1988
DOI: 10.1073/pnas.85.23.8924
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Cocrystal structure of an editing complex of Klenow fragment with DNA.

Abstract: 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 ofthe duplex DNA by the protein is stabilized by hydophobic interactions between Phe473, Leu-361, and His-666 and the last three bases at the 3' terminus. Two divalent metal ions interacting with the… Show more

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Cited by 332 publications
(328 citation statements)
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“…16), therefore allowing editing of any single-stranded DNA sequence as would be required for error-free DNA replication . Two divalent metal ions are also seen interacting with the phosphate of the 3' terminal base and are thought to be involved in the positioning and cleavage of the phosphodiester bond (Derbyshire et al, 1988;Freemont et al, 1988). Recent site-directed mutagenesis studies of all the amino acids implicated by the crystal structure to be involved in substrate binding or catalysis are in agreement with the structural observations (Derbyshire et al, 1991).…”
Section: Zif268-dna Complexmentioning
confidence: 58%
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“…16), therefore allowing editing of any single-stranded DNA sequence as would be required for error-free DNA replication . Two divalent metal ions are also seen interacting with the phosphate of the 3' terminal base and are thought to be involved in the positioning and cleavage of the phosphodiester bond (Derbyshire et al, 1988;Freemont et al, 1988). Recent site-directed mutagenesis studies of all the amino acids implicated by the crystal structure to be involved in substrate binding or catalysis are in agreement with the structural observations (Derbyshire et al, 1991).…”
Section: Zif268-dna Complexmentioning
confidence: 58%
“…However, there are subtle differences in the mode of DNA recognition and interaction displayed by these repressors, the details of which will be discussed later. On the other hand, the three helix-turn-helix repressors listed in Table 1 Beese & Steitz (1991 Beese & Steitz (1991) Freemont et al (1988) Steitz (1990) White et al (1989) Sanderson et al (1990 Burlingame et al (1985) Richmond et al (1984 is involved in the regulation of tryptophan biosynthesis by binding as a dimer to three different operator sites in the presence of its corepressor L-tryptophan (Klig et al, 1988). Binding in the absence of L-tryptophan is weak and non-specific.…”
Section: Helix-turn-helix Proteinsmentioning
confidence: 99%
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“…We conclude that the correlation between cleavage activity and metal ion pK a , the solvent deuterium isotope effect, and the results of 5Ј-sulfur replacement experiments, can all be explained by a mechanism that falls within the framework of a general two-metal-ion model proposed for a number of phosphoryl transfer reactions (9)(10)(11). The data available in the literature are consistent with a two-metal-ion model in which metal ions in sites A and B both play a role in the transition state.…”
Section: Discussionmentioning
confidence: 99%
“…This model is based on mechanisms that have been put forward to explain the activities of alkaline phosphatase and the 3Ј-5Ј exonuclease of DNA polmerase I (10,11). Similar two-metal-ion models have been proposed for a wide variety of protein and RNA enzymes that mediate phosphoryl transfer reactions (9).…”
mentioning
confidence: 99%