Fig. 5: Structure of Bd1075 and features different to other characterized LD-CPase enzymes.
From: Asymmetric peptidoglycan editing generates cell curvature in Bdellovibrio predatory bacteria
a Two orthogonal views of the Bd1075 fold, with catalytic residue C156 in space-fill form and features labeled. b Close-up view of the Bd1075 LD-CPase catalytic domain with selected residues that form the active site pocket displayed in stick form. c Close-up view of the Bd1075 NTF2 pocket, demonstrating complexation of a loop (residues 106–109 colored yellow, P107 and K108 in stick form) from a neighboring molecule in the crystal lattice. d Comparison of Bd1075 (red, 7O21: https://www.rcsb.org/structure/7O21), Csd6 (white, 4XZZ: https://www.rcsb.org/structure/4XZZ), and Pgp2 (gray, 6XJ6: https://www.rcsb.org/structure/6XJ6) structures. Helix 3 of the Bd1075 NTF2 domain (labeled ‘nH3’) and the associated loop (‘lip’) are relatively closer to the NTF2 pocket than the respective features of Csd6/Pgp2. e Close-up of the NTF2 terminus from structural alignment in d, demonstrating the relative extension of the Bd1075 C-terminus (colored yellow, includes NTF2 pocket-forming residue W303) in comparison to the shorter Csd6/Pgp2 termini (end residue colored green). The relative shifts of the nH3 helix and lip loop to constrict the NTF2 pocket are denoted by dashed arrows.
