TY - JOUR
T1 - Modeling study on the cleavage step of the self-splicing reaction in group i introns
AU - Setlik, Robert F.
AU - Garduno-Juarez, Ramon
AU - Manchester, John I.
AU - Shibata, Masayuki
AU - Omstein, Rick L.
AU - Rein, Robert
N1 - Funding Information:
This work was supported in part by a grant from NASA (NAGW-1546) and in part from the National Foundation of Cancer Research. Partial support was also provided by the Northwest College and University Association for Science (NORCUS)
Funding Information:
in afftliation with Washington State University under Contract DE-AMPb-76-RL0-2225 with the U.S. DepartmentofEnergy, Office ofEnergy Research. RF.S andJ.I.M. are grateful for support through NORCUS Laboratory Graduate Appointments. The authors also acknowledge supercomputer support at the Pittsburgh Supercomputing Center through grant DMB880048P. Pacific Northwest Laboratory is operated for the U.S. Department of Energy by Battelle Memorial Institute under Contract DE-AC06-76RLO 1830.
PY - 1993/6
Y1 - 1993/6
N2 - A 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 PI 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 EMBOJ. 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.
AB - A 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 PI 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 EMBOJ. 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.
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U2 - 10.1080/07391102.1993.10508689
DO - 10.1080/07391102.1993.10508689
M3 - Article
C2 - 8357544
AN - SCOPUS:0027253555
SN - 0739-1102
VL - 10
SP - 945
EP - 972
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
IS - 6
ER -