Solution Structures of 2 : 1 And 1 : 1 DNA Polymerase - DNA Complexes Probed By Ultracentrifugation And Small-Angle X-Ray Scattering

We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme-DNA complexes of rat DNA polymerase {beta} (Pol {beta}) 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 {beta...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 36; no. 3
Main Authors:	Tang, K.H., /Ohio State U., Niebuhr, M., /SLAC, SSRL, Aulabaugh, A., /Wyeth Res. Biophys., Pearl River, Tsai, M.D., /Ohio State U. /SLAC, SSRL
Format:	Journal Article
Language:	English
Published:	United States 30-04-2009
Subjects:	CHEM CONFIGURATION CRYSTAL STRUCTURE DNA DNA POLYMERASES FEVER LYASES MATERIALS SCIENCE SCATTERING SEDIMENTATION STRUCTURAL MODELS SWINE ULTRACENTRIFUGATION VELOCITY
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Summary:	We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme-DNA complexes of rat DNA polymerase {beta} (Pol {beta}) 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 {beta}-DNA complex, whereas only 1 : 1 Pol X-DNA complex was observed. Three-dimensional structural models for the 2 : 1 Pol {beta}-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{prime}-dRP lyase domain of the second Pol {beta} molecule with the active site of the 1 : 1 Pol {beta}-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{prime}-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{prime}-dRP lyase reaction in the crystal structures of the closed ternary enzyme-DNA-dNTP complexes, we propose that the asymmetric 2 : 1 Pol {beta}-DNA complex enhances the function of Pol {beta}.
Bibliography:	USDOE AC02-76SF00515 SLAC-REPRINT-2009-041
ISSN:	0305-1048 1362-4962