Structural motif



In an unbranched, 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 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 subtilisin.

Because the relationship between 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 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

 

  • Beta ribbon:

Extremely common. Two antiparallel beta strands connected by a tight turn of a few amino acids between them.

  • Greek key:

4 beta strands folded over into a sandwich shape.

  • Omega loop:

a loop where the residues that make up the beginning and end of the loop are very close together.

  • Helix-loop-helix:

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.

See also: structural domain


  • Beta hairpin:

See also

References

  • Prosite Database of protein families and domains
  • SCOP Structural classification of Proteins
  • CATH Class Architecture Topology Homology
  • FSSP FSSP
  • PASS2 PASS2 - Protein Alignments as Structural Superfamilies
  • SMoS SMoS - Database of Structural Motifs of Superfamily
 
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