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Theoretical analyses on the role of Mg 2+ ions in ribozyme reactions
Author(s) -
Uchimaru Tadafumi,
Uebayasi Masami,
Tanabe Kazutoshi,
Taira Kazunari
Publication year - 1993
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.7.1.8422960
Subject(s) - ribozyme , chemistry , phosphodiester bond , tetracoordinate , tetrahymena , hairpin ribozyme , stereochemistry , metal ions in aqueous solution , crystallography , vs ribozyme , ion , carboxylate , rna , biochemistry , computer graphics (images) , organic chemistry , gene , computer science , planar
To elucidate the role of the Mg 2+ ion in ribozyme reactions, we carried out ab initio molecular orbital investigations on dianionic trimethoxyphosphorane A and its Mg 2+ complex (overall a neutral molecule) as a model system for the reaction center of Tetrahymena‐ type ribozyme. Although dianionic oxyphosphorane A concentrates its negative charges on the equatorial phosphoryl oxygens, the coordination of the Mg 2+ ion between these two oxygens is unlikely. Geometry optimizations of the complex and the electrostatic potential of A both suggest that Mg 2+ coordination preferably occurs in the region between the axial oxygen and the equatorial phosphoryl oxygen. The considerations of electrostatic potential rationalize the geometries of carboxylate‐metal and phosphate‐metal interactions extracted from the Cambridge Structural Database as well. Consequently, the Mg 2+ ion at the active site of Tetrahymena‐ type ribozyme most likely lies in the regions between the axial and equatorial oxygens. The axial‐equatorial coordinations of Mg 2+ ions conceivably increase the electronegativities of the axial oxygens and facilitate cleavage of the phosphodiester bond located at the junction of the intron and the exon. It is thus likely that the Mg 2 ∗ ions play the key role in the phosphodiester cleavage reactions mediated by ribozymes.— Uchimaru, T., Uebayasi, M., Tanabe, K., Taira, K. Theoretical analyses of the role of Mg 2+ ions in ribozyme reactions. FASEB J. 7: 137‐142; 1993.