1QFE

THE STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE FROM SALMONELLA TYPHI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction.

Gourley, D.G., Shrive, A.K., Polikarpov, I., Krell, T., Coggins, J.R., Hawkins, A.R., Isaacs, N.W., Sawyer, L.

(1999) Nat Struct Biol 6: 521-525

  • DOI: 10.1038/9287
  • Primary Citation of Related Structures:  
    1QFE, 2DHQ

  • PubMed Abstract: 

    • The structures of enzymes catalyzing the reactions in central metabolic pathways are generally well conserved as are their catalytic mechanisms. The two types of 3-dehydroquinate dehydratase (DHQase) are therefore most unusual since they are unrelated at the sequence level and they utilize completely different mechanisms to catalyze the same overall reaction ...

    The structures of enzymes catalyzing the reactions in central metabolic pathways are generally well conserved as are their catalytic mechanisms. The two types of 3-dehydroquinate dehydratase (DHQase) are therefore most unusual since they are unrelated at the sequence level and they utilize completely different mechanisms to catalyze the same overall reaction. The type I enzymes catalyze a cis-dehydration of 3-dehydroquinate via a covalent imine intermediate, while the type II enzymes catalyze a trans-dehydration via an enolate intermediate. Here we report the three-dimensional structures of a representative member of each type of biosynthetic DHQase. Both enzymes function as part of the shikimate pathway, which is essential in microorganisms and plants for the biosynthesis of aromatic compounds including folate, ubiquinone and the aromatic amino acids. An explanation for the presence of two different enzymes catalyzing the same reaction is presented. The absence of the shikimate pathway in animals makes it an attractive target for antimicrobial agents. The availability of these two structures opens the way for the design of highly specific enzyme inhibitors with potential importance as selective therapeutic agents.

    Related Citations: 
    • Crystallisation of the Type I 3-Dehydroquinase from Salmonella Typhi
      Boys, C.W.G., Bury, S.M., Sawyer, L., Moore, J.D., Charles, I.G., Hawkins, A.R., Deka, R., Kleanthous, C., Coggins, J.R.
      (1992) J Mol Biol 227: 352
    Organizational Affiliation: 

    Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Scotland, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)A, B252Salmonella enterica subsp. enterica serovar TyphiMutation(s): 0 
Gene Names: aroD, STY1760, t1231
EC: 4.2.1.10
UniProt
Find proteins for P24670 (Salmonella typhi)
Explore P24670 
Go to UniProtKB:  P24670
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24670
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHS
Query on DHS
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE
C7 H10 N O4
WPZSUTUAATWRPU-KVQBGUIXSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.49α = 90
b = 45.39β = 95.48
c = 85.47γ = 90
Software Package:
Software NamePurpose
VECREFmodel building
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
VECREFphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-05
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance