1DNE

MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2

1DNE の概要

• エントリーDOI: 10.2210/pdb1dne/pdb
• 分子名称: DNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3'), NETROPSIN (3 entities in total)
• 機能のキーワード: b-dna, double helix, complexed with drug, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 7757.25

構造登録者

Coll, M.,Aymami, J.,Van Der Marel, G.A.,Van Boom, J.H.,Rich, A.,Wang, A.H.-J. (登録日: 1988-09-14, 公開日: 1989-01-09, 最終更新日: 2024-02-07)

主引用文献

Coll, M.,Aymami, J.,van der Marel, G.A.,van Boom, J.H.,Rich, A.,Wang, A.H.
Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment.
Biochemistry, 28:310-320, 1989

PubMed Abstract: The molecular structure of the complex between a minor groove binding drug (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and refined by single-crystal X-ray diffraction analysis to a final R factor of 20.0% to 2.4-A resolution. The crystal is similar to that of the other related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow minor groove of the dodecamer B-DNA double helix as expected. However, in the structural refinement the drug is found to fit the electron density in two orientations equally well, suggesting the disordered model. This agrees with the results from solution studies (chemical footprinting and NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug and DNA are provided by a combination of ionic, van der Waals, and hydrogen-bonding interactions. No bifurcated hydrogen bond is found between netropsin and DNA in this complex due to the unique dispositions of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the floor of the DNA minor groove. Two of the four AT base pairs in the ATAT stretch have low propeller twist angles, even though the DNA has a narrow minor groove. Alternating helical twist angles are observed in the ATAT stretch with lower twist in the ApT steps than in the TpA step.

PubMed: 2539859
DOI: 10.1021/bi00427a042

実験手法

X-RAY DIFFRACTION (2.4 Å)