6SFE

CRYSTAL STRUCTURE OF DHQ1 FROM SALMONELLA TYPHI COVALENTLY MODIFIED BY COMPOUND 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1002/chem.202000759
  • Primary Citation of Related Structures:  
    6SFE, 6SFG, 6SFH

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-dehydroquinate dehydratase
A, B
252Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: aroDSTY1760t1231
EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi)
Explore P24670 
Go to UniProtKB:  P24670
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24670
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L9Z (Subject of Investigation/LOI)
Query on L9Z

Download Ideal Coordinates CCD File 
C [auth A],
D [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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.119 
  • R-Value Observed: 0.120 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.144α = 90
b = 44.15β = 95.14
c = 84.634γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description