NDLI: Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity

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Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity

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Crystal structures of a ddATP-, ddTTP-, ddCTP, and ddGTP- trapped ternary complex of Klentaq1: Insights into nucleotide incorporation and selectivity

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Waksman, G. Li, Y.
Description	Country affiliation: United States Author Affiliation: Li Y ( Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.)
Abstract	The mechanism by which DNA polymerase I enzymes function has been the subject of extensive biochemical and structural studies. We previously determined the structure of a ternary complex of the large fragment of DNA polymerase I from Thermus aquaticus (Klentaq1) bound to a primer/template DNA and a dideoxycytidine 5'-triphosphate (ddCTP). In this report, we present the details of the 2.3-A resolution crystal structures of three additional ternary complexes of Klentaq1 bound to a primer/template DNA and a dideoxyguanosine 5'-triphosphate (ddGTP), a dideoxythymidine 5'-triphosphate (ddTTP), or a dideoxyadenosine 5'-triphosphate (ddATP). Comparison of the active site of the four ternary complexes reveals that the protein residues around the nascent base pair (that formed between the incoming dideoxynucleoside triphosphate [ddNTP] and the template base) form a snug binding pocket into which only a correct Watson-Crick base pair can fit. Except in the ternary complex bound to dideoxyguanosine 5'-triphosphate, there are no sequence specific contacts between the protein side chains and the nascent base pair, suggesting that steric constraints imposed by the protein onto the nascent base pair is the major contributor to nucleotide selectivity at the polymerase active site. The protein around the polymerase active site also shows plasticity, which may be responsible for the substrate diversity of the enzyme. Two conserved side chains, Q754 and R573, form hydrogen bonds with the N3 atom in the purine base and O2 atom in the pyrimidine base at the minor groove side of the base pair formed by the incorporated ddNMP and the corresponding template base in all the four ternary complexes. These hydrogen-bonding interactions may provide a means of detecting misincorporation at this position.
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science
Issue Number	6
Volume Number	10
Language	English
Publisher	Wiley-Blackwell (on behalf of The Protein Society)
Publisher Date	2001-06-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Chemistry Deoxyadenine Nucleotides Deoxycytosine Nucleotides Deoxyguanine Nucleotides Taq Polymerase Thymine Nucleotides Binding Sites Computer Simulation Dna-directed Dna Polymerase Dideoxynucleotides Kinetics Models, Molecular Nucleotides Protein Binding Protein Structure, Secondary Research Support, U.s. Gov't, P.h.s. Discipline Biochemistry
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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