4CLM

Structure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic acid derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Irreversible covalent modification of type I dehydroquinase with a stable Schiff base.

Tizon, L.Maneiro, M.Peon, A.Otero, J.M.Lence, E.Poza, S.van Raaij, M.J.Thompson, P.Hawkins, A.R.Gonzalez-Bello, C.

(2015) Org Biomol Chem 13: 706-716

  • DOI: 10.1039/c4ob01782j
  • Primary Citation of Related Structures:  
    4CLM

  • PubMed Abstract: 
  • The irreversible inhibition of type I dehydroquinase (DHQ1), the third enzyme of the shikimic acid pathway, is investigated by structural, biochemical and computational studies. Two epoxides, which are mimetics of the natural substrate, were designed ...

    The irreversible inhibition of type I dehydroquinase (DHQ1), the third enzyme of the shikimic acid pathway, is investigated by structural, biochemical and computational studies. Two epoxides, which are mimetics of the natural substrate, were designed as irreversible inhibitors of the DHQ1 enzyme and to study the binding requirements of the linkage to the enzyme. The epoxide with the S configuration caused the covalent modification of the protein whereas no reaction was obtained with its epimer. The first crystal structure of DHQ1 from Salmonella typhi covalently modified by the S epoxide, which is reported at 1.4 Å, revealed that the modified ligand is surprisingly covalently attached to the essential Lys170 by the formation of a stable Schiff base. The experimental and molecular dynamics simulation studies reported here highlight the huge importance of the conformation of the C3 carbon of the ligand for covalent linkage to this type of aldolase I enzyme, revealed the key role played by the essential His143 as a Lewis acid in this process and show the need for a neatly closed active site for catalysis.


    Organizational Affiliation

    Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain. concepcion.gonzalez.bello@usc.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-DEHYDROQUINATE DEHYDRATASEAB252Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: aroDSTY1760t1231
EC: 4.2.1.10
Find proteins for P24670 (Salmonella typhi)
Explore P24670 
Go to UniProtKB:  P24670
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WPL
Query on WPL

Download CCD File 
B
(1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid
C8 H14 O5
NMVUNDOHFYILSF-FJDLHZNMSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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: 1.40 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.59α = 90
b = 44.47β = 95.17
c = 84.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2018-02-07
    Changes: Database references, Structure summary
  • Version 1.4: 2018-08-01
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2018-08-29
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-08-28
    Changes: Data collection, Derived calculations, Structure summary