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1cvy
From Proteopedia
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CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG
Overview
Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole, (Hp) bind specific DNA sequences as antiparallel dimers in the minor, groove. The side-by-side pairings of aromatic rings in the dimer afford a, general recognition code that allows all four base-pairs to be, distinguished. To examine the structural consequences of changing the DNA, sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole, counterpart (ImPyPyPy)(2) bound to the six base-pair target site, 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a, resolution of 2.27 and 2.15 A, respectively. The structures demonstrate, that the principles of Hp/Py recognition of T.A are consistent between, different sequence contexts. However, a general structural explanation for, the non-additive reduction in binding affinity due to introduction of the, hydroxyl group is less clear. Comparison with other polyamide-DNA, cocrystal structures reveals structural themes and differences that may, relate to sequence preference.
About this Structure
1CVY is a Protein complex structure of sequences from [1] with IPY as ligand. Full crystallographic information is available from OCA.
Reference
Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:10623546
Page seeded by OCA on Sun Nov 25 02:01:04 2007
