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

Publication ,  Journal Article
Freemont, PS; Friedman, JM; Beese, LS; Sanderson, MR; Steitz, TA
Published in: Proc Natl Acad Sci U S A
December 1988

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.

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Published In

Proc Natl Acad Sci U S A

DOI

ISSN

0027-8424

Publication Date

December 1988

Volume

85

Issue

23

Start / End Page

8924 / 8928

Location

United States

Related Subject Headings

  • X-Ray Diffraction
  • Protein Conformation
  • Protein Binding
  • Nucleic Acid Conformation
  • Models, Molecular
  • DNA, Single-Stranded
  • DNA Polymerase I
  • DNA
  • Computer Simulation
 

Citation

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ICMJE
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Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R., & Steitz, T. A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci U S A, 85(23), 8924–8928. https://doi.org/10.1073/pnas.85.23.8924
Freemont, P. S., J. M. Friedman, L. S. Beese, M. R. Sanderson, and T. A. Steitz. “Cocrystal structure of an editing complex of Klenow fragment with DNA.Proc Natl Acad Sci U S A 85, no. 23 (December 1988): 8924–28. https://doi.org/10.1073/pnas.85.23.8924.
Freemont PS, Friedman JM, Beese LS, Sanderson MR, Steitz TA. Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8924–8.
Freemont, P. S., et al. “Cocrystal structure of an editing complex of Klenow fragment with DNA.Proc Natl Acad Sci U S A, vol. 85, no. 23, Dec. 1988, pp. 8924–28. Pubmed, doi:10.1073/pnas.85.23.8924.
Freemont PS, Friedman JM, Beese LS, Sanderson MR, Steitz TA. Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8924–8928.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

ISSN

0027-8424

Publication Date

December 1988

Volume

85

Issue

23

Start / End Page

8924 / 8928

Location

United States

Related Subject Headings

  • X-Ray Diffraction
  • Protein Conformation
  • Protein Binding
  • Nucleic Acid Conformation
  • Models, Molecular
  • DNA, Single-Stranded
  • DNA Polymerase I
  • DNA
  • Computer Simulation