A Molecular Model of the Complete Three-Dimensional Structure of the Klenow Fragment of Escherichia Coli DNA Polymerase I: Binding of the dNTP Substrate and Template-Primer

Prem N.S. Yadav, Janardan S. Yadav, Mukund J. Modak

Research output: Contribution to journalArticle

22 Scopus citations

Abstract

A complete three-dimensional structure of the Klenow fragment of Escherichia coli DNA polymerase I (pol I) has been proposed on the basis of molecular modeling and molecular mechanics studies using available Cα coordinates. The structure seems quite reliable because the overall surface of electrostatic potentials calculated for the molecularly modeled enzyme closely resembles that reported for the X-ray structure. The modeled structure is then used in developing a ternary complex of dTTP and (dA)25-(dT)14 poised in its active site. The orientation of both substrates in the ternary complex was primarily guided by the amino acid residues which had been known to interact with dNTP and DNA substrates from earlier studies. The proposed model (a) explains the geometrical and physicochemical relationship of the two substrates with the various critical amino acid residues involved in the binding process and (b) suggests possible roles for additional residues in the binding and/or polymerization reaction. Furthermore, the ternary complex appears to satisfy many biochemical and genetic data concerning catalytic requirements known to exist for the polymerization reaction.

Original languageEnglish (US)
Pages (from-to)2879-2886
Number of pages8
JournalBiochemistry
Volume31
Issue number11
DOIs
StatePublished - Mar 1 1992

All Science Journal Classification (ASJC) codes

  • Biochemistry

Fingerprint Dive into the research topics of 'A Molecular Model of the Complete Three-Dimensional Structure of the Klenow Fragment of Escherichia Coli DNA Polymerase I: Binding of the dNTP Substrate and Template-Primer'. Together they form a unique fingerprint.

  • Cite this