1CVX image
Deposition Date 1999-08-24
Release Date 2000-01-15
Last Version Date 2024-02-07
Entry Detail
PDB ID:
1CVX
Keywords:
Title:
CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG
Biological Source:
Source Organism:
(Taxon ID: ) (Taxon ID: )
Method Details:
Experimental Method:
Resolution:
2.27 Å
R-Value Free:
0.23
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 31
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3'
Chain IDs:A, B
Chain Length:10
Number of Molecules:2
Biological Source:
Ligand Molecules
Primary Citation
Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
J.Mol.Biol. 295 557 567 (2000)
PMID: 10623546 DOI: 10.1006/jmbi.1999.3364

Abstact

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.

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