A protein motif, also called a secondary structure motif, is a sequence of secondary protein structures, such that the sequence recurs in a variety of proteins, and specifies a characteristic three-dimensional structure.
Secondary structure motifs are usually fairly short, e.g. the 'helix-turn-helix' motif has just three elements.
A single protein may contain more than one motif.
The amino acid sequences producing a single protein motif may differ significantly, as illustrated in the next section.
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2 The DSSP Code 3 See also 4 References |
This example comes from the paper by Matsuda and colleagues cited below.
The E. coli lactose operon repressor LacI (PDB id 1lccA) and E. coli catabolite gene activator (PDB id 3gapA) both have a helix-turn-helix motif, but their amino acid sequences do not show much similarity, as shown in the table below.
Matsuda and colleagues devised a code called the 3D chain code for
representing a protein structure as a string of letters. This encoding scheme reveals the similarity between the proteins much more clearly than the amino acid sequence:
The DSSP code is frequently used to describe the most frequent secondary structures as a single letter. DSSP is an acronym for "Dictionary of Protein Secondary Structure".
Helix-turn-helix
3D chain code Amino acid sequence 1lccA TWWWWWWWKCLKWWWWWWG LYDVAEYAGVSYQTVSRVV 3gapA KWWWWWWGKCFKWWWWWWW RQEIGQIVGCSRETVGRIL The DSSP Code
Other types of structure are sometimes designated with C or L.
See also
References
