Crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase: new insights into the mechanism of tryptophan activation and implications for anti-fungal drug design

Nucleic Acids Res. 2010 Jun;38(10):3399-413. doi: 10.1093/nar/gkp1254. Epub 2010 Jan 31.

Abstract

Specific activation of amino acids by aminoacyl-tRNA synthetases is essential for maintaining translational fidelity. Here, we present crystal structures of Saccharomyces cerevisiae tryptophanyl-tRNA synthetase (sTrpRS) in apo form and in complexes with various ligands. In each complex, there is a sulfate ion bound at the active site which mimics the alpha- or beta-phosphate group of ATP during tryptophan activation. In particular, in one monomer of the sTrpRS-TrpNH(2)O complex, the sulfate ion appears to capture a snapshot of the alpha-phosphate of ATP during its movement towards tryptophan. Simulation study of a human TrpRS-Trp-ATP model shows that during the catalytic process the alpha-phosphate of ATP is driven to an intermediate position equivalent to that of the sulfate ion, then moves further and eventually fluctuates at around 2 A from the nucleophile. A conserved Arg may interact with the oxygen in the scissile bond at the transition state, indicating its critical role in the nucleophilic substitution. Taken together, eukaryotic TrpRSs may adopt an associative mechanism for tryptophan activation in contrast to a dissociative mechanism proposed for bacterial TrpRSs. In addition, structural analysis of the apo sTrpRS reveals a unique feature of fungal TrpRSs, which could be exploited in rational antifungal drug design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Monophosphate / chemistry
  • Amino Acid Sequence
  • Antifungal Agents / chemistry
  • Apoenzymes / chemistry
  • Catalytic Domain
  • Crystallography, X-Ray
  • Drug Design
  • Humans
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sulfates / chemistry
  • Transfer RNA Aminoacylation
  • Tryptophan / chemistry*
  • Tryptophan / metabolism
  • Tryptophan-tRNA Ligase / chemistry*
  • Tryptophan-tRNA Ligase / metabolism

Substances

  • Antifungal Agents
  • Apoenzymes
  • Saccharomyces cerevisiae Proteins
  • Sulfates
  • Adenosine Monophosphate
  • Tryptophan
  • Tryptophan-tRNA Ligase

Associated data

  • PDB/3KT0
  • PDB/3KT3
  • PDB/3KT6
  • PDB/3KT8