An unprecedented nucleic acid capture mechanism for excision of DNA damage.

Abstract

DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.

• Authors: Emily H Rubinson, A S Prakasha Gowda, Thomas E Spratt, Barry Gold, Brandt F Eichman
• Journal: Nature (Nature) Vol. 468 Issue 7322 Pg. 406-11 (Nov 18 2010) ISSN: 1476-4687 [Electronic] England
• PMID: 20927102 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.)

Chemical References

• Solvents
• DNA
• DNA Glycosylases

Topics

• Alkylation
• Bacillus cereus (enzymology)
• Base Sequence
• Biocatalysis
• Crystallography, X-Ray
• DNA (chemistry, genetics, metabolism)
• DNA Damage
• DNA Glycosylases (metabolism)
• DNA Repair (physiology)
• Hydrolysis
• Models, Molecular
• Nucleic Acid Conformation
• Protein Binding
• Solvents (chemistry)
• Thermodynamics