Figure 13: Structure of Bdellovibrio peptidoglycan deacetylase Bd3279.

(a) Protein fold of Bd3279, N-terminal domain coloured in blue, C-terminal catalytic domain coloured by secondary structure (TIM barrel; red α-helices, yellow β-strands). The N and C termini and disordered active site loop (parentheses) are labelled. Disulphide link between C79 and C109 is shown in stick form (labelled by asterisk) and coloured green. (b) Comparison of selected active site residues of Bd3279 and S. pneumoniae PgdA (PDB code 2C1G). Bd3279 (light tan, non-primed labels) and PgdA (light blue, prime labels) have a largely similar active site conformation, centred around a catalytic Zn ion (purple, sphere representation). Corresponding residues on the left-hand side of the figure (toward the core of the enzyme) are in better agreement than those on the right-hand side (towards solvent and the disordered loop between residues 230–249); the Bd3279 equivalent to PgdA H330’ (H231) is within this region and not observed in our structure. The conserved active site tyrosine (Y280/Y367’) is adjacent to this region and in Bd3279 takes the place of the PgdA substrate-mimic acetate ligand (labeled Ac’). The figure also demonstrates the extent of which the N-terminal domain “caps” the active site pocket – in particular, L43 contacts both H335 and Y280.