3JS3

Crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent reaction intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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This is version 1.2 of the entry. See complete history


Literature

Insights into the mechanism of type I dehydroquinate dehydratases from structures of reaction intermediates.

Light, S.H.Minasov, G.Shuvalova, L.Duban, M.E.Caffrey, M.Anderson, W.F.Lavie, A.

(2011) J Biol Chem 286: 3531-3539

  • DOI: 10.1074/jbc.M110.192831
  • Primary Citation of Related Structures:  
    3JS3, 3M7W, 3NNT

  • PubMed Abstract: 
  • The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3-dehydroquinate to 3-dehydroshikimate ...

    The biosynthetic shikimate pathway consists of seven enzymes that catalyze sequential reactions to generate chorismate, a critical branch point in the synthesis of the aromatic amino acids. The third enzyme in the pathway, dehydroquinate dehydratase (DHQD), catalyzes the dehydration of 3-dehydroquinate to 3-dehydroshikimate. We present three crystal structures of the type I DHQD from the intestinal pathogens Clostridium difficile and Salmonella enterica. Structures of the enzyme with substrate and covalent pre- and post-dehydration reaction intermediates provide snapshots of successive steps along the type I DHQD-catalyzed reaction coordinate. These structures reveal that the position of the substrate within the active site does not appreciably change upon Schiff base formation. The intermediate state structures reveal a reaction state-dependent behavior of His-143 in which the residue adopts a conformation proximal to the site of catalytic dehydration only when the leaving group is present. We speculate that His-143 is likely to assume differing catalytic roles in each of its observed conformations. One conformation of His-143 positions the residue for the formation/hydrolysis of the covalent Schiff base intermediates, whereas the other conformation positions the residue for a role in the catalytic dehydration event. The fact that the shikimate pathway is absent from humans makes the enzymes of the pathway potential targets for the development of non-toxic antimicrobials. The structures and mechanistic insight presented here may inform the design of type I DHQD enzyme inhibitors.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-dehydroquinate dehydrataseA, B, C, D258Clostridioides difficile 630Mutation(s): 0 
Gene Names: aroDCD2217CD630_22170
EC: 4.2.1.10
UniProt
Find proteins for Q186A6 (Clostridioides difficile (strain 630))
Explore Q186A6 
Go to UniProtKB:  Q186A6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHS (Subject of Investigation/LOI)
Query on DHS

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE
C7 H10 N O4
WPZSUTUAATWRPU-KVQBGUIXSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.472α = 90
b = 139.619β = 90.63
c = 66.774γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description