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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 non-contiguous 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 non-contiguous beta-strand forming hydrogen bonds with the beta-turn. Using structure-based analysis, we have detected 518 instances of the GD box in a non-redundant subset of the SCOP database comprising 3771 domains. Apart from the cradle-loop barrels, this motif is also found in a diverse set of non-homologous folds including other topologically related beta-barrels. Since non-local interactions are fundamental in the formation of protein structure, systematic identification and characterization of other non
-contiguous supersecondary structural elements is likely to prove valuable to protein structure modeling, validation, and prediction.