title: Searching for DNA lesions: structural evidence for lower- and higher-affinity DNA binding conformations of human alkyladenine DNA glycosylase.
abstract: To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, like AAG, to interact with DNA using two affinities: a lower-affinity interaction in a searching process and a higher-affinity interaction for catalytic repair. Here, we present crystal structures of AAG trapped in two DNA-bound states. The lower-affinity depiction allows us to investigate, for the first time, the conformation of this protein in the absence of a tightly bound DNA adduct. We find that active site residues of AAG involved in binding lesion bases are in a disordered state. Furthermore, two loops that contribute significantly to the positive electrostatic surface of AAG are disordered. Additionally, a higher-affinity state of AAG captured here provides a fortuitous snapshot of how this enzyme interacts with a DNA adduct that resembles a one-base loop.
authors.affiliation: Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.
authors.forename: Jeremy W
authors.initials: JW
authors.lastname: Setser
authors.forename: Gondichatnahalli M
authors.initials: GM
authors.lastname: Lingaraju
authors.forename: C Ainsley
authors.initials: CA
authors.lastname: Davis
authors.forename: Leona D
authors.initials: LD
authors.lastname: Samson
authors.forename: Catherine L
authors.initials: CL
authors.lastname: Drennan
mesh_terms: D002384:Catalysis; D018360:Crystallography, X-Ray; D018736:DNA Adducts / Q000737:chemistry; D004249:DNA Damage; D045647:DNA Glycosylases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D015894:Genome, Human; D006801:Humans; D016296:Mutagenesis; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010957:Plasmids; D011487:Protein Conformation
chemical_list: D018736:DNA Adducts; D004268:DNA-Binding Proteins; D009692:Nucleic Acid Heteroduplexes; C021565:3-methyladenine-DNA glycosylase; D045647:DNA Glycosylases