Energy analysis of chemistry for correct insertion by DNA polymerase β

doi:10.1073/pnas.0606006103

Energy analysis of chemistry for correct insertion by DNA polymerase β

^†Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599; and
^‡Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709-2233

Communicated by Robert G. Parr, University of North Carolina, Chapel Hill, NC, July 19, 2006 (received for review March 8, 2006)

Abstract

X-ray crystallographic structures of human DNA polymerase β with nonhydrolyzable analogs containing all atoms in the active site required for catalysis provide a secure starting point for a theoretical analysis (quantum mechanics/molecular mechanics) of the mechanism of chemistry without biasing of modeling assumptions as required in previous studies. These structures provide the basis for a detailed quantum mechanics/molecular mechanics study of the path for the complete transfer of a monophosphate nucleoside donor to the sugar acceptor in the active site. The reaction is largely associative with the main energetic step preceded by proton transfer from the terminal primer deoxyribose O3′ to Asp-256. The key residues that provide electrostatic stabilization of the transition state are identified and compared with those identified by mutational studies.

Footnotes

^§To whom correspondence should be addressed. E-mail: pedersen{at}email.unc.edu
Author contributions: P.L., L.C.P., V.K.B., W.A.B., S.H.W., and L.G.P. designed research; P.L. performed research; P.L., L.C.P., V.K.B., W.A.B., and S.H.W. contributed new reagents/analytic tools; P.L. analyzed data; and P.L. and L.G.P. wrote the paper.
Conflict of interest statement: No conflicts declared.
Abbreviations:

pol β,

polymerase β;

QM,

quantum mechanics;

MM,

molecular mechanics;

TS,

transition state.