Slow solvation dynamics at the active site of an enzyme: implications for catalysis

Biochemistry. 2005 Jun 28;44(25):8940-7. doi: 10.1021/bi0473915.

Abstract

Solvation dynamics at the active site of an enzyme, glutaminyl-tRNA synthetase (GlnRS), was studied using a fluorescence probe, acrylodan, site-specifically attached at cysteine residue C229, near the active site. The picosecond time-dependent fluorescence Stokes shift indicates slow solvation dynamics at the active site of the enzyme, in the absence of any substrate. The solvation dynamics becomes still slower when the substrate (glutamine or tRNA(Gln)) binds to the enzyme. A mutant Y211H-GlnRS was constructed in which the glutamine binding site is disrupted. The mutant Y211H-GlnRS labeled at C229 with acrylodan exhibited significantly different solvent relaxation, thus demonstrating that the slow dynamics is indeed associated with the active site. Implications for catalysis and specificity have been discussed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acyl-tRNA Synthetases / chemistry*
  • Amino Acyl-tRNA Synthetases / genetics
  • Amino Acyl-tRNA Synthetases / metabolism*
  • Binding Sites
  • Catalysis
  • Circular Dichroism
  • Cysteine / genetics
  • Cysteine / metabolism
  • Glutamine / metabolism
  • Hydrogen Sulfide / chemistry
  • Kinetics
  • Models, Molecular
  • Mutation / genetics
  • Protein Structure, Tertiary
  • RNA, Transfer / metabolism
  • RNA, Transfer, Gln / metabolism
  • Solvents / chemistry*
  • Spectrometry, Fluorescence
  • Substrate Specificity
  • Tyrosine / genetics
  • Tyrosine / metabolism

Substances

  • RNA, Transfer, Gln
  • Solvents
  • Glutamine
  • Tyrosine
  • RNA, Transfer
  • Amino Acyl-tRNA Synthetases
  • glutaminyl-tRNA synthetase
  • Cysteine
  • Hydrogen Sulfide