Wy. Wan et Ej. Milner-white, A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at alpha-helical N termini and in other situations, J MOL BIOL, 286(5), 1999, pp. 1651-1662
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.