Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats.
3-methyladenine DNA glycosylases initiate repair of cytotoxic and promutagenic alkylated bases in DNA. We demonstrate by comparative modelling that Bacillus cereus AlkD belongs to a new, fifth, structural superfamily of DNA glycosylases with an alpha-alpha superhelix fold comprising six HEAT-like repeats. The structure reveals a wide, positively charged groove, including a putative base recognition pocket. This groove appears to be suitable for the accommodation of double-stranded DNA with a flipped-out alkylated base. Site-specific mutagenesis within the recognition pocket identified several residues essential for enzyme activity. The results suggest that the aromatic side chain of a tryptophan residue recognizes electron-deficient alkylated bases through stacking interactions, while an interacting aspartate-arginine pair is essential for removal of the damaged base. A structural model of AlkD bound to DNA with a flipped-out purine moiety gives insight into the catalytic machinery for this new class of DNA glycosylases.
Dalhus
Bjørn
B
Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway.
Helle
Ina Høydal
IH
Backe
Paul H
PH
Alseth
Ingrun
I
Rognes
Torbjørn
T
Bjørås
Magnar
M
Laerdahl
Jon K
JK
D000478:Alkylation; D000595:Amino Acid Sequence; D001409:Bacillus cereus / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D045647:DNA Glycosylases / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D004260:DNA Repair; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D017433:Protein Structure, Secondary; D020449:Repetitive Sequences, Amino Acid
D001426:Bacterial Proteins; D004247:DNA; D045647:DNA Glycosylases