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 -helix (4) between 3 and 3, 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.