8J4H image
Deposition Date 2023-04-20
Release Date 2024-01-10
Last Version Date 2024-02-07
Entry Detail
PDB ID:
8J4H
Title:
X-ray structure of a ferric ion-binding protein A (FbpA) from Vibrio metschnikovii in complex with Danshensu (DSS)
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.01 Å
R-Value Free:
0.20
R-Value Work:
0.15
R-Value Observed:
0.16
Space Group:
P 63 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Ferric iron ABC transporter iron-binding protein
Chain IDs:A
Chain Length:309
Number of Molecules:1
Biological Source:Vibrio metschnikovii
Ligand Molecules
Primary Citation
Molecular mechanism of Fe 3+ binding inhibition to Vibrio metschnikovii ferric ion-binding protein, FbpA, by rosmarinic acid and its hydrolysate, danshensu.
Protein Sci. 33 e4881 e4881 (2024)
PMID: 38143427 DOI: 10.1002/pro.4881

Abstact

Global warming has increased the growth of pathogenic Vibrio bacteria, which can cause foodborne illnesses and death. Vibrio bacteria require iron for growth and survival. They utilize a ferric ion-binding protein (FbpA) to bind and transport Fe3+ into the cell. FbpA from Vibrio metschnikovii (Vm) is a potential target for inhibiting its growth. Rosmarinic acid (RA) can block the binding of VmFbpA to Fe3+ ; however, the molecular mechanism of Fe3+ binding and RA inhibition to VmFbpA is unclear. In this study, we used x-ray crystallography to determine the Fe3+ -binding mode of VmFbpA and the mechanism of RA inhibition. The structures revealed that in the Fe3+ bound form, Fe3+ was coordinated to VmFbpA by two Tyr residues, two HCO3 - ions, and two water molecules in a six-coordinated geometry. In contrast, in the inhibitor bound form, RA was initially bound to VmFbpA following gel filtration purification, but it was hydrolyzed to danshensu (DSS), which occupied the binding site as shown in an electron density map and reverse phase chromatography (RPC) analysis. Both RA and DSS exhibited a stronger binding affinity to VmFbpA, higher Fe3+ reduction capacity, and more potent bacteriostatic effect on V. metschnikovii compared with caffeic acid (CA), another hydrolysis product of RA. These results provide insight into the mechanism of iron acquisition by V. metschnikovii and inhibition by RA and DSS. Our findings offer clues on the development of effective strategies to prevent Vibrio infections.

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Primary Citation of related structures