336D

INTERACTION BETWEEN LEFT-HANDED Z-DNA AND POLYAMINE-3 THE CRYSTAL STRUCTURE OF THE D(CG)3 AND THERMOSPERMINE COMPLEX

336D の概要

• エントリーDOI: 10.2210/pdb336d/pdb
• 分子名称: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3'), N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: z-dna, double helix, dna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 4073.70

構造登録者

Ohishi, H.,Terasoma, N.,Nakanishi, I.,Van Der Marel, G.,Van Boom, J.H.,Rich, A.,Wang, A.H.-J.,Hakoshima, T.,Tomita, K.-I. (登録日: 1997-06-24, 公開日: 1998-04-10, 最終更新日: 2024-02-21)

主引用文献

Ohishi, H.,Terasoma, N.,Nakanishi, I.,van der Marel, G.,van Boom, J.H.,Rich, A.,Wang, A.H.,Hakoshima, T.,Tomita, K.
Interaction between left-handed Z-DNA and polyamine - 3. The crystal structure of the d(CG)3 and thermospermine complex.
FEBS Lett., 398:291-296, 1996

PubMed Abstract: The DNA fragment, d(CG)3, was co-crystallized with N-(3-amino-propyl)-N-(5-aminopropyl)-l,4 -diaminobutane (thermospermine; PA(334)), a polyamine metabolized from the nucleic acid. By using a good crystal with dimensions of 0.5 x 0.5 x 0.5 mm3, X-ray intensity data were collected up to 1.0 A resolution. Two thermospermine molecules and a magnesium cation were bound to the left-handed double-helical d(CG)3 molecule. The d(CG)3 molecule adopted the left-handed Z-conformation and two thermospermine molecules and a magnesium cation neutralized the negative charges of the phosphate groups of the d(CG)3 molecule. Furthermore, the binding modes between d(CG)3 and thermospermine were different from those of d(CG)3 complexes with PA(24), spermidine and spermine. This is the first case in which it was determined by X-ray crystallographic analysis that one of two thermospermine molecules bound three d(CG)3 duplexes which were symmetrically related to each other, and the other formed two hydrogen bonds at the N(5) and N(9) atoms with two adjacent nucleotide phosphate groups of a single d(CG)3 strand at the minor groove. Furthermore, no direct coordination bond was found between the d(CG)3 molecule and the magnesium cation.

PubMed: 8977125
DOI: 10.1016/S0014-5793(96)01225-2

実験手法

X-RAY DIFFRACTION (1 Å)