In an unbranched, chain-like biological molecule, such as a protein or a strand of RNA, a structural motif is a three-dimensional structural element or fold within the chain, which appears also in a variety of other molecules. In the context of proteins, the term is sometimes used interchangeably with "structural domain," although a domain need not be a motif nor, if it contains a motif, need not be made up of only one.
Structural alignment is a major method for discovering significant structural motifs.
Some motifs exhibit both tertiary and secondary structure, and may be regarded as a configuration of secondary structures. Such a description is the basis for many of the names that structural biologists give to particular kinds, such as the helix-turn-helix motif. This is not always true, however, as in the case of the EF-hand.
Other motifs, especially in proteins, consist of only a small number of amino acids, functional groups or functional atoms and do not depend on any secondary structure. These motifs are often directly involved in a protein's function. For example the catalytic triad made up of a serine, histidine, and aspartic acid is observed in the structures of the unrelated proteins trypsin and subtilisin.
Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not need to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure. In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" structure.
Structural motifs in proteins
In proteins, structure motifs usually consist of just a few elements, e.g. the 'helix-turn-helix' has just three. Note that while the spatial sequence of elements is the same in all instances of a motif, they may be encoded in any order within the underlying gene. Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene. Note also that even when two genes encode secondary structural elements of a motif in the same order, nevertheless they may specify somewhat different sequences of amino acids. This is true not only because of the complicated relationship between tertiary and primary structure, but because the size of the elements varies from one protein and the next.
Examples of motif types in proteins
Extremely common. Two antiparallel beta strands connected by a tight turn of a few amino acids between them.
4 beta strands folded over into a sandwich shape.
a loop where the residues that make up the beginning and end of the loop are very close together.
Consists of alpha helices bound by a looping stretch of amino acids. Important in DNA binding proteins.
Two beta strands with an alpha helix end folded over to bind a zinc ion. This motif is seen in transcription factors.