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-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'-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'-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 beta-DNA complex enhances the function of Pol beta.
Tang
Kuo-Hsiang
KH
Department of Chemistry, the Ohio State University, Columbus, OH 43210, USA.
Niebuhr
Marc
M
Aulabaugh
Ann
A
Tsai
Ming-Daw
MD
D000818:Animals; D004247:DNA / Q000737:chemistry*; D019951:DNA Polymerase beta / Q000737:chemistry*; D004260:DNA Repair; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry*; D008958:Models, Molecular; D051381:Rats; D053838:Scattering, Small Angle; D012996:Solutions; D014461:Ultracentrifugation; D014961:X-Ray Diffraction
D012996:Solutions; D004247:DNA; C109534:DNA polymerase X; D019951:DNA Polymerase beta; D004259:DNA-Directed DNA Polymerase