title: The recognition domain of the BpuJI restriction endonuclease in complex with cognate DNA at 1.3-A resolution.
abstract: Type IIS restriction endonucleases recognize asymmetric DNA sequences and cleave both DNA strands at fixed positions downstream of the recognition site. The restriction endonuclease BpuJI recognizes the asymmetric sequence 5'-CCCGT; however, it cuts at multiple sites in the vicinity of the target sequence. BpuJI consists of two physically separate domains, with catalytic and dimerization functions in the C-terminal domain and DNA recognition functions in the N-terminal domain. Here we report the crystal structure of the BpuJI recognition domain bound to cognate DNA at 1.3-A resolution. This region folds into two winged-helix subdomains, D1 and D2, interspaced by the DL subdomain. The D1 and D2 subdomains of BpuJI share structural similarity with the similar subdomains of the FokI DNA-binding domain; however, their orientations in protein-DNA complexes are different. Recognition of the 5'-CCCGT target sequence is achieved by BpuJI through the major groove contacts of amino acid residues located on both the helix-turn-helix motifs and the N-terminal arm. The role of these interactions in DNA recognition is also corroborated by mutational analysis.
authors.affiliation: Institute of Biotechnology, Graiciuno 8, 02241 Vilnius, Lithuania.
authors.forename: Rasa
authors.initials: R
authors.lastname: Sukackaite
authors.forename: Saulius
authors.initials: S
authors.lastname: Grazulis
authors.forename: Matthias
authors.initials: M
authors.lastname: Bochtler
authors.forename: Virginijus
authors.initials: V
authors.lastname: Siksnys
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004252:DNA Mutational Analysis; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000378:metabolism; D046911:Macromolecular Substances / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D011487:Protein Conformation
chemical_list: D046911:Macromolecular Substances; D004247:DNA; D015252:Deoxyribonucleases, Type II Site-Specific; C051481:GRGCYC-specific type II deoxyribonucleases