Cocrystal structure of an editing complex of Klenow fragment with DNA.

Published

Journal Article

High-resolution crystal structures of editing complexes of both duplex and single-stranded DNA bound to Escherichia coli DNA polymerase I large fragment (Klenow fragment) show four nucleotides of single-stranded DNA bound to the 3'-5' exonuclease active site and extending toward the polymerase active site. Melting of the duplex DNA by the protein is stabilized by hydrophobic interactions between Phe-473, Leu-361, and His-666 and the last three bases at the 3' terminus. Two divalent metal ions interacting with the phosphodiester to be hydrolyzed are proposed to catalyze the exonuclease reaction by a mechanism that may be related to mechanisms of other enzymes that catalyze phospho-group transfer including RNA enzymes. We suggest that the editing active site competes with the polymerase active site some 30 A away for the newly formed 3' terminus. Since a 3' terminal mismatched base pair favors the melting of duplex DNA, its binding and excision at the editing exonuclease site that binds single-stranded DNA is enhanced.

Full Text

Duke Authors

Cited Authors

  • Freemont, PS; Friedman, JM; Beese, LS; Sanderson, MR; Steitz, TA

Published Date

  • December 1988

Published In

Volume / Issue

  • 85 / 23

Start / End Page

  • 8924 - 8928

PubMed ID

  • 3194400

Pubmed Central ID

  • 3194400

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.85.23.8924

Language

  • eng

Conference Location

  • United States