Structural motif

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions.

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 have 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.

In proteins

In proteins, a structural motif describes the connectivity between secondary structural elements. An individual motif usually consists of only a few elements, e.g., the 'helix-turn-helix' motif which has just three. Note that, while the spatial sequence of elements may be identical in all instances of a motif, they may be encoded in any order within the underlying gene. In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure.

• Beta hairpin:

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

• Greek key:

Two beta strands folded over into a sandwich shape.

• Omega loop:

A loop in which 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. This motif is seen in transcription factors.

• Zinc finger:

Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins.

• Helix-turn-helix:

Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression.

• Nest:

Extremely common. Three consecutive amino acid residues form an anion-binding concavity.

• Niche:

Extremely common. Three or four consecutive amino acid residues form a cation-binding feature.

See also

• Sequence motif
• Short linear motif

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
• S4 S4: Server for Super-Secondary Structure Motif Mining

Further reading

• Chiang YS, Gelfand TI, Kister AE, Gelfand IM (2007). "New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage". Proteins. 68 (4): 915–921. doi:10.1002/prot.21473. PMID 17557333.