Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.Batra, V.K., Oertell, K., Beard, W.A., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.
(2018) Biochemistry 57: 3934-3944
- PubMed: 29874056
- DOI: 10.1021/acs.biochem.8b00418
- Primary Citation of Related Structures:
- PubMed Abstract:
We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replac ...
We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pβ and Pγ of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, dTTP, and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group, yet with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important for understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site.
Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive , Research Triangle Park , North Carolina 27709 , United States.,Department of Biological Sciences , University of Southern California , Los Angeles , California 90089-0371 , United States.,Department of Chemistry , University of Southern California , Los Angeles , California 90089-1062 , United States.