Biological Assembly 1  

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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: 113097.79 
• Atom Count: 7236 
• Residue Count: 1002 
• Unique protein chains: 1

2WKS

Structure of Helicobacter pylori Type II Dehydroquinase with a new carbasugar-thiophene inhibitor.

• DOI: 10.2210/pdb2WKS/pdb

• Classification: LYASE
• Organism(s): Helicobacter pylori (strain ATCC 700392 / 26695)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2009-06-17 Released: 2009-11-24 
• Deposition Author(s): Otero, J.M., Guardado-Calvo, P., Llamas-Saiz, A.L., Prazeres, V.F.V., Tizon, L., Castedo, L., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.206 

Literature

Synthesis and biological evaluation of new nanomolar competitive inhibitors of Helicobacter pylori type II dehydroquinase. Structural details of the role of the aromatic moieties with essential residues.

Prazeres, V.F., Tizon, L., Otero, J.M., Guardado-Calvo, P., Llamas-Saiz, A.L., van Raaij, M.J., Castedo, L., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C.

(2010) J. Med. Chem. 53: 191-200

• PubMed: 19911771 
• DOI: 10.1021/jm9010466


• PubMed Abstract: 
  

The shikimic acid pathway is essential to many pathogens but absent in mammals. Enzymes in its pathway are therefore appropriate targets for the development of novel antibiotics. Dehydroquinase is the third enzyme of the pathway, catalyzing the reversible dehydratation of 3-dehydroquinic acid to form 3-dehydroshikimic acid. Here we present the synthesis of novel inhibitors with high affinity for Helicobacter pylori type II dehydroquinase and efficient inhibition characteristics. The structure of Helicobacter pylori type II dehydroquinase in complex with the most potent inhibitor shows that the aromatic functional group interacts with the catalytic Tyr22 by pi-stacking, expelling the Arg17 side chain, which is essential for catalysis, from the active site. The structure therefore explains the favorable properties of the inhibitor and will aid in design of improved antibiotics.

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Related Citations: 

• Progress in Type II Dehydroquinase Inhibitors: From Concept to Practice.
  Gonzalez-Bello, C.,Castedo, L.
  (2007) Med.Res.Rev. 27: 177
• Competitive Inhibitors of Helicobacter Pylori Type II Dehydroquinase: Synthesis, Biological Evaluation, and NMR Studies.
  Prazeres, V.F.V.,Sanchez-Sixto, C.,Castedo, L.,Shuh, S.W.,Lamb, H.,Hawkins, A.R.,Canada, F.J.,Jimenez-Barbero, J.,Gonzalez-Bello, C.
  (2008) Chemmedchem 3: 756




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Organizational Affiliation: 

Laboratorio de Quimica Organica (CSIC) y Departamento de Quimica Organica, Facultad de Quimica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CB6	A, B, C, D, E, F	(1R,4S,5R)-1,4,5-trihydroxy-3-[(5-methyl-1-benzothiophen-2-yl)methoxy]cyclohex-2-ene-1-carboxylic acid C17 H18 O6 S BNUWPGVZRDEWEX-ISTRZQFTSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CB6	Ki: 130 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.206 
• Space Group: I 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 157.850	α = 90.00
b = 157.850	β = 90.00
c = 99.780	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-06-17 
• Released Date: 2009-11-24 
• Deposition Author(s): Otero, J.M., Guardado-Calvo, P., Llamas-Saiz, A.L., Prazeres, V.F.V., Tizon, L., Castedo, L., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History 

• Version 1.0: 2009-11-24
  Type: Initial release
• Version 1.1: 2011-06-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-02-14
  Type: Database references