Nucleic Acids Research Advance Access originally published online on April 2, 2008
Nucleic Acids Research 2008 36(9):2948-2957; doi:10.1093/nar/gkn138
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2008, Vol. 36, No. 9 2948-2957
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Mismatched dNTP incorporation by DNA polymerase β does not proceed via globally different conformational pathways
1Departments of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA, 2Genomics Research Center, Academia Sinica, Taiwan, 3Stanford Synchrotron Radiation Laboratory, MS99, SLAC, Menlo Park, CA 94025, 4Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA, 5Institute of Bioinformatics and Structural Biology, National Tsing Hua University and 6Institute of Biological Chemistry, Academia Sinica, Taiwan
*To whom correspondence should be addressed. Tel: 886 2 2789 9930 ext. 341; Fax: 886 2 2789 8811; Email: tsai{at}chemistry.ohio-state.edu
Correspondence may also be addressed to Kuo-Hsiang Tang. Tel: 614 292 6771; Fax: 614 292 6773; Email: jtang{at}chemistry.ohio-state.edu
Received December 17, 2007. Revised March 7, 2008. Accepted March 12, 2008.
Understanding how DNA polymerases control fidelity requires elucidation of the mechanisms of matched and mismatched dNTP incorporations. Little is known about the latter because mismatched complexes do not crystallize readily. In this report, we employed small-angle X-ray scattering (SAXS) and structural modeling to probe the conformations of different intermediate states of mammalian DNA polymerase β (Pol β) in its wild-type and an error-prone variant, I260Q. Our structural results indicate that the mismatched ternary complex lies in-between the open and the closed forms, but more closely resembles the open form for WT and the closed form for I260Q. On the basis of molecular modeling, this over-stabilization of mismatched ternary complex of I260Q is likely caused by formation of a hydrogen bonding network between the side chains of Gln260, Tyr296, Glu295 and Arg258, freeing up Asp192 to coordinate MgdNTP. These results argue against recent reports suggesting that mismatched dNTP incorporations follow a conformational path distinctly different from that of matched dNTP incorporation, or that its conformational closing is a major contributor to fidelity.
The coordinates of free I260Q have been deposited to PDB (2VAN).