PDBsum entry 146d

DNA

PDB id: 146d

Contents

DNA/RNA

Ligands

DDA-DDA ×2

DDA-DDL-MDA ×2

CRH ×2

Metals

_MG

PDB id:

146d

Name:

DNA

Title:

Solution structure of the mithramycin dimer-DNA complex

Structure:

DNA (5'-d( Tp Cp Gp Cp Gp A)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Other_details: chemically synthesized

NMR struc:

2 models

Authors:

M.Sastry,D.J.Patel

Key ref:

M.Sastry and D.J.Patel (1993). Solution structure of the mithramycin dimer-DNA complex. Biochemistry, 32, 6588-6604. PubMed id: 8329387 DOI: 10.1021/bi00077a012

Date:

09-Nov-93 Release date: 31-Mar-95

DNA/RNA chains

T-C-G-C-G-A 6 bases

T-C-G-C-G-A 6 bases

DOI no: 10.1021/bi00077a012

Biochemistry 32:6588-6604 (1993)

PubMed id: 8329387

Solution structure of the mithramycin dimer-DNA complex.

M.Sastry, D.J.Patel.

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)