Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase

Cell. 2000 Nov 22;103(5):793-803. doi: 10.1016/s0092-8674(00)00182-3.

Abstract

Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine / chemistry
  • Binding Sites
  • Crystallography, X-Ray
  • Hydrolysis
  • Isoleucine / chemistry*
  • Models, Chemical
  • Models, Molecular
  • Proline / chemistry
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA, Transfer, Val / chemistry*
  • RNA, Transfer, Val / metabolism
  • Thermus thermophilus / chemistry
  • Threonine / chemistry*
  • Valine / chemistry*
  • Valine-tRNA Ligase / chemistry*
  • Valine-tRNA Ligase / metabolism

Substances

  • RNA, Transfer, Val
  • Isoleucine
  • Threonine
  • Proline
  • Valine-tRNA Ligase
  • Valine
  • Adenosine