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PDBsum entry 1nyr

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1nyr
Jmol
Contents
Protein chains
642 a.a. *
Ligands
ATP ×2
THR ×2
Metals
_ZN ×3
Waters ×216
* Residue conservation analysis
PDB id:
1nyr
Name: Ligase
Title: Structure of staphylococcus aureus threonyl-tRNA synthetase complexed with atp
Structure: Threonyl-tRNA synthetase 1. Chain: a, b. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.239     R-free:   0.313
Authors: A.Torres-Larios,R.Sankaranarayanan,B.Rees,A.C.Dock-Bregeon, D.Moras
Key ref:
A.Torres-Larios et al. (2003). Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. J Mol Biol, 331, 201-211. PubMed id: 12875846 DOI: 10.1016/S0022-2836(03)00719-8
Date:
13-Feb-03     Release date:   28-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8NW68  (SYT_STAAW) -  Threonine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
645 a.a.
642 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.3  - Threonine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+
L-threonine
Bound ligand (Het Group name = THR)
corresponds exactly
+ tRNA(Thr)
= AMP
+ diphosphate
+ L-threonyl-tRNA(Thr)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   4 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0022-2836(03)00719-8 J Mol Biol 331:201-211 (2003)
PubMed id: 12875846  
 
 
Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase.
A.Torres-Larios, R.Sankaranarayanan, B.Rees, A.C.Dock-Bregeon, D.Moras.
 
  ABSTRACT  
 
The crystal structures of threonyl-tRNA synthetase (ThrRS) from Staphylococcus aureus, with ATP and an analogue of threonyl adenylate, are described. Together with the previously determined structures of Escherichia coli ThrRS with different substrates, they allow a comprehensive analysis of the effect of binding of all the substrates: threonine, ATP and tRNA. The tRNA, by inserting its acceptor arm between the N-terminal domain and the catalytic domain, causes a large rotation of the former. Within the catalytic domain, four regions surrounding the active site display significant conformational changes upon binding of the different substrates. The binding of threonine induces the movement of as much as 50 consecutive amino acid residues. The binding of ATP triggers a displacement, as large as 8A at some C(alpha) positions, of a strand-loop-strand region of the core beta-sheet. Two other regions move in a cooperative way upon binding of threonine or ATP: the motif 2 loop, which plays an essential role in the first step of the aminoacylation reaction, and the ordering loop, which closes on the active site cavity when the substrates are in place. The tRNA interacts with all four mobile regions, several residues initially bound to threonine or ATP switching to a position in which they can contact the tRNA. Three such conformational switches could be identified, each of them in a different mobile region. The structural analysis suggests that, while the small substrates can bind in any order, they must be in place before productive tRNA binding can occur.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. A color-coded representation of the mobile regions in the catalytic domain. The apo structure is in gray. The substrates threonine and ATP are represented in the active site. The mobile regions are: 1, the ordering loop, residues 301-317, in yellow as in the EcThrRS+tRNA structure; 2, the motif 2 loop, residues 363-377, in magenta as in EcDN-ThrRS+ThrAMS; 3, the threonine loop, residues 417-466, in red as in EcDN-ThrRS+threonine; 4, the ATP loop, residues 468-480, in green as in SaThrRS+ATP. This Figure and the following ones have been prepared with the program DINO (http://www.dino3d.org).
Figure 5.
Figure 5. Annealed omit maps in the active site of ThrRS from S. aureus, contoured at 1.5s. The substrates and the solvent molecules were omitted from the simulated annealing refinement and the calculation of the electron density maps. (a) SaThrRS:ATP structure, subunit A of the dimer, showing ATP in the bent conformation. (b) SaThrRS:ATP structure, subunit B. (c) and (d) SaThrRS+ThrAMS structure in subunits A and B of the dimer, respectively. For consistency, the amino acid numbering of E. coli ThrRS is used here for S. aureus (the positions shown are occupied by the same amino acid in the two systems, except for Glu484, replaced by a triptophan in E. coli).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 331, 201-211) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20122268 S.Wu, T.Liu, and R.B.Altman (2010).
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues.
  BMC Struct Biol, 10, 4.  
18997014 A.Minajigi, and C.S.Francklyn (2008).
RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 17748-17753.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
18611382 L.Klipcan, I.Levin, N.Kessler, N.Moor, I.Finarov, and M.Safro (2008).
The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase.
  Structure, 16, 1095-1104.
PDB code: 3cmq
  18931432 S.Shimizu, E.C.Juan, Y.I.Miyashita, Y.Sato, M.M.Hoque, K.Suzuki, M.Yogiashi, M.Tsunoda, A.C.Dock-Bregeon, D.Moras, T.Sekiguchi, and A.Takénaka (2008).
Crystallization and preliminary crystallographic studies of putative threonyl-tRNA synthetases from Aeropyrum pernix and Sulfolobus tokodaii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 903-910.  
16374837 J.Ishijima, Y.Uchida, C.Kuroishi, C.Tuzuki, N.Takahashi, N.Okazaki, K.Yutani, and M.Miyano (2006).
Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution.
  Proteins, 62, 1133-1137.
PDB code: 1v4p
16675947 S.Bilokapic, T.Maier, D.Ahel, I.Gruic-Sovulj, D.Söll, I.Weygand-Durasevic, and N.Ban (2006).
Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition.
  EMBO J, 25, 2498-2509.
PDB codes: 2cim 2cj9 2cja 2cjb
15746292 Y.Ye, and A.Godzik (2005).
Multiple flexible structure alignment using partial order graphs.
  Bioinformatics, 21, 2362-2369.  
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.  
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 code is shown on the right.