Mapping Functional Substrate–Enzyme Interactions in the pol β Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs

Batra, Vinod K.; Oertell, Keriann; Beard, William A.; Kashemirov, Boris A.; McKenna, Charles E.; Goodman, Myron F.; Wilson, Samuel H.

doi:10.1021/acs.biochem.8b00418

Mapping Functional Substrate–Enzyme Interactions in the pol β Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs

Journal Article · Wed Jun 06 00:00:00 EDT 2018 · Biochemistry

DOI:https://doi.org/10.1021/acs.biochem.8b00418· OSTI ID:1463717

Batra, Vinod K. ^[1]; Oertell, Keriann ^[2]; Beard, William A. ^[1]; Kashemirov, Boris A. ^[2]; ^[2]; ^[2]; ^[1]

National Inst. of Health (NIH), Triangle Park, MD (United States)
Univ. of Southern California, Los Angeles, CA (United States)

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. Lastly, 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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Inst. of Health (NIH); USDOE Office of Science (SC)

OSTI ID:: 1463717

Journal Information:: Biochemistry, Journal Name: Biochemistry Journal Issue: 26 Vol. 57; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

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New chirally modified bisphosphonates for synthesis of individual beta,gamma-CHX-deoxynucleotide diastereomers Haratipour, Pouya; Minard, Corinne; Nakhjiri, Maryam Phosphorus, Sulfur, and Silicon and the Related Elements, Vol. 194, Issue 4-6 https://doi.org/10.1080/10426507.2018.1540482	journal	March 2019

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