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M109496200v1
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Papers In Press, published online ahead of print November 14, 2001
J. Biol. Chem, 10.1074/jbc.M109496200
Submitted on October 2, 2001
Revised on November 8, 2001
Accepted on November 14, 2001

Holliday junction resolution is modulated by archaeal chromatin components in vitro

Mamuka Kvaratskhelia, Benjamin N. Wardleworth, Charles S. Bond, Jonathon M. Fogg, David M. J. Lilley, and Malcolm F. White

Biomolecular Sciences, St. Andrews University, St. Andrews, Scotland KY16 9ST

Corresponding Author: mfw2{at}st-andrews.ac.uk

The Holliday junction-resolving enzyme Hjc is conserved in the archaea, and probably plays a role analogous to that of E. coli RuvC in the pathway of homologous recombination. Hjc specifically recognises four-way DNA junctions, cleaving them without sequence preference to generate recombinant DNA duplex products. Hjc imposes an X-shaped global conformation on the bound DNA junction and distorts base stacking around the point of cleavage, three nucleotides 3’ of the junction centre. We show that Hjc is auto-inhibitory under single turnover assay conditions, and that this can be relieved by the addition of either competitor duplex DNA or the architectural dsDNA binding protein Sso7d – i.e. by approximating in vivo conditions more closely. Using a combination of isothermal titration calorimetry and fluorescent resonance energy transfer, we demonstrate that multiple Hjc dimers can bind to each synthetic four-way junction, and provide evidence for significant distortion of the junction structure at high protein:DNA ratios. Analysis of crystal packing interactions in the crystal structure of Hjc suggests a molecular basis for this auto-inhibition. The wider implications of these findings for the quantitative study of DNA:protein interactions is discussed.


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