9E9B | pdb_00009e9b

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Literature

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.

(2025) Acta Crystallogr F Struct Biol Commun 

  • DOI: https://doi.org/10.1107/S2053230X25006181
  • Primary Citation of Related Structures:  
    9E9B, 9MNN

  • PubMed Abstract: 

    Menaquinones (vitamin K 2 ) 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.


  • Organizational Affiliation

    Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase583Listeria monocytogenes 10403SMutation(s): 1 
Gene Names: menDLMRG_01292
EC: 2.2.1.9
UniProt
Find proteins for A0A0H3GD77 (Listeria monocytogenes serotype 1/2a (strain 10403S))
Explore A0A0H3GD77 
Go to UniProtKB:  A0A0H3GD77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3GD77
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.025α = 90
b = 176.025β = 90
c = 100.144γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marsden FundNew ZealandM1208
Other governmentGermanyGerman Academic Exchange Service/Deutscher Akademischer Austauschdienst (DAAD)

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release