1L9W

CRYSTAL STRUCTURE OF 3-DEHYDROQUINASE FROM SALMONELLA TYPHI COMPLEXED WITH REACTION PRODUCT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity.

Lee, W.H.Perles, L.A.Nagem, R.A.Shrive, A.K.Hawkins, A.Sawyer, L.Polikarpov, I.

(2002) Acta Crystallogr.,Sect.D 58: 798-804

  • Primary Citation of Related Structures:  1GQN

  • PubMed Abstract: 
  • The type I 3-dehydroquinate dehydratase (DHQase) which catalyses the reversible dehydration of 3-dehydroquinic acid to 3-dehydroshikimic acid is involved in the shikimate pathway for the biosynthesis of aromatic compounds. The shikimate pathway is ab ...

    The type I 3-dehydroquinate dehydratase (DHQase) which catalyses the reversible dehydration of 3-dehydroquinic acid to 3-dehydroshikimic acid is involved in the shikimate pathway for the biosynthesis of aromatic compounds. The shikimate pathway is absent in mammals, which makes structural information about DHQase vital for the rational design of antimicrobial drugs and herbicides. The crystallographic structure of the type I DHQase from Salmonella typhi has now been determined for the native form at 1.78 A resolution (R = 19.9%; R(free) = 24.7%). The structure of the modified enzyme to which the product has been covalently bound has also been determined but in a different crystal form (2.1 A resolution; R = 17.7%; R(free) = 24.5%). An analysis of the three available crystal forms has provided information about the physiological dimer interface. The enzyme relies upon the closure of a lid-like loop to complete its active site. As the lid-loop tends to stay in the closed position, dimerization appears to play a role in biasing the arrangement of the loop towards its open position, thus facilitating substrate access.


    Organizational Affiliation

    Laboratório Nacional de Luz Síncrotron/LNLS, Campinas, SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-dehydroquinate dehydratase aroD
A, B, C, D
252Salmonella typhiGene Names: aroD
EC: 4.2.1.10
Find proteins for P24670 (Salmonella typhi)
Go to UniProtKB:  P24670
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHS
Query on DHS

Download SDF File 
Download CCD File 
A, B, C, D
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: 2.1 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.610α = 90.00
b = 158.560β = 93.61
c = 85.890γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-26
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2012-02-08
    Type: Derived calculations