146D

SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX

146D の概要

• エントリーDOI: 10.2210/pdb146d/pdb
• 分子名称: DNA (5'-D(*TP*CP*GP*CP*GP*A)-3'), beta-D-Olivopyranose-(1-3)-beta-D-Olivopyranose, 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-Olivopyranose, ... (5 entities in total)
• 機能のキーワード: dna, mithramycin dimer
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 5821.10

構造登録者

Sastry, M.,Patel, D.J. (登録日: 1993-11-09, 公開日: 1995-03-31, 最終更新日: 2024-05-22)

主引用文献

Sastry, M.,Patel, D.J.
Solution structure of the mithramycin dimer-DNA complex.
Biochemistry, 32:6588-6604, 1993

PubMed Abstract: We have characterized the NMR parameters for the complexes formed by the Mg(2+)-coordinated mithramycin dimer with self-complementary d(T-G-G-C-C-A) and d(T-C-G-C-G-A) duplexes. The solution structure of the latter complex has been determined using a combined NMR-molecular dynamics study including relaxation matrix refinement. The Mg(2+)-coordinated mithramycin dimer-d(T-C-G-C-G-A) complex exhibits a 2-fold center of symmetry with the divalent cation coordinated aglycons positioned opposite the central (G3-C4).(G3-C4) segment such that the aglycon C8 hydroxyl oxygens form symmetrical sequence-specific hydrogen bonds to guanine amino protons in the complex. The C-D-E trisaccharide segments of each monomer in the mithramycin dimer adopt extended conformations, are positioned inside the minor groove, and are directed toward either end of the duplex. The C-D saccharide component of one monomer and the aglycon of the other monomer in the mithramycin dimer share a widened minor groove with the hydrophobic edges of the C and D sugars interacting with individual strands of the duplex. The E-sugar ring is positioned in the floor of the minor groove, and its hydroxyl-bearing face interacts with both strands of the duplex through hydrogen-bonding and hydrophobic intermolecular interactions. The A-B disaccharide and the hydrophilic side chain form intermolecular contacts with the sugar-phosphate backbone in the complex. The antiparallel alignment of divalent cation coordinated monomers in the mithramycin dimer results in the two outwardly directed C-D-E trisaccharide segments generating a right-handed continuous hexasaccharide domain that spans six base pairs in the minor groove of the duplex. The solution structure of the mithramycin dimer-DNA complex reported in this study and the solution structure of the chromomycin dimer-DNA complex reported previously [Gao, X., Mirau, P., & Patel, D. J. (1992) J. Mol. Biol. 223, 259-279] show global similarities, as well as local differences that are of interest. All four nucleotides in the tetranucleotide segment of the duplex centered about the sequence-specific (G-C).(G-C) step adopt A-DNA sugar puckers and glycosidic torsion angles in the chromomycin dimer-DNA complex, while only the central cytidine adopts an A-DNA sugar pucker and glycosidic torsion angle in the mithramycin dimer-DNA complex.(ABSTRACT TRUNCATED AT 400 WORDS)

PubMed: 8329387
DOI: 10.1021/bi00077a012

実験手法

SOLUTION NMR