Motions of the fingers subdomain of Klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases

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Abstract

Various kinetic studies on nucleotide incorporation by DNA polymerases have established that a rate-limiting step occurs that is crucial in the mechanism of discrimination between correct versus incorrect nucleotide. Crystallographic studies have indicated that this step may be due to a large open-to-closed conformational transition affecting the fingers subdomain. However, there is no direct evidence to support this hypothesis. In order to investigate whether or not the open-to-closed conformational transition affecting the fingers subdomain is rate limiting, we have developed a fluorescence resonance energy transfer (FRET) system, which monitors motions of the fingers subdomain. We establish that the closing of the fingers subdomain is significantly faster than the kinetically determined rate-limiting step. We propose that the rate-limiting step occurs after the closing of the fingers subdomain and is caused by local reorganization events in the active site. Copyright ©2005 by Elsevier Inc.

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Rothwell, P. J., Mitaksov, V., & Waksman, G. (2005). Motions of the fingers subdomain of Klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases. Molecular Cell, 19(3), 345–355. https://doi.org/10.1016/j.molcel.2005.06.032

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