A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations

Side-chain hydroxyl residues in protein crystal structures often form hydro gen bonds with main-chain atoms. The most common bond arrangement is a four to five residue motif in which a serine or threonine is the first residue forming two characteristic hydrogen bonds to residues ahead of it in sequen ce. We call them ST-motifs, by analogy with the term Asx-motif we suggested for the related motifs with aspartate and asparagine residues. ST-motifs a re common, there being just under one and a half in a typical protein subun it. Asx-motifs are even more common, such that 9% of the residues of an ave rage protein consist of Asx or ST-motifs. Of the ST-motifs, three-quarters are at helical N termini, and the rest occur by themselves or in conjunctio n with beta-bulge loops. A third of all alpha-helices have either ST-motifs or Asx-motifs at their N termini. Previous work has emphasised the occurre nce of the capping box at alpha-helical N termini, but the capping box occu rs in only 5% of alpha-helical N termini; also, we point out that it can be regarded as a subset of the ST-motif (or, occasionally, of the Asx-motif). By comparing related sequences, the rates which amino acid residues at the first position of ST or Asx-motifs interchange during evolution are examin ed. Serine right arrow over left arrow threonine, and aspartate right arrow over left arrow asparagine, interchange is rapid; inter-pair exchange is s lower, but much faster than exchange with other amino acid residues. This i s consistent with the general similarity of ST-motifs and Asx-motifs combin ed with some subtle structural differences between them that are described. (C) 1999 Academic Press.