The glmS Ribozyme Cofactor is a General Acid-Base Catalyst

被引:35
作者
Viladoms, Julia
Fedor, Martha J. [1 ]
机构
[1] Scripps Res Inst, Dept Mol Biol, Dept Chem Physiol, La Jolla, CA 92037 USA
关键词
DELTA VIRUS RIBOZYME; SELF-CLEAVAGE; HAMMERHEAD RIBOZYME; RIBONUCLEASE-A; RNA; RIBOSWITCH; MECHANISM; BINDING; SITE; GLUCOSAMINE-6-PHOSPHATE;
D O I
10.1021/ja307021f
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
The glmS ribozyme is the first natural self-cleaving ribozyme known to require a cofactor. The D-glucosamine-6-phosphate (GlcN6P) cofactor has been proposed to serve as a general acid, but its role in the catalytic mechanism has not been established conclusively. We surveyed GlcN6P-like molecules for their ability to support self cleavage of the glmS ribozyme and found a strong correlation between the pH dependence of the cleavage reaction and the intrinsic acidity of the cofactors. For cofactors with low binding affinities, the contribution to rate enhancement was proportional to their intrinsic acidity. This linear free energy relationship between cofactor efficiency and acid dissociation constants is consistent with a mechanism in which the cofactors participate directly in the reaction as general acid-base catalysts. A high value for the Bronsted coefficient (beta similar to 0.7) indicates that a significant amount of proton transfer has already occurred in the transition state. The glmS ribozyme is the first self-cleaving RNA to use an exogenous acid-base catalyst.
引用
收藏
页码:19043 / 19049
页数:7
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