2XB9

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

Summary for 2XB9

• Entry DOI: 10.2210/pdb2xb9/pdb
• Related: 1J2Y 2C4V 2C4W 2C57 2WKS 2XB8
• Descriptor: 3-DEHYDROQUINATE DEHYDRATASE, (1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID, CITRIC ACID, ... (4 entities in total)
• Functional Keywords: lyase, amino acid biosynthesis
• Biological source: HELICOBACTER PYLORI
• Total number of polymer chains: 3
• Total formula weight: 56310.46

Authors

Otero, J.M.,Tizon, L.,Llamas-Saiz, A.L.,Fox, G.C.,Gonzalez-Bello, C.,van Raaij, M.J. (deposition date: 2010-04-08, release date: 2010-09-15, Last modification date: 2023-12-20)

Primary citation

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.
Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids.
Chemmedchem, 5:1726-, 2010

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.

PubMed: 20815012
DOI: 10.1002/CMDC.201000281

Experimental method

X-RAY DIFFRACTION (2.75 Å)