1EG6

CRYSTAL STRUCTURE ANALYSIS OF D(CG(5-BRU)ACG) COMPLEXES TO A PHENAZINE

Summary for 1EG6

• Entry DOI: 10.2210/pdb1eg6/pdb
• Descriptor: 5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3', COBALT (III) ION, BROMIDE ION, ... (5 entities in total)
• Functional Keywords: drug-dna complex, intercalation, major groove binding, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 4241.30

Authors

Cardin, C.J.,Denny, W.A.,Hobbs, J.R.,Thorpe, J.H. (deposition date: 2000-02-14, release date: 2001-01-03, Last modification date: 2024-02-07)

Primary citation

Thorpe, J.H.,Hobbs, J.R.,Todd, A.K.,Denny, W.A.,Charlton, P.,Cardin, C.J.
Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG](2) with a topoisomerase poison in the presence of Co(2+) ions.
Biochemistry, 39:15055-15061, 2000

PubMed Abstract: The structure of the duplex d[CG(5-BrU)ACG](2) bound to 9-bromophenazine-4-carboxamide has been solved through MAD phasing at 2.0 A resolution. It shows an unexpected and previously unreported intercalation cavity stabilized by the drug and novel binding modes of Co(2+) ions at certain guanine N7 sites. For the intercalation cavity the terminal cytosine is rotated to pair with the guanine of a symmetry-related duplex to create a pseudo-Holliday junction geometry, with two such cavities linked through the minor groove interactions of the N2/N3 guanine sites at an angle of 40 degrees, creating a quadruplex-like structure. The mode of binding of the drug is shown to be disordered, with the major conformations showing the side chain bound to the N7 position of adjacent guanines. The other end of the duplex exhibits a terminal base fraying in the presence of Co(2+) ions linking symmetry-related guanines, causing the helices to intertwine through the minor groove. The stabilization of the structure by the intercalating drug shows that this class of compound may bind to DNA junctions as well as duplex DNA or to strand-nicked DNA ('hemi-intercalated'), as in the cleavable complex. This suggests a structural basis for the dual poisoning of topoisomerase I and II enzymes by this family of drugs.

PubMed: 11106483
DOI: 10.1021/bi001749p

Experimental method

X-RAY DIFFRACTION (2 Å)