title: How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.
abstract: Restriction endonucleases Ecl18kI and PspGI/catalytic domain of EcoRII recognize CCNGG and CCWGG sequences (W stands for A or T), respectively. The enzymes are structurally similar, interact identically with the palindromic CC:GG parts of their recognition sequences and flip the nucleotides at their centers. Specificity for the central nucleotides could be influenced by the strength/stability of the base pair to be disrupted and/or by direct interactions of the enzymes with the flipped bases. Here, we address the importance of these contributions. We demonstrate that wt Ecl18kI cleaves oligoduplexes containing canonical, mismatched and abasic sites in the central position of its target sequence CCNGG with equal efficiencies. In contrast, substitutions in the binding pocket for the extrahelical base alter the Ecl18kI preference for the target site: the W61Y mutant prefers only certain mismatched substrates, and the W61A variant cuts exclusively at abasic sites, suggesting that pocket interactions play a major role in base discrimination. PspGI and catalytic domain of EcoRII probe the stability of the central base pair and the identity of the flipped bases in the pockets. This 'double check' mechanism explains their extraordinary specificity for an A/T pair in the flipping position.
authors.affiliation: Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania.
authors.forename: Gintautas
authors.initials: G
authors.lastname: Tamulaitis
authors.forename: Mindaugas
authors.initials: M
authors.lastname: Zaremba
authors.forename: Roman H
authors.initials: RH
authors.lastname: Szczepanowski
authors.forename: Matthias
authors.initials: M
authors.lastname: Bochtler
authors.forename: Virginijus
authors.initials: V
authors.lastname: Siksnys
mesh_terms: D019943:Amino Acid Substitution; D020029:Base Pairing; D001665:Binding Sites; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D008958:Models, Molecular; D013379:Substrate Specificity
chemical_list: D004247:DNA; C114636:endodeoxyribonuclease Ecl18kI; C046545:CCWGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific