title: Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding.
abstract: The nucleotide excision repair pathway corrects many structurally unrelated DNA lesions. Damage recognition in bacteria is performed by UvrA, a member of the ABC ATPase superfamily whose functional form is a dimer with four nucleotide-binding domains (NBDs), two per protomer. In the 3.2 A structure of UvrA from Bacillus stearothermophilus, we observe that the nucleotide-binding sites are formed in an intramolecular fashion and are not at the dimer interface as is typically found in other ABC ATPases. UvrA also harbors two unique domains; we show that one of these is required for interaction with UvrB, its partner in lesion recognition. In addition, UvrA contains three zinc modules, the number and ligand sphere of which differ from previously published models. Structural analysis, biochemical experiments, surface electrostatics, and sequence conservation form the basis for models of ATP-modulated dimerization, UvrA-UvrB interaction, and DNA binding during the search for lesions.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
authors.forename: Danaya
authors.initials: D
authors.lastname: Pakotiprapha
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Inuzuka
authors.forename: Brian R
authors.initials: BR
authors.lastname: Bowman
authors.forename: Geri F
authors.initials: GF
authors.lastname: Moolenaar
authors.forename: Nora
authors.initials: N
authors.lastname: Goosen
authors.forename: David
authors.initials: D
authors.lastname: Jeruzalmi
authors.forename: Gregory L
authors.initials: GL
authors.lastname: Verdine
mesh_terms: D000244:Adenosine Diphosphate / Q000737:chemistry; D000251:Adenosine Triphosphatases / Q000737:chemistry* / Q000378:metabolism; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D004265:DNA Helicases / Q000737:chemistry* / Q000378:metabolism; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000378:metabolism; D001411:Geobacillus stearothermophilus / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011487:Protein Conformation; D025941:Protein Interaction Mapping; D055672:Static Electricity; D016335:Zinc Fingers
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D000244:Adenosine Diphosphate; D004706:Endodeoxyribonucleases; D000251:Adenosine Triphosphatases; D004265:DNA Helicases