Fig. 3

Characteristics of bacterial avidins. Avidins are made of beta barrels and their oligomeric state vary from loose dimeric assembly to very stable tetramer. a Structure of tetrameric chicken avidin with four bound biotin ligands (PDB 2AVI). The biotin molecules are represented as sticks and coloured according to the atom (C, gray; N, blue; O, red; S, yellow). The conserved residues indicated by black stars in e are indicated by black spheres, representing C-alpha atoms of residues 10, 15, 20, 27, 29, 30, 49, 51, 64, 66, 67, 68, 77, 80, 81, 93, 95, 116 and 120. b Structure of rhizavidin showing dimeric assembly (PDB 3EW2). c The biotin-binding site has very high structural complementarity with the ligand, represented here by chicken avidin monomeric subunit with bound biotin (PDB 2AVI). d Closer view of the area indicated in a. e Multiple sequence alignment of verified avidins. The black stars indicate highly conserved residues, which are also visualized in a and d. Red stars indicate residues in direct contact with the bound biotin ligand. Secondary structure elements (according to chicken avidin) are indicated by arrows above the alignment. f Groupwise sequence features of putative bacterial avidins. Sequence logos of the identified clades of the phylogeny tree of putative avidins were used to build sequence logos. Those logos were then aligned manually using the secondary structure elements as a guide. The residues are colored according to the chemical characteristics of the residues, as indicated in the legend