7RML

Neisseria meningitidis Methylenetetrahydrofolate reductase in complex with FAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Biochemical and structural characterization of meningococcal methylenetetrahydrofolate reductase.

Pantong, W.Pederick, J.L.Maenpuen, S.Tinikul, R.Jayapalan, J.J.Jovcevski, B.Wegener, K.L.Bruning, J.B.Salaemae, W.

(2023) Protein Sci 32: e4654-e4654

  • DOI: https://doi.org/10.1002/pro.4654
  • Primary Citation of Related Structures:  
    7RML

  • PubMed Abstract: 

    Methylenetetrahydrofolate reductase (MTHFR) is a key metabolic enzyme in colonization and virulence of Neisseria meningitidis, a causative agent of meningococcal diseases. Here, the biochemical and structural properties of MTHFR from a virulent strain of N. meningitidis serogroup B (NmMTHFR) were characterized. Unlike other orthologs, NmMTHFR functions as a unique homohexamer, composed of three homo-dimerization partners, as shown in our 2.7 Å resolution crystal structure. Six active sites were formed solely within monomers and located away from the oligomerization interfaces. Flavin adenine dinucleotide cofactor formed hydrogen bonds with conserved sidechains, positioning its isoalloxazine ring adjacent to the overlapping binding sites of nicotinamide adenine dinucleotide (NADH) coenzyme and CH 2 -H 4 folate substrate. NmMTHFR utilized NADH (K m  = 44 μM) as an electron donor in the NAD(P)H-CH 2 -H 4 folate oxidoreductase assay, but not nicotinamide adenine dinucleotide phosphate (NADPH) which is the donor required in human MTHFR. In silico analysis and mutagenesis studies highlighted the significant difference in orientation of helix α7A (Phe215-Thr225) with that in the human enzyme. The extended sidechain of Met221 on helix α7A plays a role in stabilizing the folded structure of NADH in the hydrophobic box. This supports the NADH specificity by restricting the phosphate group of NADPH that causes steric clashes with Glu26. The movement of Met221 sidechain allows the CH 2 -H 4 folate substrate to bind. The unique topology of its NADH and CH 2 -H 4 folate binding pockets makes NmMTHFR a promising drug target for the development of new antimicrobial agents that may possess reduced off-target side effects.


  • Organizational Affiliation

    Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5,10-methylenetetrahydrofolate reductase
A, B, C
298Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: metFNMB0943
EC: 1.5.1.20
UniProt
Find proteins for Q9JZQ3 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZQ3 
Go to UniProtKB:  Q9JZQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JZQ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.444α = 90
b = 146.598β = 90
c = 86.9γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references, Refinement description
  • Version 1.2: 2023-06-14
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description