DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI

By K. E. Flick, M. Jurica, R. Monnat, Barry L. Stoddard. 1998

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3D-DART: a DNA structure modelling server (2009, background): “DNA often changes its conformation as a result of interactions with various ligands; especially binding to proteins can result in large conformational changes such as helical kinks (1) or local helical untwisting (2).”
Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site. (2000, methodology): “The wild-type product complex structure has been solved and reported previously (Brookhaven PDB 1A73) (Flick et al., 1998).”
Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease (2007, methodology): “These sequencedependent effects may be further amplified by DNA substrate deformation in this region of the I-PpoI substrate complex, and thus interfere with correct positioning of the scissile phosphate (Figures 1 and 4) ( 21 ,26).”
Mh1 domain of Smad is a degraded homing endonuclease. (2001, background): “Its structure has been determined in complex with DNA (PDB entry 1a73).(39) The enzyme is composed of three subdomains, two of which have structural equivalents in MH1 Smad (Figure 1(a), blue/yellow and purple/green).”