Crystal Structure of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium with close loop conformation.

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

Starting Model: experimental
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A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate binding.

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

(2011) Biochemistry 50: 2357-2363

  • DOI: https://doi.org/10.1021/bi102020s
  • Primary Citation of Related Structures:  
    3L2I, 3O1N, 3OEX

  • PubMed Abstract: 

    Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. We present three crystal structures of the Salmonella enterica type I DHQD that address the functionality of a surface loop that is observed to close over the active site following substrate binding. Two wild-type structures with differing loop conformations and kinetic and structural studies of a mutant provide evidence of both direct and indirect mechanisms of involvement of the loop in substrate binding. In addition to allowing amino acid side chains to establish a direct interaction with the substrate, closure of the loop necessitates a conformational change of a key active site arginine, which in turn positions the substrate productively. The absence of DHQD in humans and its essentiality in many pathogenic bacteria make the enzyme a target for the development of nontoxic antimicrobials. The structures and ligand binding insights presented here may inform the design of novel type I DHQD inhibiting molecules.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-dehydroquinate dehydratase
A, B, C, D
255Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: aroDSTM1358
Find proteins for P58687 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P58687 
Go to UniProtKB:  P58687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58687
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.147α = 90
b = 75.757β = 102.65
c = 94.263γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description