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Modeling study on the cleavage step of the self-splicing reaction in group I intronsA three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.
Document ID
20050000460
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
Authors
Setlik, R. F.
(Roswell Park Cancer Institute Buffalo, New York 14263)
Garduno-Juarez, R.
Manchester, J. I.
Shibata, M.
Ornstein, R. L.
Rein, R.
Date Acquired
August 22, 2013
Publication Date
June 1, 1993
Publication Information
Publication: Journal of biomolecular structure & dynamics
Volume: 10
Issue: 6
ISSN: 0739-1102
Subject Category
Life Sciences (General)
Distribution Limits
Public
Copyright
Other
Keywords
NASA Discipline Exobiology
NASA Program Exobiology
Non-NASA Center
NASA Discipline Number 52-20

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