2GLM

Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with Compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 

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

  • DOI: 10.1074/jbc.M705566200
  • Primary Citation of Related Structures:  

  • 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 esse ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
A, B, C, D, E, F
171Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: fabZ
EC: 4.2.1.59
Find proteins for O25928 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25928
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCB
Query on SCB

Download SDF File 
Download CCD File 
A
2-CHLORO-5-(5-{(E)-[(2Z)-3-(2-METHOXYETHYL)-4-OXO-2-(PHENYLIMINO)-1,3-THIAZOLIDIN-5-YLIDENE]METHYL}-2-FURYL)BENZOIC ACID
C24 H19 Cl N2 O5 S
BLYOIVXXTIAFFL-QPVYCHHJSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BEN
Query on BEN

Download SDF File 
Download CCD File 
A, B, C, D, E
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SCBKi: 4300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.052α = 90.00
b = 100.534β = 90.00
c = 186.142γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CrystalCleardata reduction
CNSrefinement
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2007-12-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance