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1.78 Angstrom Crystal Structure of the Salmonella enterica 3-Dehydroquinate Dehydratase (aroD) in Complex with Quinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of schiff base formation.

Light, S.H.Antanasijevic, A.Krishna, S.N.Caffrey, M.Anderson, W.F.Lavie, A.

(2014) Biochemistry 53: 872-880

  • DOI: 10.1021/bi4015506
  • Primary Citation of Related Structures:  4GUJ, 4IUO

  • PubMed Abstract: 
  • A component of the shikimate biosynthetic pathway, dehydroquinate dehydratase (DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ) to 3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine forms a Schiff base intermediate with DHQ. ...

    A component of the shikimate biosynthetic pathway, dehydroquinate dehydratase (DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ) to 3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine forms a Schiff base intermediate with DHQ. The Schiff base acts as an electron sink to facilitate the catalytic dehydration. To address the mechanism of Schiff base formation, we determined structures of the Salmonella enterica wild-type DHQD in complex with the substrate analogue quinate and the product analogue shikimate. In addition, we determined the structure of the K170M mutant (Lys170 being the Schiff base forming residue) in complex with quinate. Combined with nuclear magnetic resonance and isothermal titration calorimetry data that revealed altered binding of the analogue to the K170M mutant, these structures suggest a model of Schiff base formation characterized by the dynamic interplay of opposing forces acting on either side of the substrate. On the side distant from the substrate 3-carbonyl group, closure of the enzyme's β8-α8 loop is proposed to guide DHQ into the proximity of the Schiff base-forming Lys170. On the 3-carbonyl side of the substrate, Lys170 sterically alters the position of DHQ's reactive ketone, aligning it at an angle conducive for nucleophilic attack. This study of a type I DHQD reveals the interplay between the enzyme and substrate required for the correct orientation of a functional group constrained within a cyclic substrate.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases and Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , Chicago, Illinois 60611, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-dehydroquinate dehydratase
A, B
255Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: aroD
EC: 4.2.1.10
Find proteins for P58687 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P58687
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QIC
Query on QIC

Download SDF File 
Download CCD File 
A, B
(1S,3R,4S,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid
Quinic acid
C7 H12 O6
AAWZDTNXLSGCEK-WYWMIBKRSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QICKd: 230000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.669α = 90.00
b = 74.427β = 100.57
c = 63.135γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description