Structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms

Bailey, M.; Given, F.M.; Ho, N.A.T.; Pearce, F.G.; Allison, T.M.; Johnston, J.M.

doi:10.1107/S2053230X25006181

Figure 3
(a) ThDP and Mg²⁺ (yellow) binding in the LmoMenD (PDB entry 9e9b) active site. (b) Intermediate I (IntI; rose) formation in the LmoMenD (PDB entry 9mnn) active site. The residues comprising the active site originate from the PYR (green) and PP (blue) domains, with the catalytic glutamate (Glu56) highlighted (*). Water molecules are depicted as orange spheres and polar contacts as black dashes. (c) ThDP (PDB entry 9e9b; yellow) and intermediate I (PDB entry 9mnn; rose) in their respective 2mF_o − DF_c electron-density maps (contoured at 1σ; grey). (d) Overlay of the apo (PDB entry 3lq1; grey), ThDP-bound (PDB entry 9e9b; green) and intermediate I-bound (PDB entry 9mnn; blue) active sites, with residues differing between the structures shown as sticks. (e) Overlay of the apo (PDB entry 3lq1; grey) and ThDP-bound (PDB entry 9e9b; green) LmoMenD monomers, with regions becoming ordered upon cofactor binding highlighted in orange. (f) Overlay of the apo (PDB entry 3lq1; grey) and ThDP-bound (PDB entry 9e9b; PYR domain, green; PP domain, blue) active sites, with regions becoming ordered upon cofactor binding highlighted in orange and ThDP in the active site shown as yellow sticks.

STRUCTURAL BIOLOGY
COMMUNICATIONS

ISSN: 2053-230X

Volume 81| Part 8| August 2025| Pages 348-357

https://doi.org/10.1107/S2053230X25006181

Open

access

Search IUCr Journals		doi		Advanced search
Author		volume	page