PROSITE documentation PDOC00499

Avidin-like domain signature and profile

Avidin [1] is a minor constituent of egg white in several groups of oviparous vertebrates. Avidin, which was discovered in the 1920's, takes its name from the avidity with which it binds biotin. These two molecules bind so strongly that it is highly difficult to separate them. Streptavidin is a protein produced by Streptomyces avidinii which also binds biotin and whose sequence is evolutionary related to that of avidin.

Avidin and streptavidin both form homotetrameric complexes of non-covalently associated chains. Each chain forms a very strong and specific non-covalent complex with one molecule of biotin.

The dimeric avidin sub-family includes several members, all originating from different bacterial sources: rhizavidin from Rhizobium etli, shwanavidin from Shewanella denitrificans, hoefavidin from Hoeflea phototrophica DFL-43, afifavidin from Afifella pfennigii and wilavidin from a member of the class γproteobacteria. Members of the sub-family exhibit a dimeric (1-4 dimer) rather than a tetrameric structure. These proteins are characterized by the lack of the critical Trp of the tetrameric avidins but retain compensatory elements that result in remarkably high affinities toward biotin, comparable to those of the tetrameric forms. Members of the dimeric sub-family are also characterized by a conserved disulfide bridge in the vicinity of the biotin-binding site that was shown to be essential for the high affinity toward biotin [2,3,4,5].

Fibropellins I and III [6] are proteins that form the apical lamina of the sea urchin embryo, a component of the extracellular matrix. These two proteins have a modular structure composed of a CUB domain (see <PDOC00908>), followed by a variable number of EGF repeats (see <PDOC00021>) and a C-terminal avidin-like domain. The fibropellin avidin-like domain forms a homotetramer incapable of binding biotin [7].

The three-dimensional structures of streptavidin [8,9], avidin [10] and dimeric bacterial avidin [2,3,4,5] have been determined and revealed them to share a common fold: an eight stranded anti-parallel β-barrel with a repeated +1 topology enclosing an internal ligand binding site (see <PDB:1AVD>).

As a signature sequence for the avidin-like domain we selected a conserved motif located in its C-terminal section. We also developed a profile that covers the entire avidin-like domain.