Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.31 kDa 
• Atom Count: 3741 
• Residue Count: 474 
• Unique protein chains: 1

2XB9

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

• DOI: 10.2210/pdb2XB9/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-08 Released: 2010-09-15 
• Deposition Author(s): Otero, J.M., Tizon, L., Llamas-Saiz, A.L., Fox, G.C., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.250 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

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

• PubMed: 20815012 
• DOI: 10.1002/cmdc.201000281
• Primary Citation of Related Structures:  
  2XB8, 2XB9


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A, B, C	167	Helicobacter pylori	Mutation(s): 0  EC: 4.2.1.10
Find proteins for Q48255 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore Q48255  Go to UniProtKB:  Q48255

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XNW	A, B	(1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID C15 H18 O7 KDOXKRDIRCHNDT-YODMDTAWSA-N
CIT	C	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
XNW	Ki :  170   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.250 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.56	α = 90
b = 100.56	β = 90
c = 105.449	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-08 
• Released Date: 2010-09-15 
Deposition Author(s): Otero, J.M., Tizon, L., Llamas-Saiz, A.L., Fox, G.C., Gonzalez-Bello, C., van Raaij, M.J.

Revision History 

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2018-02-07
  Changes: Database references