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


This is version 1.1 of the entry. See complete history


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 26: 8035-8044

  • DOI: 10.1002/chem.202000759
  • Primary Citation of Related Structures:  
    6SFE, 6SFH, 6SFG

  • 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 shown that the 2-hydroxyethylammonium derivative 3 has in vitro activity since it causes the covalent modification of the catalytic lysine residue of DHQ1 ...

    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

    Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago, de Compostela, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-dehydroquinate dehydrataseA, B238Staphylococcus aureusMutation(s): 0 
Gene Names: aroDSAB0760
EC: 4.2.1.10
Find proteins for Q2YWJ9 (Staphylococcus aureus (strain bovine RF122 / ET3-1))
Explore Q2YWJ9 
Go to UniProtKB:  Q2YWJ9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9Z
Query on L9Z

Download Ideal Coordinates CCD File 
C [auth A], F [auth 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 Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LI
Query on LI

Download Ideal Coordinates CCD File 
E [auth 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  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references