Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII

Shuntaro Takahashi, Hisao Matsuno, Hiroyuki Furusawa, Yoshio Okahata

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

EcoRII is a homodimer with two domains consisting of a DNA-binding N terminus and a catalytic C terminus and recognizes two specific sequences on DNA. It shows a relatively complicated cleavage reaction in bulk solution. After binding to either recognition site, EcoRII cleaves the other recognition site of the same DNA (cis-binding) strand and/or the recognition site of the other DNA (trans-binding) strand. Although it is difficult to separate these two reactions in bulk solution, we could simply obtain the binding and cleavage kinetics of only the cis-binding by following the frequency (mass) changes of a DNA-immobilized quartz-crystal microbalance (QCM) responding to the addition of EcoRII in aqueous solution. We obtained the maximum binding amounts (Δmmax), the dissociation constants (Kd), the binding and dissociation rate constants (kon and koff), and the catalytic cleavage reaction rate constants (kcat) for wildtype EcoRII, the N-terminal-truncated form (EcoRII N-domain), and the mutant derivatives in its C-terminal domain (K263A and R330A). It was determined from the kinetic analyses that the N-domain, which covers the catalytic C-domain in the absence of DNA, preferentially binds to the one DNA recognition site while transforming EcoRII into an active form allosterically, and then the secondary C-domain binds to and cleaves the other recognition site of the DNA strand.

Original languageEnglish
Pages (from-to)15023-15030
Number of pages8
JournalJournal of Biological Chemistry
Volume283
Issue number22
DOIs
Publication statusPublished - May 30 2008
Externally publishedYes

Fingerprint

DNA Restriction Enzymes
Monitoring
DNA
Immobilized Nucleic Acids
Rate constants
Quartz Crystal Microbalance Techniques
Kinetics
Quartz crystal microbalances
Catalytic Domain
Reaction rates
Derivatives

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII. / Takahashi, Shuntaro; Matsuno, Hisao; Furusawa, Hiroyuki; Okahata, Yoshio.

In: Journal of Biological Chemistry, Vol. 283, No. 22, 30.05.2008, p. 15023-15030.

Research output: Contribution to journalArticle

Takahashi, Shuntaro ; Matsuno, Hisao ; Furusawa, Hiroyuki ; Okahata, Yoshio. / Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII. In: Journal of Biological Chemistry. 2008 ; Vol. 283, No. 22. pp. 15023-15030.
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