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Functional analysis of hairpin ribozyme active site architecture

Academic Article
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Overview

authors

  • Cottrell, J. W.
  • Kuzmin, Y. I.
  • Fedor, Martha

publication date

  • May 2007

journal

  • Journal of Biological Chemistry  Journal

abstract

  • The hairpin ribozyme is a small catalytic motif found in plant satellite RNAs where it catalyzes a reversible self-cleavage reaction during processing of replication intermediates. Crystallographic studies of hairpin ribozymes have provided high resolution views of the RNA functional groups that comprise the active site and stimulated biochemical studies that probed the contributions of nucleobase functional groups to catalytic chemistry. The dramatic loss of activity that results from perturbation of active site architecture points to the importance of positioning and orientation in catalytic rate acceleration. The current study focuses on the network of noncovalent interactions that align nucleophilic and leaving group oxygens in the orientation required for the S(N)2-type reaction mechanism and orient the active site nucleobases near the reactive phosphate to facilitate catalytic chemistry. Nucleotide modifications that alter or eliminate individual hydrogen bonding partners had different effects on the activation barrier to catalysis, the stability of ribozyme complexes in the ground state, and the internal equilibrium between cleavage and ligation of bound products. Furthermore, substitution of hydrogen bond donors and acceptors with seemingly equivalent pairs sometimes had very different functional consequences. These biochemical analyses augment high resolution structural information to provide insights into the functional significance of active site architecture.

subject areas

  • Crystallography, X-Ray
  • Databases, Protein
  • Hydrogen Bonding
  • Models, Molecular
  • Nucleic Acid Conformation
  • RNA, Catalytic
  • RNA, Plant
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Identity

International Standard Serial Number (ISSN)

  • 0021-9258

Digital Object Identifier (DOI)

  • 10.1074/jbc.M700451200

PubMed ID

  • 17351263
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Additional Document Info

start page

  • 13498

end page

  • 13507

volume

  • 282

issue

  • 18

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