6SFG

CRYSTAL STRUCTURE OF DHQ1 FROM SALMONELLA TYPHI COVALENTLY MODIFIED BY COMPOUND 9

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

wwPDB Validation 3D Report Full Report



Literature

Self-Immolation of a Bacterial Dehydratase Enzyme by its Epoxide Product.

Lence, E., Maneiro, M., Sanz-Gaitero, M., van Raaij, M.J., Thompson, P., Hawkins, A.R., Gonzalez-Bello, C.

(2020) Chemistry 

  • DOI: 10.1002/chem.202000759
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Disabling the bacterial capacity to cause infection is an innovative approach that has attracted significant attention to fight against superbugs. A relevant target for anti-virulence drug discovery is the type I dehydroquinase (DHQ1) enzyme. It was ...

    Disabling the bacterial capacity to cause infection is an innovative approach that has attracted significant attention to fight against superbugs. A relevant target for anti-virulence drug discovery is the type I dehydroquinase (DHQ1) enzyme. It was shown that the 2-hydroxyethylammonium derivative 3 has in vitro activity since it causes the covalent modification of the catalytic lysine residue of DHQ1. As this compound does not bear reactive electrophilic centers, how the chemical modification occurs is intriguing. We report here an integrated approach, which involves biochemical studies, X-ray crystallography and computational studies on the reaction path using combined quantum mechanics/molecular mechanics Umbrella Sampling Molecular Dynamics, that evidences that DHQ1 catalyzes its self-immolation by transforming the unreactive 2-hydroxyethylammonium group in 3 into an epoxide that triggers the lysine covalent modification. This finding might open opportunities for the design of lysine-targeted irreversible inhibitors bearing a 2-hydroxyethylammonium moiety as an epoxide proform, which to our knowledge has not been reported previously.

    Organizational Affiliation: 

    Universidade de Santiago de Compostela, Organic Chemistry, Jenaro de la Fuente s/n, 15782, Santiago de Compostela, SPAIN.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-dehydroquinate dehydratase
A
252Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: aroD, STY1760, t1231
EC: 4.2.1.10
Find proteins for P24670 (Salmonella typhi)
Go to UniProtKB:  P24670
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSQ
Query on FSQ
Download CCD File 
A
(1~{S},3~{R},4~{S},5~{R})-3-methyl-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic Acid
C8 H14 O5
OFMSIUGUPGSXKY-SKHQTKALSA-N		 Ligand Interaction
FQZ
Query on FQZ
Download CCD File 
A
(1~{R},3~{S},4~{R},5~{R})-3-methyl-4,5-bis(hydroxyl)cyclohexane-1-carboxylic acid
C8 H14 O4
OBDLOCPYNMEWCH-BDVNFPICSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.582α = 90
b = 114.158β = 90
c = 42.478γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainBFU2017-82207-P

Revision History 

  • Version 1.0: 2020-04-15
    Type: Initial release