structural motif
/ moh-TEEF /
Below the level of a whole domain, proteins are full of small, recurring patterns — a couple of helices arranged just so, a hairpin of two strands, a little loop that grips a metal ion. These mini-patterns, repeated across many proteins, are called motifs. If a domain is a word, a motif is a common syllable or letter combination that shows up again and again.
The term is used two related ways. A structural motif (sometimes called supersecondary structure) is a small, recognizable arrangement of a few secondary-structure elements — for example, the helix-turn-helix, two short helices set at an angle that together fit into the major groove of DNA, or the beta-hairpin of two strands joined by a tight turn. A sequence motif is a short, conserved stretch of amino-acid sequence that signals a particular function or modification site, such as a few residues that mark where a sugar gets attached. The two often go together: a conserved sequence frequently folds into a conserved shape.
Motifs are useful because they are predictive. Spot a helix-turn-helix and you can bet the protein binds DNA; spot a particular sequence motif and you can guess it will be phosphorylated or glycosylated. They are the building blocks one rung below domains, and recognizing them is how biologists make quick, educated guesses about a protein's job from its sequence or structure alone — a guess to be tested, not a certainty, since the same shape can occasionally do different things.
The helix-turn-helix motif — two short alpha helices joined by a turn — appears in countless proteins that switch genes on and off; one helix lies in the DNA's major groove and reads the bases there.
A motif is a small, reusable arrangement that often signals a specific function.
A motif is smaller than a domain: a domain folds and is stable on its own, while a motif is a recurring sub-pattern that usually needs the rest of the fold around it. The same shape can occasionally serve more than one function, so motifs predict, they do not prove.