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.203     R-free:   0.250
Authors: R.Fukunaga,S.Fukai,R.Ishitani,O.Nureki,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Fukunaga et al. (2004). Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine. J Biol Chem, 279, 8396-8402. PubMed id: 14672940 DOI: 10.1074/jbc.M312830200
08-May-03     Release date:   23-Mar-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P56690  (SYI_THET8) -  Isoleucine--tRNA ligase
1043 a.a.
179 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Isoleucine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl- tRNA(Ile)
+ L-isoleucine
+ tRNA(Ile)
+ 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  


DOI no: 10.1074/jbc.M312830200 J Biol Chem 279:8396-8402 (2004)
PubMed id: 14672940  
Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.
R.Fukunaga, S.Fukai, R.Ishitani, O.Nureki, S.Yokoyama.
Isoleucyl-tRNA synthetase (IleRS) links tRNA(Ile) with not only its cognate isoleucine but also the nearly cognate valine. The CP1 domain of IleRS deacylates, or edits, the mischarged Val-tRNA(Ile). We determined the crystal structures of the Thermus thermophilus IleRS CP1 domain alone, and in its complex with valine at 1.8- and 2.0-A resolutions, respectively. In the complex structure, the Asp(328) residue, which was shown to be critical for the editing reaction against Val-tRNA(Ile) by a previous mutational analysis, recognizes the valine NH(3)(+) group. The valine side chain binding pocket is only large enough to accommodate valine, and the placement of an isoleucine model in this location revealed that the additional methylene group of isoleucine would clash with His(319). The H319A mutant of Escherichia coli IleRS reportedly deacylates the cognate Ile-tRNA(Ile) in addition to Val-tRNA(Ile), indicating that the valine-binding mode found in this study represents that in the Val-tRNA(Ile) editing reaction. Analyses of the Val-tRNA(Ile) editing activities of T. thermophilus IleRS mutants revealed the importance of Thr(228), Thr(229), Thr(230), and Asp(328), which are coordinated with water molecules in the present structure. The structural model for the Val-adenosine moiety of Val-tRNA(Ile) bound in the IleRS editing site revealed some interesting differences in the substrate binding and recognizing mechanisms between IleRS and T. thermophilus leucyl-tRNA synthetase. For example, the carbonyl oxygens of the amino acids are located opposite to each other, relative to the adenosine ribose ring, and are differently recognized.
  Selected figure(s)  
Figure 2.
FIG. 2. Valine-binding mode. A, F[o] - F[c] omit map electron densities for valine, contoured at 4.0 . Although the electron density for valine in the full-length IleRS was not resolved well, this study yielded a quite sharp electron density and we could determine the valine coordinates unambiguously. B, ball and stick representation of the active site residues, valine, and water molecules bound at the post-transfer editing site. Ionic bonds and hydrogen bonds recognizing valine are shown by dashed yellow lines (stereo view). C, the CP1 domain editing active site, rotated by 90° (stereo view)
Figure 7.
FIG. 7. Structural model of the 3'-OH valylated adenosine moiety of Val-tRNA^Ile (stereo view). The two water molecules are located in the same places as in the determined structure (light blue). Ionic bonds and hydrogen bonds are shown by dashed blue lines. The water molecule hydrogen bonding to Thr228 and Thr230 is favorably located to act as a nucleophile in the ester bond hydrolysis reaction.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 8396-8402) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20557293 X.L.Zhou, M.Tan, M.Wang, X.Chen, and E.D.Wang (2010).
Post-transfer editing by a eukaryotic leucyl-tRNA synthetase resistant to the broad-spectrum drug AN2690.
  Biochem J, 430, 325-333.  
19020078 M.T.Boniecki, M.T.Vu, A.K.Betha, and S.A.Martinis (2008).
CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 19223-19228.  
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.  
16155583 M.Tukalo, A.Yaremchuk, R.Fukunaga, S.Yokoyama, and S.Cusack (2005).
The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation.
  Nat Struct Mol Biol, 12, 923-930.
PDB codes: 2bte 2byt
15775966 M.W.Zhao, B.Zhu, R.Hao, M.G.Xu, G.Eriani, and E.D.Wang (2005).
Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution.
  EMBO J, 24, 1430-1439.  
  16508082 R.Fukunaga, R.Ishitani, O.Nureki, and S.Yokoyama (2005).
Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 30-32.  
16155584 R.Fukunaga, and S.Yokoyama (2005).
Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition.
  Nat Struct Mol Biol, 12, 915-922.  
15388946 R.Fukunaga, and S.Yokoyama (2004).
Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues.
  Acta Crystallogr D Biol Crystallogr, 60, 1900-1902.  
15388951 R.Fukunaga, and S.Yokoyama (2004).
Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 60, 1916-1918.  
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.