Biology Reference
In-Depth Information
CHAPTER ONE
The Hammerhead Ribozyme:
Structure, Catalysis, and Gene
Regulation
William G. Scott, Lucas H. Horan, Monika Martick
The Center for the Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa
Cruz, Santa Cruz, California, USA
Contents
1. Discovery and Context
2
1.1 Biological context
2
1.2 A prototype ribozyme
3
2. The Minimal Sequence
4
2.1 Enzymology
5
2.2 Crystal structure
7
2.3 Experimental discord
8
3. The Full-Length Sequence
8
3.1 Biological context
9
3.2 Enzymology
9
3.3 Crystal structure
10
3.4 Resolution of experimental discord
11
3.5 Mechanistic proposals
13
4. Hammerhead Ribozymes in Mammalian Gene Regulation
14
References
20
Abstract
The hammerhead ribozyme has long been considered a prototype for understanding
RNA catalysis, but discrepancies between the earlier crystal structures of a minimal ham-
merhead self-cleaving motif and various biochemical investigations frustrated attempt
to understand hammerhead ribozyme catalysis in terms of structure. With the discovery
that a tertiary contact distal from the ribozyme
s active site greatly enhances its catalytic
prowess, and the emergence of new corresponding crystal structures of full-length
hammerhead ribozymes, a unified understanding of catalysis in terms of the structure
is now possible. A mechanism in which the invariant residue G12 functions as a general
base, and the 2
0
-OHmoiety of the invariant G8, itself forming a tertiary base pair with the
invariant C3, is the general acid, appears consistent with both the crystal structure and
biochemical experimental results. Originally discovered in the context of plant satellite
'
