1VTD

UNUSUAL HELICAL PACKING IN CRYSTALS OF DNA BEARING A MUTATION HOT SPOT

Summary for 1VTD

• Entry DOI: 10.2210/pdb1vtd/pdb
• Descriptor: DNA (5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3'), DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3') (2 entities in total)
• Functional Keywords: b-dna, double helix, dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 7327.77

Authors

Timsit, Y.,Westhof, E.,Fuchs, R.P.P.,Moras, D. (deposition date: 1996-12-12, release date: 2011-07-13, Last modification date: 2023-12-27)

Primary citation

Timsit, Y.,Westhof, E.,Fuchs, R.P.,Moras, D.
Unusual helical packing in crystals of DNA bearing a mutation hot spot.
Nature, 341:459-462, 1989

PubMed Abstract: The target sequence of the restriction enzyme NarI (GGCGCC) is a hot spot for the -2 frameshift mutagenesis (GGCGCC----GGCC) induced by the chemical carcinogens such as N-2-acetyl-aminofluorene. Of the guanine residues, all of which show equal reactivity towards the carcinogen, only binding to the 3'-most proximal guanine within the NarI site is able to trigger the frameshift event. We selected the non-palindromic dodecamer d(ACCGGCGCCACA), whose sequence corresponds to the most mutagenic NarI site in pBR322 DNA; for X-ray structure analysis. Its molecular structure determined at 2.8 A resolution reveals significant deviations from the structure of canonical B-form DNA, with partial opening of three G-C base pairs, high propeller twist values and sequence-dependent three-centred hydrogen bonds. This crystal structure shows a novel kind of packing in which helices are locked together by groove-backbone interactions. The partial opening of G-C base pairs is induced by interactions of phosphate anionic oxygen atoms with the amino group of cytosine bases. This provides a model for close approach of DNA molecules during biological processes, such as recombination.

PubMed: 2797169
DOI: 10.1038/341459a0

Experimental method

X-RAY DIFFRACTION (2.8 Å)