9E9B

Crystal structure of L. monocytogenes MenD with Mg2+ and ThDP bound

Summary for 9E9B

• Entry DOI: 10.2210/pdb9e9b/pdb
• Descriptor: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase, THIAMINE DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: sephchc synthase decarboxylase thdp-dependent enzyme, transferase
• Biological source: Listeria monocytogenes 10403S
• Total number of polymer chains: 1
• Total formula weight: 65379.12

Authors

Klein, M.,Given, F.M.,Ho, N.A.T.,Allison, T.M.,Johnston, J.M. (deposition date: 2024-11-08, release date: 2025-07-30, Last modification date: 2025-08-13)

Primary citation

Bailey, M.,Given, F.M.,Ho, N.A.T.,Pearce, F.G.,Allison, T.M.,Johnston, J.M.
Structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms.
Acta Crystallogr.,Sect.F, 81:348-357, 2025

PubMed Abstract: Menaquinones (vitamin K) are a family of redox-active small lipophilic molecules that serve as vital electron carriers in many bacterial electron-transport pathways. The ThDP-dependent enzyme 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC) synthase (MenD) catalyses the first irreversible step in bacterial classical menaquinone biosynthesis via a series of reactions involving covalent ThDP-bound intermediates. We report structures of MenD from the pathogen Listeria monocytogenes (LmoMenD) in its ThDP cofactor-bound and in-crystallo captured intermediate I-bound forms. Analysis of the structures revealed that LmoMenD adopts the typical three-domain ThDP-dependent fold observed for MenD orthologs, while a combination of structure, size-exclusion chromatography, mass photometry and small-angle X-ray scattering analysis showed that the enzyme has a homotetrameric quaternary structure. While both of the ligand-bound structures reported here were very similar, comparison with an apo form from the PDB revealed a closing down of the active site in the ligand-bound forms, with more complete models suggesting lower levels of disorder around key regions of the active site that interface with ThDP or the captured intermediate. Enzyme kinetics characterization showed the enzyme was active and enabled allosteric inhibition to be measured. There was weak inhibition of enzyme activity in the presence of 1,4-dihydroxy-2-naphthoic acid, an allosteric regulator of Mycobacterium tuberculosis MenD and downstream metabolite in the menaquinone-biosynthesis pathway.

PubMed: 40673487
DOI: 10.1107/S2053230X25006181

Experimental method

X-RAY DIFFRACTION (2.61 Å)