4CNO

Structure of the Salmonella typhi Type I dehydroquinase inhibited by a 3-dehydroquinic acid derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into substrate binding and catalysis in bacterial type I dehydroquinase.

Maneiro, M.Peon, A.Lence, E.Otero, J.M.Van Raaij, M.J.Thompson, P.Hawkins, A.R.Gonzalez-Bello, C.

(2014) Biochem. J. 462: 415-424

  • DOI: 10.1042/BJ20140614

  • PubMed Abstract: 
  • Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonell ...

    Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonella typhi in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, was solved at 1.5 Å. The present study reveals a previously unknown key role for conserved Glu46, Phe145 and Met205 and Gln236, Pro234 and Ala233 residues, with the latter three being located in the flexible substrate-covering loop. Gln236 was shown to be responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 was found to be key in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis. The present study could be useful in the rational design of inhibitors of this challenging and recognized target for the development of novel herbicides and antimicrobial agents.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEHYDROQUINATE DEHYDRATASE
A, B, C, D
252Salmonella typhiMutation(s): 0 
Gene Names: aroD
EC: 4.2.1.10
Find proteins for P24670 (Salmonella typhi)
Go to UniProtKB:  P24670
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9PY
Query on 9PY

Download SDF File 
Download CCD File 
A, B, C, D
(2R)-2-METHYL-3-DEHYDROQUINIC ACID
C8 H12 O6
YHBCRPWBCJOXAZ-MIZGGHSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 78.670α = 90.00
b = 39.406β = 104.68
c = 155.130γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
SCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2018-02-07
    Type: Database references