title: The cis-Pro touch-turn: a rare motif preferred at functional sites.
abstract: A new motif of three-dimensional (3D) protein structure is described, called the cis-Pro touch-turn. In this four-residue, three-peptide motif, the central peptide is cis. Residue 2, which precedes the proline, has phi, psi values either in the "prePro region" of the Ramachandran plot near -130 degrees, 75 degrees or in the Lalpha region near +60 degrees, +60 degrees. The Calpha(1)-Calpha(4) distance is 4-5 A and the two flanking peptides lie parallel to one another, making van der Waals contact rather than a hydrogen bond. Apparently, this arrangement is locally unfavorable and therefore rare, usually occurring only if needed for biological function. Of the 12 examples in a 500-protein database, cis-Pro touch-turns are found at the catalytic sites of pectate lyase, Ni-Fe hydrogenase, glucoamylase, xylanase, and opine dehydrogenase and at the primary binding sites of ribonuclease H, type I DNA polymerase, ribotoxin, and phage gene 3 protein. In each of these protein families, the touch-turns serve different roles; their functional importance is supported by conservation and mutagenesis data. In analyzing the conservation patterns of these 3D motifs, new methods for in-depth quality evaluation of the structural bioinformatic data are employed to distinguish between significant exceptions and errors
authors.affiliation: Department of Biochemistry, Duke University, Durham, North Carolina 27710-3711, USA.
authors.forename: Lizbeth L
authors.initials: LL
authors.lastname: Videau
authors.forename: W Bryan
authors.initials: WB
authors.lastname: Arendall
authors.forename: Jane S
authors.initials: JS
authors.lastname: Richardson
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D020134:Catalytic Domain; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry; D008958:Models, Molecular; D011485:Protein Binding; D013329:Structure-Activity Relationship
chemical_list: D004798:Enzymes