title: A new protein architecture for processing alkylation damaged DNA: the crystal structure of DNA glycosylase AlkD.
abstract: DNA glycosylases safeguard the genome by locating and excising chemically modified bases from DNA. AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from from those of other DNA repair proteins. The crystal structure of Bacillus cereus AlkD presented here shows that the protein is composed exclusively of helical HEAT-like repeats, which form a solenoid perfectly shaped to accommodate a DNA duplex on the concave surface. Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA. We report 7mG excision and DNA binding activities of AlkD mutants, along with a comparison of alkylpurine DNA glycosylase structures. Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases.
authors.affiliation: Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Emily H
authors.initials: EH
authors.lastname: Rubinson
authors.forename: Audrey H
authors.initials: AH
authors.lastname: Metz
authors.forename: Jami
authors.initials: J
authors.lastname: O'Quin
authors.forename: Brandt F
authors.initials: BF
authors.lastname: Eichman
mesh_terms: D000478:Alkylation; D000595:Amino Acid Sequence; D001409:Bacillus cereus / Q000201:enzymology / Q000235:genetics; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004249:DNA Damage / Q000235:genetics*; D045647:DNA Glycosylases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008760:Methylguanidine / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D040681:Structural Homology, Protein
chemical_list: D008760:Methylguanidine; D004247:DNA; D045647:DNA Glycosylases