The GD box: a widespread noncontiguous supersecondary structural element.

ABSTRACT: Identification and characterization of recurrent supersecondary structural elements is central to understanding the rules governing protein tertiary structure. Here, we describe the GD box, a widespread noncontiguous supersecondary element, which we initially found in a group of topologically distinct but homologous beta-barrels--the cradle-loop barrels. The GD box is similar both in sequence and structure and comprises two short unpaired beta-strands connected by an orthogonal type-II beta-turn and a noncontiguous beta-strand forming hydrogen bonds with the beta-turn. Using structure-based analysis, we have detected 518 instances of the GD box in a nonredundant subset of the SCOP database comprising 3771 domains. Apart from the cradle-loop barrels, this motif is also found in a diverse se

SUBMITTER: Alva V 

PROVIDER: S-EPMC2777370 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature