A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes.
Published
Journal Article
The two ribozymes of hepatitis delta virus (HDV) cleave faster in divalent metal ions than in monovalent cations, and a variety of divalent metal ions can act as catalysts in supporting these higher rates. Although the ribozymes are closely related in sequence and structure, they display a different metal ion preference; the genomic form cleaves moderately faster in Mg2+ than in Ca2+ while the reverse is true for the antigenomic ribozyme. This difference raises questions about understanding the catalytic role of the metal ion in the reaction. We found that the metal ion reactivity preference correlated with the identity of a single nucleotide 5' of the cleavage site (-1 position). It is a U in the genomic sequence and a C in the antigenomic sequence. With both ribozymes, the reactivity preference for Mg2+ and Ca2+ could be reversed with a change at this position (C to U or U to C). Moreover, with an A at position -1, there was a relative increase in cleavage rates in low concentrations of Mn2+ for both ribozymes. Metal ion reactivity preference was also linked to changes in pH, and the pH-rate profiles could be shifted with nucleotide changes at position -1. Together, the data provide biochemical evidence in support of an organized active site, as seen in the crystal structures, where at least one metal ion, an ionizable group, and the conformation of the phosphate backbone at the cleavage site interact in concert to promote cleavage.
Full Text
Duke Authors
Cited Authors
- Perrotta, AT; Been, MD
Published Date
- May 1, 2007
Published In
Volume / Issue
- 46 / 17
Start / End Page
- 5124 - 5130
PubMed ID
- 17417876
Pubmed Central ID
- 17417876
International Standard Serial Number (ISSN)
- 0006-2960
Digital Object Identifier (DOI)
- 10.1021/bi602569x
Language
- eng
Conference Location
- United States