2XB8

Structure of Mycobacterium tuberculosis type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3- dehydroquinic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids.

Peon, A.Otero, J.M.Tizon, L.Prazeres, V.F.V.Llamas-Saiz, A.L.Fox, G.C.van Raaij, M.J.Lamb, H.Hawkins, A.R.Gago, F.Castedo, L.Gonzalez-Bello, C.

(2010) Chemmedchem 5: 1726

  • DOI: 10.1002/cmdc.201000281
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding mode of several substrate analogues, (2R)-2-benzyl-3-dehydroquinic acids 4, which are potent reversible competitive inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by struc ...

    The binding mode of several substrate analogues, (2R)-2-benzyl-3-dehydroquinic acids 4, which are potent reversible competitive inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway, has been investigated by structural and computational studies. The crystal structures of Mycobacterium tuberculosis and Helicobacter pylori DHQ2 in complex with one of the most potent inhibitor, p-methoxybenzyl derivative 4 a, have been solved at 2.40 Å and 2.75 Å, respectively. This has allowed the resolution of the M. tuberculosis DHQ2 loop containing residues 20-25 for the first time. These structures show the key interactions of the aromatic ring in the active site of both enzymes and additionally reveal an important change in the conformation and flexibility of the loop that closes over substrate binding. The loop conformation and the binding mode of compounds 4 b-d has been also studied by molecular dynamics simulations, which suggest that the benzyl group of inhibitors 4 prevent appropriate orientation of the catalytic tyrosine of the loop for proton abstraction and disrupts its basicity.


    Related Citations: 
    • Inducible Overproduction of the Aspergillus Nidulans Pentafunctional Arom Protein and the Type-I and -II 3-Dehydroquinases from Salmonella Typhi and Mycobacterium Tuberculosis.
      Moore, J.D.,Lamb, H.K.,Garbe, T.,Servos, S.,Dougan, G.,Charles, I.G.,Hawkins, A.R.
      (1992) Biochem.J. 287: 173
    • Crystallization of a Type II Dehydroquinase from Mycobacterium Tuberculosis.
      Gourley, D.G.,Coggins, J.R.,Isaacs, N.W.,Moore, J.D.,Charles, I.G.,Hawkins, A.R.
      (1994) J.Mol.Biol. 241: 488


    Organizational Affiliation

    Departamento de Química Orgánica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-DEHYDROQUINATE DEHYDRATASE
A
146Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: aroQ (aroD)
EC: 4.2.1.10
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPX7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XNW
Query on XNW

Download SDF File 
Download CCD File 
A
(1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID
(2R)-2-METHOXYBENZYL-3-DEHYDROQUINIC ACID
C15 H18 O7
KDOXKRDIRCHNDT-YODMDTAWSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
XNWKi: 26 nM BINDINGMOAD
XNWKi: 26 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 126.520α = 90.00
b = 126.520β = 90.00
c = 126.520γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-09-28
    Type: Database references, Refinement description, Version format compliance
  • Version 1.2: 2018-02-07
    Type: Database references