Ribozyme catalysis from the major groove of group II intron domain 5

Mol Cell. 1998 Feb;1(3):433-41. doi: 10.1016/s1097-2765(00)80043-x.

Abstract

The most highly conserved nucleotides in D5, an essential active site component of group II introns, consist of an AGC triad, of which the G is invariant. To understand how this G participates in catalysis, the mechanistic contribution of its functional groups was examined. We observed that the exocyclic amine of G participates in ground state interactions that stabilize D5 binding from the minor groove. In contrast, each major groove heteroatom of the critical G (specifically N7 or O6) is essential for chemistry. Thus, major groove atoms in an RNA helix can participate in catalysis, despite their presumed inaccessibility. N7 or O6 of the critical G could engage in critical tertiary interactions with the rest of the intron or they could, together with phosphate oxygens, serve as a binding site for catalytic metal ions.

Publication types

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

MeSH terms

  • Binding Sites / physiology
  • Introns / physiology*
  • Kinetics
  • Nucleic Acid Conformation*
  • Nucleotides / chemistry
  • Protein Structure, Tertiary
  • RNA Splicing / genetics*
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / genetics
  • RNA, Catalytic / metabolism*

Substances

  • Nucleotides
  • RNA, Catalytic