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Figure 1 | BMC Structural Biology

Figure 1

From: Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalis

Figure 1

Comparison of avidin, streptavidin and xenavidin. A, Structural alignment of avidin [PDB: 1AVD] (red), streptavidin [PDB: 1MK5] (cyan) and xenavidin (reported here; [PDB: 2UYW] (blue)). The A subunits of each protein are shown as ribbons. The bound biotin of xenavidin is shown as sticks. Loops connecting β-strands (for example, L1,2 connecting strands β1 and β2) as well as the amino (N) and carboxyl (C) termini are labelled. The α1-helix (H1) is also indicated. B, Selected residues around the biotin-binding pocket are shown as sticks and are labelled according to xenavidin. Biotin molecules are shown (1, xenavidin; 2 avidin; and 3 streptavidin). C, Structure-based sequence alignment created based on the ensemble of aligned structures shown in A. The secondary structure elements of avidin (β-strands 1-8, arrows; α-helix, H1) are indicated, and residues are numbered according to avidin (top) and xenavidin (bottom). Identical (red background) and physicochemically similar amino acid residues (red letters) are boxed. Potential N-glycosylation sites are indicated with an asterisk. Residues hydrogen bonded to biotin are indicated by triangles (side-chain interaction) or squares (main-chain interaction). Spheres denote residues involved in hydrophobic effect or van der Waals interactions with biotin. Interacting residues from a neighbouring subunit are indicated with an open circle. Colouring scheme for the symbols: black, conserved in all three proteins; green, conserved in xenavidin and avidin only; blue, unique to xenavidin; red, unique to avidin; and cyan, unique to streptavidin. For additional information, see Methods.

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