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Protein motif

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.

Table of contents
1 Helix-turn-helix
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:
3D chain code Amino acid sequence

The DSSP Code

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".

Other types of structure are sometimes designated with C or L.

See also

DNA motif


Hideo Matsuda, Fumihiro Taniguchi, Akihiro Hashimoto. An Approach to Detection of Protein Structural Motifs using an Encoding Scheme of Backbone Conformations. Proc. of 2nd Pacific Symposium on Biocomputing, pp.280-291 (January, 1997).
W. Kabsch and C. Sander. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen Bonded and Geometrical Features. Biopolymers 22: 2577-2637 (1983).