4UMA

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.bioorg.2014.08.003
  • Primary Citation of Related Structures:  

  • 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 bet ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
A, B, C, D
351Neisseria meningitidis serogroup B (strain MC58)Mutation(s): 0 
Gene Names: aroG
EC: 2.5.1.54
Find proteins for Q9K169 (Neisseria meningitidis serogroup B (strain MC58))
Go to UniProtKB:  Q9K169
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GZ3
Query on GZ3

Download SDF File 
Download CCD File 
A, B, C, D
(E)-2-METHYL-3-PHOSPHONOACRYLATE
C4 H7 O5 P
XGDAHZFVQMTYCT-NSCUHMNNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GZ3Ki: 3900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.495α = 90.00
b = 136.501β = 96.41
c = 76.157γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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