Fig. 4: Crystal structure of NanR in complex with Neu5Ac and Zn²⁺.

a The E. coli NanR monomer has two domains—an N-terminal DNA-binding domain (green) and C-terminal effector-binding domain (beige). The DNA-binding domain contains a highly conserved winged helix–turn–helix motif (left panel) where the wing is defined by an antiparallel two-stranded β-sheet (blue). The C-terminal domain is arranged into an antiparallel, all-α-helical bundle (right inset, rainbow). Helix α4 (purple) is a flexible linker connecting the two domains. b Cartoon/surface representation of the asymmetric domain-swapped dimeric structure formed by an exchange between monomers via the α4-helix (pink). The Neu5Ac-bound and Neu5Ac-free monomers are shown in beige and blue, respectively. c The effector binding site is located within a large polar cavity of the C-terminal domain. The direct or water-mediated hydrogen-bonding residues (gray sticks) that coordinate Neu5Ac in its β-anomeric form and hold Zn²⁺ in an octahedral geometry are indicated, while water molecules are depicted as yellow spheres. d An overlay of the Neu5Ac-bound C-terminal domain (beige) and Neu5Ac-free C-terminal domain (blue) illustrates the effector-induced conformational changes. e An overlay of the Neu5Ac-bound monomer (beige) and Neu5Ac-free monomer (blue) further illustrates effector-induced conformational changes. f Surface depiction of Neu5Ac-bound (beige) and Neu5Ac-free (blue) monomers shows that the binding of Neu5Ac compresses the monomer around the α4-helix (purple) relative to the Neu5Ac-free monomer by 28.3 Å. g Cartoon representation of the interface between the Neu5Ac-bound monomer (beige) and the Neu5Ac-free monomer (blue), facilitated by salt-bridge interactions.