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: 16.24 kDa 
• Atom Count: 1193 
• Residue Count: 142 
• Unique protein chains: 1

4B6P

Structure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2S)-2-Perfluorobenzyl-3-dehydroquinic acid

• DOI: 10.2210/pdb4B6P/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2012-08-14 Released: 2012-12-19 
• Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Lence, E., Tizon, L., Peon, A., Prazeres, V.F.V., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.223 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 

Literature

Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids.

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

(2013) ACS Chem Biol 8: 568-577

• PubMed: 23198883 
• DOI: 10.1021/cb300493s
• Primary Citation of Related Structures:  
  4B6P, 4B6Q, 4B6R, 4B6S, 4B6O


• PubMed Abstract: 
  

The structural changes caused by the substitution of the aromatic moiety in (2S)-2-benzyl-3-dehydroquinic acids and its epimers in C2 by electron-withdrawing or electron-donating groups in type II dehydroquinase enzyme from M. tuberculosis and H. pylori has been investigated by structural and computational studies. Both compounds are reversible competitive inhibitors of this enzyme, which is essential in these pathogenic bacteria. The crystal structures of M. tuberculosis and H. pylori in complex with (2S)-2-(4-methoxy)benzyl- and (2S)-2-perfluorobenzyl-3-dehydroquinic acids have been solved at 2.0, 2.3, 2.0, and 1.9 Å, respectively. The crystal structure of M. tuberculosis in complex with (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid is also reported at 1.55 Å. These crystal structures reveal key differences in the conformation of the flexible loop of the two enzymes, a difference that depends on the presence of electron-withdrawing or electron-donating groups in the aromatic moiety of the inhibitors. This loop closes over the active site after substrate binding, and its flexibility is essential for the function of the enzyme. These differences have also been investigated by molecular dynamics simulations in an effort to understand the significant inhibition potency differences observed between some of these compounds and also to obtain more information about the possible movements of the loop. These computational studies have also allowed us to identify key structural factors of the H. pylori loop that could explain its reduced flexibility in comparison to the M. tuberculosis loop, specifically by the formation of a key salt bridge between the side chains of residues Asp18 and Arg20.

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Organizational Affiliation: 

Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Edificio CACTUS, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEHYDROQUINATE DEHYDRATASE	A	146	Mycobacterium tuberculosis	Mutation(s): 0  EC: 4.2.1.10
Find proteins for P9WPX7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPX7  Go to UniProtKB:  P9WPX7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2HN	A	(1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid C14 H11 F5 O6 ZNZHQTVBMHBUCF-GLOYCNQYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
2HN	Ki:  74   nM  Binding MOAD
2HN	Ki :  74   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.223 
• R-Value Work: 0.169 
• R-Value Observed: 0.172 
• Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.27	α = 90
b = 126.27	β = 90
c = 126.27	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-14 
• Released Date: 2012-12-19 
Deposition Author(s): Otero, J.M., Llamas-Saiz, A.L., Lence, E., Tizon, L., Peon, A., Prazeres, V.F.V., Lamb, H., Hawkins, A.R., Gonzalez-Bello, C., van Raaij, M.J.

Revision History 

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-03-20
  Changes: Other
• Version 1.2: 2013-03-27
  Changes: Database references
• Version 1.3: 2013-08-07
  Changes: Non-polymer description
• Version 1.4: 2018-01-17
  Changes: Database references