Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion
Abstract
Faithful transmission and maintenance of genetic material is primarily fulfilled by DNA polymerases. During DNA replication, these enzymes catalyze incorporation of deoxynucleotides into a DNA primer strand based on Watson-Crick complementarity to the DNA template strand. Through the years, research on DNA polymerases from every family and reverse transcriptases has revealed structural and functional similarities, including a conserved domain architecture and purported two-metal-ion mechanism for nucleotidyltransfer. However, it is equally clear that DNA polymerases possess distinct differences that often prescribe a particular cellular role. Indeed, a unified kinetic mechanism to explain all aspects of DNA polymerase catalysis, including DNA binding, nucleotide binding and incorporation, and metal-ion-assisted nucleotidyltransfer (i.e., chemistry), has been difficult to define. In particular, the contributions of enzyme conformational dynamics to several mechanistic steps and their implications for replication fidelity are complex. Moreover, recent time-resolved X-ray crystallographic studies of DNA polymerases have uncovered a third divalent metal ion present during DNA synthesis, the function of which is currently unclear and debated within the field. In this review, we survey past and current literature describing the structures and kinetic mechanisms of DNA polymerases from each family to explore every major mechanistic step while emphasizing the impact of enzyme conform…
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DNA and RNA polymerases function with multiple Mg2+ ions in their active site, with the highest affinity binding having a Kd of ~50-100 μM.
“DNA and RNA polymerases function with multiple Mg2+ ions in their active site,79 with the highest affinity binding having a Kd of ∼50–100 μM.80”
From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [79]
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Metals in Motion: Understanding Labile Metal Pools in Bacteria
Helmann, J. D. (2025) · Biochemistry · doi:10.1021/acs.biochem.4c00726 · Cited by 49 · see citing works
- Authors
- Raper, A. T., Reed, A. J., & Suo, Z.
- Affiliations
- The Ohio State University (US)
- Corresponding author
- Suo, Zucai
- Venue
- Chemical Reviews
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-06-04
- Volume
- 118
- Issue
- 12
- Pages
- 6000-6025
- ISSN
- 0009-2665 (ISSN-L)
- 1520-6890
- OpenAlex
- W2805276053
- Cited by
- 83
- References
- 11
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 12 · 2023: 7 · 2022: 13 · 2021: 8 · 2020: 12 · 2019: 13 · 2018: 4
- FWCI
- 0.47
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Chemical Reviews (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Division of Molecular and Cellular Biosciences (MCB-1716168)
- Ohio State University
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- DNA polymerase, conformational dynamics, two-metal-ion mechanism, DNA replication fidelity, DNA binding, nucleotide incorporation, reverse transcriptase, time-resolved crystallography
- MeSH terms
- DNA, DNA-Directed DNA Polymerase, Humans, Kinetics, Metals, Protein Conformation, Crystallography, X-Ray, Molecular Dynamics Simulation
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