Classification of the nucleolytic ribozymes based upon catalytic mechanism

F1000Res. 2019 Aug 19:8:F1000 Faculty Rev-1462. doi: 10.12688/f1000research.19324.1. eCollection 2019.

Abstract

The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2'-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. A major part of this arises from concerted general acid-base catalysis. Recent identification of new ribozymes has expanded the group to a total of nine and this provides a new opportunity to identify sub-groupings according to the nature of the general base and acid. These include nucleobases, hydrated metal ions, and 2'-hydroxyl groups. Evolution has selected a number of different combinations of these elements that lead to efficient catalysis. These differences provide a new mechanistic basis for classifying these ribozymes.

Keywords: Nucleolytic ribozymes; general acid-base catalysis; metal ions.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Catalysis
  • Phosphorus
  • RNA / metabolism*
  • RNA, Catalytic*

Substances

  • RNA, Catalytic
  • Phosphorus
  • RNA