3O1N

1.03 Angstrom Crystal Structure of Q236A Mutant Type I Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-dehydroquinate dehydratase
A, B
276Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
Gene Names: aroDSTM1358
EC: 4.2.1.10
UniProt
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 1
  • Diffraction Data: https://doi.org/10.18430/M33O1N
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.433α = 104.23
b = 46.476β = 97.5
c = 55.79γ = 98.7
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-11
    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