2GLL

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori

DOI: 10.2210/pdb2GLL/pdb

Classification: LYASE
Organism(s): Helicobacter pylori SS1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-04-05 Released: 2007-03-13
Deposition Author(s): Zhang, L., Liu, W., Shen, X., Jiang, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.255
R-Value Work: 0.214

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for catalytic and inhibitory mechanisms of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ).

Zhang, L., Liu, W., Hu, T., Du, L., Luo, C., Chen, K., Shen, X., Jiang, H.

(2008) J Biol Chem 283: 5370-5379

PubMed: 18093984 Search on PubMed
DOI: 10.1074/jbc.M705566200
Primary Citation of Related Structures:
2GLM, 2GLL, 2GLV, 2GLP

PubMed Abstract:

beta-Hydroxyacyl-acyl carrier protein dehydratase (FabZ) is an important enzyme for the elongation cycles of both saturated and unsaturated fatty acids biosyntheses in the type II fatty acid biosynthesis system (FAS II) pathway. FabZ has been an essential target for the discovery of compounds effective against pathogenic microbes. In this work, to characterize the catalytic and inhibitory mechanisms of FabZ, the crystal structures of the FabZ of Helicobacter pylori (HpFabZ) and its complexes with two newly discovered inhibitors have been solved. Different from the structures of other bacterial FabZs, HpFabZ contains an extra short two-turn alpha-helix (alpha4) between alpha3 and beta3, which plays an important role in shaping the substrate-binding tunnel. Residue Tyr-100 at the entrance of the tunnel adopts either an open or closed conformation in the crystal structure. The crystal structural characterization, the binding affinity determination, and the enzymatic activity assay of the HpFabZ mutant (Y100A) confirm the importance of Tyr-100 in catalytic activity and substrate binding. Residue Phe-83 at the exit tunnel was also refined in two alternative conformations, leading the tunnel to form an L-shape and U-shape. All these data thus contributed much to understanding the catalytic mechanism of HpFabZ. In addition, the co-crystal structures of HpFabZ with its inhibitors have suggested that the enzymatic activity of HpFabZ could be inhibited either by occupying the entrance of the tunnel or plugging the tunnel to prevent the substrate from accessing the active site. Our study has provided some insights into the catalytic and inhibitory mechanisms of FabZ, thus facilitating antibacterial agent development.

Organizational Affiliation:

Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201203, China. hljiang@mail.shcnc.ac.cn

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase	A, B, C, D, E, F	171	Helicobacter pylori SS1	Mutation(s): 0 Gene Names: fabZ EC: 4.2.1 (PDB Primary Data), 4.2.1.59 (UniProt)
Find proteins for O25928 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25928 Go to UniProtKB: O25928
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain H [A] SDF format, chain J [B] SDF format, chain K [B] SDF format, chain M [C] SDF format, chain N [C] SDF format, chain Q [E] SDF format, chain R [E] SDF format, chain T [F] MOL2 format, chain H [A] MOL2 format, chain J [B] MOL2 format, chain K [B] MOL2 format, chain M [C] MOL2 format, chain N [C] MOL2 format, chain Q [E] MOL2 format, chain R [E] MOL2 format, chain T [F]	A, B, C, E, F	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain I [B] SDF format, chain L [C] SDF format, chain O [D] SDF format, chain P [E] SDF format, chain S [F] MOL2 format, chain G [A] MOL2 format, chain I [B] MOL2 format, chain L [C] MOL2 format, chain O [D] MOL2 format, chain P [E] MOL2 format, chain S [F]	A, B, C, D, E, F	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction