The term "motif" when used in structural biology tends to refer to one of two cases:
A particular amino-acid sequence that characterises a biochemical function.
A set of secondary structure elements that defines a functional or structural role.
There are a great number of protein sequence motifs identified, many of which have well defined structural or functional roles. One such example is the so-called zinc finger motif which is readily identified from the following consensus sequence pattern (where "X" represents any amino acid):
Cys - X(2-4) - Cys - X(3) - Phe - X(5) - Leu - X(2) - His - X(3) - His
Coordination of the zinc ion by 4 amino acid residues forces a particular folding of the protein backbone, giving rise to the nickname zinc finger:
The example structure, displayed to the right, that serves to illustrate the motif is that of Zif268 protein-DNA complex from Mus musculus. In this example (a C2H2 class zinc finger) the conserved cysteine and histidine residues form ligands to a zinc ion whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the recogniton helices to bind to the major groove of the DNA.
