3B7J image
Entry Detail
PDB ID:
3B7J
Keywords:
Title:
Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with juglone
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2007-10-31
Release Date:
2008-09-02
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.22
R-Value Work:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:(3R)-hydroxymyristoyl-acyl carrier protein dehydratase
Chain IDs:A, B, C, D, E, F
Chain Length:159
Number of Molecules:6
Biological Source:Helicobacter pylori
Primary Citation
Natural product juglone targets three key enzymes from Helicobacter pylori: inhibition assay with crystal structure characterization
ACTA PHARMACOL.SIN. 29 870 876 (2008)
PMID: 18565285 DOI: 10.1111/j.1745-7254.2008.00808.x

Abstact

AIM To investigate the inhibition features of the natural product juglone (5- hydroxy-1,4-naphthoquinone) against the three key enzymes from Helicobacter pylori (cystathionine gamma-synthase [HpCGS], malonyl-CoA:acyl carrier protein transacylase [HpFabD], and beta-hydroxyacyl-ACP dehydratase [HpFabZ]). METHODS An enzyme inhibition assay against HpCGS was carried out by using a continuous coupled spectrophotometric assay approach. The inhibition assay of HpFabD was performed based on the alpha-ketoglutarate dehydrogenase-coupled system, while the inhibition assay for HpFabZ was monitored by detecting the decrease in absorbance at 260 nm with crotonoyl-CoA conversion to beta -hydroxybutyryl-CoA. The juglone/FabZ complex crystal was obtained by soaking juglone into the HpFabZ crystal, and the X-ray crystal structure of the complex was analyzed by molecular replacement approach. RESULTS Juglone was shown to potently inhibit HpCGS, HpFabD, and HpFabZ with the half maximal inhibitory concentration IC50 values of 7.0 +/-0.7, 20 +/-1, and 30 +/-4 micromol/L, respectively. An inhibition-type study indicated that juglone was a non-competitive inhibitor of HpCGS against O-succinyl- L-homoserine (Ki=alphaKi=24 micromol/L), an uncompetitive inhibitor of HpFabD against malonyl-CoA (alphaKi=7.4 micromol/L), and a competitive inhibitor of HpFabZ against crotonoyl-CoA (Ki=6.8 micromol/L). Moreover, the crystal structure of the HpFabZ/juglone complex further revealed the essential binding pattern of juglone against HpFabZ at the atomic level. CONCLUSION HpCGS, HpFabD, and HpFabZ are potential targets of juglone.

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