What are sequence features?

Sequence features are groups of amino acids that confer certain characteristics upon a protein, and may be important for its overall function. Such features include:

• active sites, which contain amino acids involved in catalytic activity. For example, the enzyme lipase, which catalyses the formation and hydrolysis of fats, has two amino acid residues (a histidine followed by a glycine) that are essential for its catalytic activity.
• binding sites, containing amino acids that are directly involved in binding molecules or ions, like the iron-binding site of haemoglobin.
• post-translational modification (PTM) sites, which contain residues known to be chemically modified (phosphorylated, palmitoylated, acetylated, etc) after the process of protein translation.
• repeats, which are typically short amino acid sequences that are repeated within a protein, and may confer binding or structural properties upon it.

Sequence features differ from domains in that they are usually quite small (often only a few amino acids long), whereas domains represent entire structural or functional units of the protein (Figure 8). Sequence features are often nested within domains – a protein kinase domain, for example, usually contains a protein kinase active site.

Proteins can also be classified according to the sequence features they contain. For example, ferredoxins are sulphur-iron proteins that mediate electron transfer in a variety of biological redox reactions, including the photosynthetic process. They can be divided into several groups according to the nature of their iron-sulphur cluster (find more information about ferredoxins).

In the 2Fe-2S ferredoxins (which bind a cluster of two iron (Fe) and two sulphur (S) atoms), there are 4 cysteines residues involved in iron-sulphur binding. The 2Fe-2S binding site is shown on the  ferredoxin 3D-structure in Figure 9.