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Nucleic Acids Research Advance Access published online on December 15, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm1101
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© 2007 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.

Structured Biology

Solution structures of 2 : 1 and 1 : 1 DNA polymerase–DNA complexes probed by ultracentrifugation and small-angle X-ray scattering

Kuo-Hsiang Tang1,2, Marc Niebuhr3, Ann Aulabaugh4 and Ming-Daw Tsai1,2,5,*

1Department of Chemistry and Department of 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, 4Wyeth Research Biophysics/Enzymology-Screening Sciences, Pearl River, NY 10965, USA and 5Institute of Biological Chemistry, Academia Sinica, Taiwan

*To whom correspondence should be addressed. Tel: +886 2 2789 9930; Fax: +886 2 2789 8811; Email: tsai{at}chemistry.ohio-state.edu

Received November 9, 2007. Revised November 25, 2007. Accepted November 25, 2007.

We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme–DNA complexes of rat DNA polymerase β (Pol β) and African swine fever virus DNA polymerase X (ASFV Pol X) with one-nucleotide gapped DNA. The results indicated formation of a 2 : 1 Pol β–DNA complex, whereas only 1 : 1 Pol X–DNA complex was observed. Three-dimensional structural models for the 2 : 1 Pol β–DNA and 1 : 1 Pol X–DNA complexes were generated from the SAXS experimental data to correlate with the functions of the DNA polymerases. The former indicates interactions of the 8 kDa 5'-dRP lyase domain of the second Pol β molecule with the active site of the 1 : 1 Pol β–DNA complex, while the latter demonstrates how ASFV Pol X binds DNA in the absence of DNA-binding motif(s). As ASFV Pol X has no 5'-dRP lyase domain, it is reasonable not to form a 2 : 1 complex. Based on the enhanced activities of the 2 : 1 complex and the observation that the 8 kDa domain is not in an optimal configuration for the 5'-dRP lyase reaction in the crystal structures of the closed ternary enzyme–DNA–dNTP complexes, we propose that the asymmetric 2 : 1 Pol β–DNA complex enhances the function of Pol β.


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