Structural Motifs

Structural motifs are short segments of protein 3D structure, which are spatially close but not necessarily adjacent in the sequence. Structural motifs may be conserved in a large number of different proteins (10). Their role may be structural or functional.

An example of a structural motif that generally performs a structural role is a beta-turn (Figure 17). A beta turn consists of four consecutive residues where the polypeptide chain folds back on itself by nearly 180 degrees (11).

 Beta turn structural motif

Figure 17 Beta turn structural motif. The four residues are shown in stick representation, the strands

are as cartoon arrows. Nitrogen is shown in blue, oxygen in red and the chiral carbon of Glycine residue in yellow.

An example of a structural motif that has an important functional role is the helix-turn-helix motif (Figure 18) which can bind DNA. This is a structural feature that is difficult to identify from the amino acid sequence alone.

The transcription factor SATB1

Figure 18: The transcription factor SATB1 (right: green and blue) contains a helix-turn-helix motif (blue) that can to bind DNA (left).

PDBe offers a service specific for structural motifs and functional sites: Motifs and Sites (PDBeMotif). PDBeMotif can be used to examine the characteristics of the binding sites of single proteins or classes of proteins by combining protein sequence, chemical structure and 3D data in a single search.