PDBsum entry: 2c57

Lyase

PDB id: 2c57

Contents

Protein chains

164 a.a. *

(+ 2 more) 153 a.a. *

Ligands

FA1 ×12

* Residue conservation analysis

PDB id:

2c57

Name:

Lyase

Title:

H.Pylori type ii dehydroquinase in complex with fa1

Structure:

3-dehydroquinate dehydratase. Chain: a, b, c, d, e, f, g, h, i, j, k, l. Synonym: 3-dehydroquinase, type ii dhqase. Engineered: yes

Source:

Helicobacter pylori. Organism_taxid: 210. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: plyss.

Biol. unit:

Dodecamer (from PDB file)

Resolution:

3.10Å R-factor: 0.210 R-free: 0.237

Authors:

D.A.Robinson,A.J.Lapthorn

Key ref:

D.A.Robinson et al. (2006). Crystal structures of Helicobacter pylori type II dehydroquinase inhibitor complexes: new directions for inhibitor design. J Med Chem, 49, 1282-1290. PubMed id: 16480265 DOI: 10.1021/jm0505361

Date:

26-Oct-05 Release date: 22-Feb-06

Protein chains

Q48255  (AROQ_HELPY) -  3-dehydroquinate dehydratase

Seq: 167 a.a.

Struc: 164 a.a.

Protein chains

Q48255  (AROQ_HELPY) -  3-dehydroquinate dehydratase

Seq: 167 a.a.

Struc: 153 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.2.1.10 - 3-dehydroquinate dehydratase.
• Pathway: Shikimate and Chorismate Biosynthesis
• Reaction: 3-dehydroquinate = 3-dehydroshikimate + H₂O

3-dehydroquinate (Bound ligand (Het Group name = FA1) matches with 92.31% similarity) = 3-dehydroshikimate + H(2)O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: cellular amino acid biosynthetic process (2 terms)
• Biochemical function: lyase activity (2 terms)

Added reference

DOI no: 10.1021/jm0505361

J Med Chem 49:1282-1290 (2006)

PubMed id: 16480265

Crystal structures of Helicobacter pylori type II dehydroquinase inhibitor complexes: new directions for inhibitor design.

D.A.Robinson, K.A.Stewart, N.C.Price, P.A.Chalk, J.R.Coggins, A.J.Lapthorn.

ABSTRACT

The crystal structures of the type II dehydroquinase (DHQase) from Helicobacter pylori in complex with three competitive inhibitors have been determined. The inhibitors are the substrate analogue 2,3-anhydroquinate (FA1), citrate, and an oxoxanthene sulfonamide derivative (AH9095). Despite the very different chemical nature of the inhibitors, in each case the primary point of interaction with the enzyme is via the residues that bind the C1 functionalities of the substrate, 3-dehydroquinate, i.e., N76, H102, I103, and H104. The DHQase/AH9095 complex crystal structure shows that sulfonamides can form a scaffold for nonsubstrate-like inhibitors and identifies a large conserved hydrophobic patch at the entrance to the active site as a locus that can be exploited in the development of new ligands.