Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity

Biochemistry ◽  
1988 ◽  
Vol 27 (18) ◽  
pp. 6716-6725 ◽  
Author(s):  
Robert D. Kuchta ◽  
Patricia Benkovic ◽  
Stephen J. Benkovic
Keyword(s):  
Dna Polymerase ◽  
Kinetic Mechanism ◽  
High Fidelity ◽  
Dna Polymerase I ◽  
Polymerase I

scholarly journals The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an “Ajar” Intermediate Conformation in the Nucleotide Selection Mechanism

2011 ◽  
Vol 286 (22) ◽  
pp. 19758-19767 ◽  
Author(s):  
Eugene Y. Wu ◽  
Lorena S. Beese
Keyword(s):  
Dna Polymerase ◽  
Reaction Pathway ◽  
Insertion Site ◽  
Nucleoside Triphosphate ◽  
High Fidelity ◽  
Dna Polymerase I ◽  
Closed Conformation ◽  
Active Site Tyrosine ◽  
Pass Through ◽  
Polymerase I

To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established “open” and “closed” states. In this “ajar” conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.

scholarly journals Role of High-Fidelity Escherichia coli DNA Polymerase I in Replication Bypass of a Deoxyadenosine DNA-Peptide Cross-Link

2011 ◽  
Vol 193 (15) ◽  
pp. 3815-3821 ◽  
Author(s):  
K. Yamanaka ◽  
I. G. Minko ◽  
S. E. Finkel ◽  
M. F. Goodman ◽  
R. S. Lloyd
Keyword(s):  
Escherichia Coli ◽  
Dna Polymerase ◽  
High Fidelity ◽  
Cross Link ◽  
Dna Polymerase I ◽  
Polymerase I

Kinetic mechanism of DNA polymerase I (Klenow)

Biochemistry ◽  
1987 ◽  
Vol 26 (25) ◽  
pp. 8410-8417 ◽  
Author(s):  
R. D. Kuchta ◽  
V. Mizrahi ◽  
P. A. Benkovic ◽  
K. A. Johnson ◽  
S. J. Benkovic
Keyword(s):  
Dna Polymerase ◽  
Kinetic Mechanism ◽  
Dna Polymerase I ◽  
Polymerase I

scholarly journals Characteristics of DNA polymerase I from an extreme thermophile, Thermus scotoductus strain K1

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Ani Saghatelyan ◽  
Hovik Panosyan ◽  
Armen Trchounian ◽  
Nils‐Kåre Birkeland
Keyword(s):  
Dna Polymerase ◽  
Extreme Thermophile ◽  
Dna Polymerase I ◽  
Polymerase I
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