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.

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, 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 also because the size of the elements varies from one protein and the next.

• Beta hairpin:

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 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:

See also

• Motif domain
• 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.