Mapping Functional Substrate-Enzyme Interactions in the Pol β Active Site Through Chemical Biology: Structural Responses to Acidity Modification of Incoming DNTPs

Overview

Journal Biochemistry

Specialty Biochemistry

Date 2018 Jun 7

PMID 29874056

Citations 6

Authors

Vinod K Batra

Keriann Oertell

William A Beard

Boris A Kashemirov

Charles E McKenna

Myron F Goodman

Samuel H Wilson

Affiliations

Soon will be listed here.

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 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.

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