1cw9
From Proteopedia
|
DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE
Overview
The response of double-helical DNA to torsional stress may be a driving, force for many processes acting on DNA. The 1.55-A crystal structure of a, duplex DNA oligonucleotide d(CCAGGCCTGG)(2) with an engineered crosslink, in the minor groove between the central guanine bases depicts how the, duplex can accommodate such torsional stress. We have captured in the same, crystal two rather different conformational states. One duplex contains a, strained crosslink that is stabilized by calcium ion binding in the major, groove, directly opposite the crosslink. For the other duplex, the strain, in the crosslink is relieved through partial rupture of a base pair and, partial extrusion of a cytosine accompanied by helix bending. The sequence, used is the target sequence for the HaeIII methylase, and this partially, flipped cytosine is the same nucleotide targeted for extrusion by the, enzyme. Molecular dynamics simulations of these structures show an, increased mobility for the partially flipped-out cytosine.
About this Structure
1CW9 is a Protein complex structure of sequences from [1] with CA as ligand. Full crystallographic information is available from OCA.
Reference
A structural snapshot of base-pair opening in DNA., van Aalten DM, Erlanson DA, Verdine GL, Joshua-Tor L, Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11809-14. PMID:10518532
Page seeded by OCA on Sun Nov 25 02:01:53 2007
