Assessing the Potential Effects of Active Site Mg²⁺ Ions in the glmS Ribozyme-Cofactor Complex.

ABSTRACT: Ribozymes employ diverse catalytic strategies in their self-cleavage mechanisms, including the use of divalent metal ions. This work explores the effects of Mg²⁺ ions in the active site of the glmS ribozyme-GlcN6P cofactor complex using computational methods. Deleterious and potentially beneficial effects of an active site Mg²⁺ ion on the self-cleavage reaction were identified. The presence of a Mg²⁺ ion near the scissile phosphate oxygen atoms at the cleavage site was determined to be deleterious, and thereby anticatalytic, due to electrostatic repulsion of the cofactor, disruption of key hydrogen-bonding interactions, and obstruction of nucleophilic attack. On the other hand, the presence of a Mg²⁺ ion at another position in the active site, th

SUBMITTER: Zhang S 

PROVIDER: S-EPMC5117136 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature