Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.05 kDa 
• Atom Count: 2371 
• Modelled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 1

6SFG

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

• PDB DOI: 10.2210/pdb6SFG/pdb

• Classification: LYASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-01 Released: 2020-04-15 
• Deposition Author(s): Sanz-Gaitero, M., Lence, E., Maneiro, M., Thompson, R., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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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 

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

• PubMed: 32259333 
• DOI: 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A	252	Salmonella enterica subsp. enterica serovar Typhi	Mutation(s): 0  Gene Names: aroD, STY1760, t1231 EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi) Explore P24670  Go to UniProtKB:  P24670

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FSQ (Subject of Investigation/LOI)	C [auth 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
FQZ (Subject of Investigation/LOI)	B [auth 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

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 = 46.582	α = 90
b = 114.158	β = 90
c = 42.478	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-01 
• Released Date: 2020-04-15 
Deposition Author(s): Sanz-Gaitero, M., Lence, E., Maneiro, M., Thompson, R., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2017-82207-P

Revision History  

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