Three-dimensional structure of a hammerhead ribozyme [see comments]

Pley HW; Flaherty KM; McKay DB

Department of Structural Biology, Stanford University School of Medicine, California 94305-5400.

Nature 372: 68-74 (1994)

Abstract
The hammerhead ribozyme is a small catalytic RNA motif made up of three base-paired stems and a core of highly conserved, non-complementary nucleotides essential for catalysis. The X-ray crystallographic structure of a hammerhead RNA-DNA ribozyme-inhibitor complex at 2.6 A resolution reveals that the base-paired stems are A-form helices and that the core has two structural domains. The first domain is formed by the sequence 5'-CUGA following stem I and is a sharp turn identical to the uridine turn of transfer RNA, whereas the second is a non-Watson-Crick three-base-pair duplex with a divalent-ion binding site. The phosphodiester backbone of the DNA inhibitor strand is splayed out at the phosphate 5' to the cleavage site. The structure indicates that the ribozyme may destabilize a substrate strand in order to facilitate twisting of the substrate to allow cleavage of the scissile bond.

Mesh Headings

Base Sequence

Binding Sites

Crystallography, X-Ray

DNA

Models, Molecular

Molecular Sequence Data

Nucleic Acid Conformation*

RNA, Catalytic*

Support, Non-U.S. Gov't

Support, U.S. Gov't, P.H.S.

Unique Identifier: 95059400

Chemical Identifiers (Names)

(RNA, Catalytic)

9007-49-2 (DNA)