Crystal structure and mechanistic investigation of the twister ribozyme

• Published in: Nature chemical biology Vol. 10; no. 9; pp. 739 - 744
• Main Authors: Liu, Yijin, Wilson, Timothy J, McPhee, Scott A, Lilley, David M J
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-09-2014; Nature Publishing Group
• Subjects: 631/337/1910; 631/535/1266; 631/92/500; 631/92/609; Acids; Adenine - chemistry; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Catalysis; Cell Biology; Chemistry; Chemistry/Food Science; Conserved Sequence; Crystal structure; Crystallography, X-Ray; Enzymes; Medical research; Models, Molecular; Nucleic Acid Conformation; Oryza - chemistry; Proteins; RNA - chemistry; RNA, Catalytic - chemistry; RNA, Plant - chemistry
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/nchembio.1587

The twister ribozyme is a recently discovered self-cleaving RNA that has wide distribution in bacteria and eukaryotes. A crystal structure of a twister ribozyme reveals a double-pseudoknot core that positions a conserved guanine near the scissile phosphate where it participates in general acid-base catalysis.
We present a crystal structure at 2.3-Å resolution of the recently described nucleolytic ribozyme twister. The RNA adopts a previously uncharacterized compact fold based on a double-pseudoknot structure, with the active site at its center. Eight highly conserved nucleobases stabilize the core of the ribozyme through the formation of one Watson-Crick and three noncanonical base pairs, and the highly conserved adenine 3′ of the scissile phosphate is bound in the major groove of an adjacent pseudoknot. A strongly conserved guanine nucleobase directs its Watson-Crick edge toward the scissile phosphate in the crystal structure, and mechanistic evidence supports a role for this guanine as either a general base or acid in a concerted, general acid-base–catalyzed cleavage reaction.