title: Twisting of the DNA-binding surface by a beta-strand-bearing proline modulates DNA gyrase activity.
abstract: DNA gyrase is the only topoisomerase capable of introducing (-) supercoils into relaxed DNA. The C-terminal domain of the gyrase A subunit (GyrA-CTD) and the presence of a gyrase-specific 'GyrA-box' motif within this domain are essential for this unique (-) supercoiling activity by allowing gyrase to wrap DNA around itself. Here we report the crystal structure of Xanthomonas campestris GyrA-CTD and provide the first view of a canonical GyrA-box motif. This structure resembles the GyrA-box-disordered Escherichia coli GyrA-CTD, both adopting a non-planar beta-pinwheel fold composed of six seemingly spirally arranged beta-sheet blades. Interestingly, structural analysis revealed that the non-planar architecture mainly stems from the tilted packing seen between blades 1 and 2, with the packing geometry likely being defined by a conserved and unusual beta-strand-bearing proline. Consequently, the GyrA-box-containing blade 1 is placed at an angled spatial position relative to the other DNA-binding blades, and an abrupt bend is introduced into the otherwise flat DNA-binding surface. Mutagenesis studies support that the proline-induced structural twist contributes directly to gyrase's (-) supercoiling activity. To our knowledge, this is the first demonstration that a beta-strand-bearing proline may impact protein function. Potential relevance of beta-strand-bearing proline to disease phenylketonuria is also noted.
authors.affiliation: Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan.
authors.forename: Tung-Ju
authors.initials: TJ
authors.lastname: Hsieh
authors.forename: Tien-Jui
authors.initials: TJ
authors.lastname: Yen
authors.forename: Te-Sheng
authors.initials: TS
authors.lastname: Lin
authors.forename: Hsun-Tang
authors.initials: HT
authors.lastname: Chang
authors.forename: Shu-Yun
authors.initials: SY
authors.lastname: Huang
authors.forename: Chun-Hua
authors.initials: CH
authors.lastname: Hsu
authors.forename: Lynn
authors.initials: L
authors.lastname: Farh
authors.forename: Nei-Li
authors.initials: NL
authors.lastname: Chan
mesh_terms: D000595:Amino Acid Sequence; D018360:Crystallography, X-Ray; D027081:DNA Gyrase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004250:DNA Topoisomerases, Type II / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis; D011392:Proline / Q000032:analysis / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016959:Xanthomonas campestris / Q000201:enzymology*
chemical_list: D004268:DNA-Binding Proteins; D021122:Protein Subunits; D011392:Proline; D027081:DNA Gyrase; D004250:DNA Topoisomerases, Type II