PDBsum entry: 1nyr

Ligase

PDB id: 1nyr

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

Protein chains

Q8NW68  (SYT_STAAW) -  Threonyl-tRNA synthetase

Seq: 645 a.a.

Struc: 642 a.a.

Enzyme reactions

• Enzyme class: E.C.6.1.1.3 - Threonine--tRNA ligase.
• 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 

• 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.