6SFH

CRYSTAL STRUCTURE OF DHQ1 FROM Staphylococcus aureus COVALENTLY MODIFIED BY LIGAND 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

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, B
238Staphylococcus aureusMutation(s): 0 
Gene Names: aroDSAB0760
EC: 4.2.1.10
Find proteins for Q2YWJ9 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Go to UniProtKB:  Q2YWJ9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9Z
Query on L9Z

Download CCD File 
A, B
(1~{S},3~{S},4~{S},5~{R})-3-(aminomethyl)-3,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid
C8 H15 N O5
YNLZKDMNCIPLRS-GCJQMDKQSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LI
Query on LI

Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.934α = 90
b = 36.148β = 99.95
c = 85.599γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



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