2KBD

5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3'

Summary for 2KBD

• Entry DOI: 10.2210/pdb2kbd/pdb
• Descriptor: DNA (5'-D(*CP*TP*GP*GP*GP*GP*AP*CP*TP*TP*TP*CP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*GP*AP*AP*AP*GP*TP*CP*CP*CP*CP*AP*G)-3') (2 entities in total)
• Functional Keywords: dna structure, modelling, deoxyribonucleic acid, dna
• Total number of polymer chains: 2
• Total formula weight: 9798.36

Authors

Tisne, C.,Hantz, E.,Hartmann, B.,Delepierre, M. (deposition date: 1998-12-07, release date: 1998-12-09, Last modification date: 2023-12-27)

Primary citation

Tisne, C.,Hantz, E.,Hartmann, B.,Delepierre, M.
Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex.
J.Mol.Biol., 279:127-142, 1998

PubMed Abstract: 1H and 31P NMR spectroscopy have been used together with molecular modelling to determine the fine structure of a non-palindromic 16 bp DNA containing the NF-kappa B binding site. Much emphasis has been placed upon NMR optimization of both two-dimensional 31P NMR techniques to extract structural information defining the phosphodiester backbone conformation and selective homonuclear 2D COSY experiments to determine sugar conformations. NMR data show evidence for a dynamic behaviour of steps flanking the ten base-pairs of the NF-kappa B binding site. A BI-BII equilibrium at these steps is demonstrated and two models for each extreme conformation are proposed in agreement with NMR data. In the refined BII structures, the NF-kappa B binding site exhibits an intrinsic curvature towards the major groove that is magnified by the four flanking steps in the BII conformation. Furthermore, the base-pairs are translated into the major groove. Thus, we present a novel mode of dynamic intrinsic curvature compatible with the DNA curvature observed in the X-ray structure of the p50-DNA complex.

PubMed: 9636705
DOI: 10.1006/jmbi.1998.1757

Experimental method

SOLUTION NMR