Analysis on substrate specificity of escherichia coli ribonuclease P using shape variants of pre-tRNA

Proposal of subsites model for substrate shape recognition

Satoshi Suwa, Yasuhiro Nagai, Akihiro Fujimoto, Yo Kikuchi, Terumichi Tanaka

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

We prepared a series of shape variants of a pre-tRNA and examined substrate shape recognition by bacterial RNase P ribozyme and holoenzyme. Cleavage site analysis revealed two new subsites for accepting the T-arm and the bottom half of pre-tRNA in the substrate-binding site of the enzyme. These two subsites take part in cleavage site selection of substrate by the enzyme: the cleavage site is not always selected according to the relative position of the 3′-CCA sequence of the substrate. Kinetic studies indicated that the substrate shape is recognized mainly in the transition state of the reaction, and neither the shape nor position of either the T-arm or the bottom half of the substrate affected the Michaelis complex formation. These results strongly suggest that the 5′ and 3′ termini of a substrate are trapped by the enzyme first, then the position and the shape of the T-arm and the bottom half are examined by the cognate subsites. From these facts, we propose a new substrate recognition model that can explain many experimental facts that have been seen as enigmatic.

Original languageEnglish
Pages (from-to)151-160
Number of pages10
JournalJournal of Biochemistry
Volume145
Issue number2
DOIs
Publication statusPublished - 2009 Feb
Externally publishedYes

Fingerprint

Ribonuclease P
RNA Precursors
Substrate Specificity
Escherichia coli
Substrates
Enzymes
Catalytic RNA
Holoenzymes
Binding Sites
Site selection
Kinetics

Keywords

  • C5 protein
  • M1 RNA
  • Ribozyme
  • RNase P
  • Subsite

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

Cite this

Analysis on substrate specificity of escherichia coli ribonuclease P using shape variants of pre-tRNA : Proposal of subsites model for substrate shape recognition. / Suwa, Satoshi; Nagai, Yasuhiro; Fujimoto, Akihiro; Kikuchi, Yo; Tanaka, Terumichi.

In: Journal of Biochemistry, Vol. 145, No. 2, 02.2009, p. 151-160.

Research output: Contribution to journalArticle

Suwa, Satoshi ; Nagai, Yasuhiro ; Fujimoto, Akihiro ; Kikuchi, Yo ; Tanaka, Terumichi. / Analysis on substrate specificity of escherichia coli ribonuclease P using shape variants of pre-tRNA : Proposal of subsites model for substrate shape recognition. In: Journal of Biochemistry. 2009 ; Vol. 145, No. 2. pp. 151-160.
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