4UIO

Structure of the Salmonella typhi Type I Dehydroquinase covalently inhibited by a 3-dehydroquinic acid derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report



Literature

Chemical Modification of a Dehydratase Enzyme Involved in Bacterial Virulence by an Ammonium Derivative: Evidence of its Active Site Covalent Adduct.

Gonzalez-Bello, C.Tizon, L.Lence, E.Otero, J.M.van Raaij, M.J.Martinez-Guitian, M.Beceiro, A.Thompson, P.Hawkins, A.R.

(2015) J Am Chem Soc 137: 9333-9343

  • DOI: 10.1021/jacs.5b04080
  • Primary Citation of Related Structures:  
    4UIO

  • PubMed Abstract: 
  • The first example of an ammonium derivative that causes a specific modification of the active site of type I dehydroquinase (DHQ1), a dehydratase enzyme that is a promising target for antivirulence drug discovery, is described. The resolution at 1.35 ...

    The first example of an ammonium derivative that causes a specific modification of the active site of type I dehydroquinase (DHQ1), a dehydratase enzyme that is a promising target for antivirulence drug discovery, is described. The resolution at 1.35 Å of the crystal structure of DHQ1 from Salmonella typhi chemically modified by this ammonium derivative revealed that the ligand is covalently attached to the essential Lys170 through the formation of an amine. The detection by mass spectroscopy of the reaction intermediates, in conjunction with the results of molecular dynamics simulations, allowed us to explain the inhibition mechanism and the experimentally observed differences between S. typhi and Staphylococcus aureus enzymes. The results presented here reveal that the replacement of Phe225 in St-DHQ1 by Tyr214 in Sa-DHQ1 and its hydrogen bonding interaction with the conserved water molecule observed in several crystal structures protects the amino adduct against further dehydration/aromatization reactions. In contrast, for the St-DHQ1 enzyme, the carboxylate group of Asp114, with the assistance of this water molecule, would trigger the formation of a Schiff base that can undergo further dehydration reactions until full aromatization of the cyclohexane ring is achieved. Moreover, in vitro antivirulence studies showed that the reported compound is able to reduce the ability of Salmonella Enteritidis to kill A459 respiratory cells. These studies have identified a good scaffold for the design of irreversible inhibitors that can be used as drugs and has opened up new opportunities for the development of novel antivirulence agents by targeting the DHQ1 enzyme.


    Organizational Affiliation

    ‡Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASEA252Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: aroDSTY1760t1231
EC: 4.2.1.10
Find proteins for P24670 (Salmonella typhi)
Explore P24670 
Go to UniProtKB:  P24670
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VAU
Query on VAU

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A
(1~{R},3~{R},4~{S},5~{R})-3-methyl-1,3,4,5-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid
C8 H14 O6
AQOKFKYCBLFIKH-IXROVEORSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.399α = 90
b = 42.327β = 105.13
c = 84.828γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2017-12-27
    Changes: Database references, Structure summary
  • Version 2.0: 2018-08-29
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary