The Closing Mechanism of DNA Polymerase I at Atomic Resolution

Authors

• Bill R. Miller III
• Loreena S. Beese
• Carol A. Parish, University of RichmondFollow
• Eugene Y. Wu, University of RichmondFollow

Abstract

Highlights

• DNA polymerase X-ray structure provides starting structure to investigate closing
• MD simulations provide atomistic details of DNA polymerase closing
• Propose sequence of events in prechemistry DNA polymerase active site assembly
• Identify a conserved histidine as a potential proton acceptor to initiate catalysis

Summary 
DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase I bound to DNA in the open conformation with a dNTP present in the active site. We use this structure to computationally simulate the open to closed transition of DNA polymerase in the presence of a Watson-Crick base pair. Our microsecond simulations allowed us to characterize the key steps involved in active site assembly, and propose the sequence of events involved in the prechemistry steps of DNA polymerase catalysis. They also reveal new features of the polymerase mechanism, such as a conserved histidine as a potential proton acceptor from the primer 3′-hydroxyl.

Document Type

Article

Publication Date

9-1-2015

Publisher Statement

Copyright © 2015 Elsevier Ltd. All rights reserved.

Recommended Citation

Miller, Bill R. III; Beese, Loreena S.; Parish, Carol A.; and Wu, Eugene Y., "The Closing Mechanism of DNA Polymerase I at Atomic Resolution" (2015). Biology Faculty Publications. 358.
https://scholarship.richmond.edu/biology-faculty-publications/358