PDBsum entry 1pfe

DNA/antibiotic

PDB id: 1pfe

Contents

DNA/RNA

Ligands

DSN-ALA-N2C-NCY-MVA-DSN-ALA-NCY-N2C-MVA

QUI ×2

Metals

_CL

Waters ×80

PDB id:

1pfe

Name:

DNA/antibiotic

Title:

Echinomycin-(gcgtacgc)2 complex

Structure:

5'-d( Gp Cp Gp Tp Ap Cp Gp C)-3'. Chain: a. Engineered: yes. Echinomycin. Chain: b. Synonym: quinomycin a

Source:

Synthetic: yes. Streptomyces echinatus. Organism_taxid: 67293

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.10Å R-factor: 0.146 R-free: 0.168

Authors:

J.A.Cuesta-Seijo

Key ref:

J.A.Cuesta-Seijo and G.M.Sheldrick (2005). Structures of complexes between echinomycin and duplex DNA. Acta Crystallogr D Biol Crystallogr, 61, 442-448. PubMed id: 15805599 DOI: 10.1107/S090744490500137X

Date:

26-May-03 Release date: 08-Jun-04

DNA/RNA chain

G-C-G-T-A-C-G-C 8 bases

DOI no: 10.1107/S090744490500137X

Acta Crystallogr D Biol Crystallogr 61:442-448 (2005)

PubMed id: 15805599

Structures of complexes between echinomycin and duplex DNA.

J.A.Cuesta-Seijo, G.M.Sheldrick.

ABSTRACT

The structure of the bis-intercalation complex of the depsipeptide antibiotic echinomycin with (CGTACG)2 has been redetermined at a higher resolution (1.4 A) and new high-resolution structures (1.1-1.5 A) are reported for the complexes of echinomycin with (GCGTACGC)2 (at both low and high ionic strengths) and (ACGTACGT)2. The structures show the expected Hoogsteen pairing for the base pairs flanking the intercalating chromophores on the outside and Watson-Crick pairing for both base pairs enclosed by the echinomycin. In the octamer complexes but not the hexamer complex, the echinomycin molecule, which would possess a molecular twofold axis were it not for the thioacetal bridge, shows twofold disorder. In all the structures the stacking of the base pairs and chromophores is extended by intermolecular stacking. The structures provide more precise details of the hydrogen bonding and other interactions between the bis-intercalating antibiotics and the duplex DNA than were previously available.

Selected figure(s)

Figure 2.
Figure 2 The echinomycin (GCGTACGC)[2] complex GE1 (a) showing the protruding thioacetal bridges, (b) diagrammatic representation of the base and chromophore stacking showing also the stacking to symmetry-equivalent molecules (the asymmetric unit is shown in black) and (c) rotated 180° from (a) showing the chromophores.

Figure 5.
Figure 5 (a) The thioacetal bridge in the structure GE1 showing the twofold disorder (2F[o] - F[c] map contoured at 1 [sigma] ); (b) a superposition of the (not disordered) echinomycin molecule in the C2 structure on itself after rotation of 180° about the molecular pseudo-twofold axis.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 442-448) copyright 2005.

Figures were selected by the author.