Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase - the importance of accommodating the active site water

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water.

Heyes, L.C.Reichau, S.Cross, P.J.Jameson, G.B.Parker, E.J.

(2014) Bioorg Chem 57: 242

  • DOI: https://doi.org/10.1016/j.bioorg.2014.08.003
  • Primary Citation of Related Structures:  
    4UMA, 4UMB, 4UMC

  • PubMed Abstract: 

    3-Deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first committed step of the shikimate pathway, which produces the aromatic amino acids as well as many other aromatic metabolites. DAH7PS catalyses an aldol-like reaction between phosphoenolpyruvate and erythrose 4-phosphate. Three phosphoenolpyruvate mimics, (R)-phospholactate, (S)-phospholactate and vinyl phosphonate [(E)-2-methyl-3-phosphonoacrylate], were found to competitively inhibit DAH7PS from Neisseria meningitidis, which is the pathogen responsible for bacterial meningitis. The most potent inhibitor was the vinyl phosphonate with a Ki value of 3.9±0.4μM. We report for the first time crystal structures of these compounds bound in the active site of a DAH7PS enzyme which reveals that the inhibitors bind to the active site of the enzyme in binding modes that mimic those of the predicted oxocarbenium and tetrahedral intermediates of the enzyme-catalysed reaction. Furthermore, the inhibitors accommodate the binding of a key active site water molecule. Together, these observations provide strong evidence that this active site water participates directly in the DAH7PS reaction, enabling the facial selectivity of the enzyme-catalysed reaction sequence to be delineated.

  • Organizational Affiliation

    Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand. Electronic address: emily.parker@canterbury.ac.nz.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
351Neisseria meningitidis MC58Mutation(s): 0 
Gene Names: aroGNMB0307
Find proteins for Q9K169 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9K169 
Go to UniProtKB:  Q9K169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K169
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0V5

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
O [auth D]
(2R)-2-(phosphonooxy)propanoic acid
C3 H7 O6 P
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
P [auth D]
O4 P
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
Binding Affinity Annotations 
IDSourceBinding Affinity
0V5 Binding MOAD:  4UMB Ki: 9.90e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.439α = 90
b = 133.733β = 90
c = 147.237γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Data collection