scholarly journals Hydrogen-Bonding Capability of a Templating Difluorotoluene Nucleotide Residue in an RB69 DNA Polymerase Ternary Complex

2011 ◽  
Vol 133 (26) ◽  
pp. 10003-10005 ◽  
Author(s):  
Shuangluo Xia ◽  
William H. Konigsberg ◽  
Jimin Wang
Keyword(s):  
Hydrogen Bonding ◽  
Dna Polymerase ◽  
Ternary Complex ◽  
Nucleotide Residue

Hydrogen-Bonding Interactions at the DNA Terminus Promote Extension from Methylguanine Lesions by Human Extender DNA Polymerase ζ

Biochemistry ◽  
2018 ◽  
Vol 57 (41) ◽  
pp. 5978-5988 ◽  
Author(s):  
Michael H. Räz ◽  
Shana J. Sturla ◽  
Hailey L. Gahlon
Keyword(s):  
Hydrogen Bonding ◽  
Dna Polymerase ◽  
Hydrogen Bonding Interactions

Nucleotides with Altered Hydrogen Bonding Capacities Impede Human DNA Polymerase η by Reducing Synthesis in the Presence of the Major Cisplatin DNA Adduct

2015 ◽  
Vol 137 (14) ◽  
pp. 4728-4734 ◽  
Author(s):  
Arman Nilforoushan ◽  
Antonia Furrer ◽  
Laura A. Wyss ◽  
Barbara van Loon ◽  
Shana J. Sturla
Keyword(s):  
Hydrogen Bonding ◽  
Dna Polymerase ◽  
Dna Adduct ◽  
Human Dna

scholarly journals Importance of Hydrogen Bonding for Efficiency and Specificity of the Human Mitochondrial DNA Polymerase

2007 ◽  
Vol 283 (21) ◽  
pp. 14402-14410 ◽  
Author(s):  
Harold R. Lee ◽  
Sandra A. Helquist ◽  
Eric T. Kool ◽  
Kenneth A. Johnson
Keyword(s):  
Mitochondrial Dna ◽  
Hydrogen Bonding ◽  
Dna Polymerase ◽  
Human Mitochondrial Dna ◽  
Mitochondrial Dna Polymerase

Importance of Terminal Base Pair Hydrogen-Bonding in 3‘-End Proofreading by the Klenow Fragment of DNA Polymerase I†

Biochemistry ◽  
2000 ◽  
Vol 39 (10) ◽  
pp. 2626-2632 ◽  
Author(s):  
Juan C. Morales ◽  
Eric T. Kool
Keyword(s):  
Hydrogen Bonding ◽  
Dna Polymerase ◽  
Base Pair ◽  
Klenow Fragment ◽  
Dna Polymerase I ◽  
Polymerase I

scholarly journals Base Pair Hydrogen Bonding and the Selectivity of a DNA Polymerase

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Harold R Lee ◽  
Kenneth A. Johnson
Keyword(s):  
Hydrogen Bonding ◽  
Dna Polymerase ◽  
Base Pair

scholarly journals Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Metal Ion ◽  
Ternary Complex ◽  
Critical Role ◽  
Divalent Metal ◽  
Binary Complex ◽  
Divalent Metal Ions ◽  
Divalent Metal Ion ◽  
Initial Binding

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

scholarly journals Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO–POL enzyme

2020 ◽  
Vol 48 (6) ◽  
pp. 3165-3180
Author(s):  
Shreya Ghosh ◽  
Yehuda Goldgur ◽  
Stewart Shuman
Keyword(s):  
Crystal Structures ◽  
Dna Polymerase ◽  
Ternary Complex ◽  
Structural Features ◽  
Reverse Transcriptase Activity ◽  
Dna Polymerase I ◽  
Polymerase Domain ◽  
Open Conformation ◽  
Rna:Dna Hybrid ◽  
Polymerase I

Abstract Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5′ exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3′-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain—especially the O helix—to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3′ exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO–POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.

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