ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12.

Bickle, Thomas A.; Brack, Christine; Yuan, Robert

doi:10.1073/pnas.75.7.3099

Cited by 54 publications

(45 citation statements)

References 12 publications

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“…When the distance between a pair of sites was increased from 0.4 to 2.4 kb, the distribution of random cleavages between the sites expanded accordingly (Figure 4). Random cleavage has been observed between pairs of sites separated by as little as 100 bp and as much as 7 kb (Adler & Nathans, 1973;Bickle et al, 1978;Rosamund et al, 1979;Yuan et al, 1980;Dryden et al, 1997). Overall, our data for random cleavages on linear DNA concur with the collision model of Studier & Bandyopadhyay (1988).…”

Section: Random and Localised Cleavages By Ecor124imentioning

confidence: 91%

Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I

Szczelkun

Janscak

Firman

et al. 1997

Journal of Molecular Biology

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Section: Random and Localised Cleavages By Ecor124imentioning

confidence: 91%

Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I

Szczelkun

Janscak

Firman

et al. 1997

Journal of Molecular Biology

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“…An alternative explanation for the preponderance of single loops might be that the enzyme remains bound to DNA at both translocation points but not at its recognition site. This seems less likely, however, because both EcoK and EcoB appear to remain bound at the recognition site after reacting (in the presence of ATP) with linear DNAs that have a single recognition site (12,14).…”

Section: Methodsmentioning

confidence: 99%

“…Previous work on EcoB and EcoK has been interpreted to mean that the enzymes remain bound at their recognition site throughout the reaction and translocate DNA past themselves for long distances to reach their cleavage sites, forming simple or supertwisted loops in the process (9,(12)(13)(14). It was further concluded that EcoB can translocate DNA from only one side of the asymmetric recognition sequence (the 5' side, as usually written) (9) and that EcoK is capable of translocating DNA from either side (13); but the mechanism for selecting cleavage sites remained a mystery.…”

Section: Methodsmentioning

confidence: 99%

Model for how type I restriction enzymes select cleavage sites in DNA.

Studier

Bandyopadhyay

1988

Proc. Natl. Acad. Sci. U.S.A.

133

145

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Under appropriate conditions, digestion of phage T7 DNA by the type I restriction enzyme EcoK produces an orderly progression of discrete DNA fragments. AU details of the fragmentation pattern can be explained on the basis of the known properties of type I enzymes, together with two further assumptions: (i) in the ATP-stimulated translocation reaction, the enzyme bound at the recognition sequence translocates DNA toward itself from both directions simultaneously; and (is) when translocation causes neighboring enzymes to meet, they cut the DNA between them. The kinetics of digestion at 37TC indicates that the rate of translocation of DNA from each side of a bound enzyme is about 200 base pairs per second, and the cuts are completed within 15-25 sec of the time neighboring enzymes meet. The resulting DNA fragments each contain a single recognition site with an enzyme (or subunit) remaining bound to it. At high enzyme concentrations, such fragments can be further degraded, apparently by cooperation between the specifically bound and excess enzymes. This model is consistent with a substantial body of previous work on the nuclease activity ofEcoB and EcoK, and it explains in a simple way how cleavage sites are selected.The type I restriction enzymes EcoB and EcoK have a complex mode ofaction (reviewed in refs. 1-3). They act only on double-stranded DNA that contains a unique recognition sequence, TGAN8TGCT for EcoB and AACN6GTGC for EcoK (N = any nucleotide). Specific binding to these sites requires S-adenosylmethionine, and further reactions require (or, in the case of methylation, are stimulated by) ATP. In the presence of ATP, the state of methylation of the recognition sequence determines the course of the reaction: if both strands are methylated, the enzyme falls off the DNA; if one strand is methylated, the enzyme rapidly methylates the second strand; if neither strand is methylated, the enzyme hydrolyzes large amounts of ATP, translocates considerable lengths ofDNA, and cuts the DNA at seemingly random sites far from the recognition sequence. In the nucleolytic mode, the enzyme is used up in the reaction, apparently remaining bound at its recognition site. The effect of this complex set of reactions is to maintain resident DNA intact but to degrade unmethylated foreign DNA.One puzzling aspect of the nuclease activity of EcoB and EcoK has been how cleavage sites are selected in the DNA. We believe we have now discovered how this is done.

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“…The restriction pathway is presumed to be initiated by the ATP-dependent conformational change originally reported for EcoKI (19) but analyzed only recently by footprinting (137). EcoKI remains the best-studied R-M complex in terms of sequence-specific binding, the effect of the cofactor AdoMet on representatives of the type IB and IC enzymes being less easy to assess because it is difficult to separate AdoMet from these enzymes (41, 133; P. Janscak and T. A. Bickle, personal communication).…”

Section: R-m Complexmentioning

confidence: 99%

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Murray

2000

Microbiol Mol Biol Rev

402

481

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SUMMARY Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.

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ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12.

Abstract: ATP induces a conformational change in the Escherichia coli K-12

Cited by 54 publications

References 12 publications

Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I

Selection of non-specific DNA cleavage sites by the type IC restriction endonuclease EcoR124I

Model for how type I restriction enzymes select cleavage sites in DNA.

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

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