info:eu-repo/semantics/article
Topology of Type II REases revisited; structural classes and the common conserved core
Fecha
2007-04Registro en:
Niv, Masha Y.; Ripoll, Daniel R.; Vila, Jorge Alberto; Liwo, Adam; Vanamee, Éva S.; et al.; Topology of Type II REases revisited; structural classes and the common conserved core; Oxford University Press; Nucleic Acids Research; 35; 7; 4-2007; 2227-2237
0305-1048
1362-4962
CONICET Digital
CONICET
Autor
Niv, Masha Y.
Ripoll, Daniel R.
Vila, Jorge Alberto
Liwo, Adam
Vanamee, Éva S.
Aggarwal, Aneel K.
Weinstein, Harel
Scheraga, Harold A.
Resumen
Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five β-strands flanked by two α-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure.