STRUCTURAL AND MECHANISTIC ENZYMOLOGY OF NUCLEOTIDE INCORPORATION BY A-FAMILY DNA POLYMERASES
Open Access
- Author:
- Almishwat, Mohammad Ali
- Graduate Program:
- Biochemistry, Microbiology, and Molecular Biology
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- September 24, 2019
- Committee Members:
- James Gregory Ferry, Dissertation Advisor/Co-Advisor
James Gregory Ferry, Committee Chair/Co-Chair
Susan Hafenstein, Committee Member
David Scott Gilmour, Committee Member
Squire J Booker, Outside Member
Amie Kathleen Boal, Committee Member
Ken Keiler, Program Head/Chair - Keywords:
- DNA polymerase
A-family
DNA replication
DNA
Nucleotide incorporation
time-resolved
structural enzymology
X-ray crystallography
high-fidelity - Abstract:
- DNA-dependent DNA and RNA polymerases are essential enzymes to gene expression and regulation. DNA polymerases, the enzymes responsible for carrying out and regulating the faithful transmission of an organisms genetic material through the process of DNA replication have been extensively characterized, however, the exact mechanism by which a high fidelity DNA polymerase preferentially incorporates a correct nucleotide, and differentially excludes an incorrect nucleotide during DNA replication is not fully understood. Structural studies of various DNA polymerases and their complexes with DNA have provided a great deal of insight into how catalysis in nucleotide incorporation occurs, and have also provided empirical models of how fidelity is brought about and sustained in these enzymes during DNA replication. This dissertation describes ongoing work to elucidate the mechanism of high-fidelity nucleotide incorporation during DNA replication by an A-family DNA polymerase, employing biochemical and structural studies to dissect the structural and mechanistic changes that occur during nucleotide binding and phosphodiester bond formation between the incoming nucleotide and the growing primer strand. Time-resolved X-ray crystallography is used to monitor and study in real-time, at atomic resolution, the mechanism of nucleotide incorporation in crystallo. This method has been successful in studying the mechanistic details of several enzymes, and we show here that it can be used to directly observe and monitor the sequential structural and mechanistic changes in an A-family DNA polymerase and its bound substrate DNA that are brought about by nucleotide binding to the DNA polymerase active site and subsequent catalysis.