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Updated: Jun 17, 2025
Essential Metal Uptake in Gram-negative Bacteria: X-ray Fluorescence, Radioisotopes, and Cell Fractionation
Published on: February 1, 2018
Crystal structure of pectocin M1 reveals diverse conformations and interactions during its initial step via the
Nawee Jantarit1,2, Hideaki Tanaka1,2, Yuxi Lin3
1Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan.
Abstract:
Pectocin M1 (PM1), the bacteriocin from phytopathogenic Pectobacterium carotovorum which causes soft rot disease, has a unique ferredoxin domain that allows it to use FusA of the plant ferredoxin uptake system. To probe the structure-based mechanism of PM1 uptake, we determined the X-ray structure of full-length PM1, containing an N-terminal ferredoxin and C-terminal catalytic domain connected by helical linker, at 2.04 Å resolution. Based on published FusA structure and NMR data for PM1 ferredoxin domain titrated with FusA, we modeled docking of the ferredoxin domain with FusA. Combining the docking models with the X-ray structures of PM1 and FusA enables us to propose the mechanism by which PM1 undergoes dynamic domain rearrangement to translocate across the target cell outer membrane.
Insights
Pectocin M1 (PM1), a bacteriocin, uses a unique ferredoxin domain to enter plant cells. This study reveals its structure and proposes a mechanism for translocation across the outer membrane.
Area of Science:
- Microbiology
- Structural Biology
- Biochemistry
Background:
- Pectobacterium carotovorum causes soft rot disease in plants.
- Pectocin M1 (PM1) is a bacteriocin produced by P. carotovorum.
- PM1 possesses a unique ferredoxin domain for interaction with plant ferredoxin uptake systems.
Purpose of the Study:
- To elucidate the structure-based mechanism of PM1 uptake into plant cells.
- To determine the X-ray structure of full-length PM1.
Main Methods:
- X-ray crystallography of full-length PM1 at 2.04 Å resolution.
- Integration of published FusA structure data.
- Nuclear Magnetic Resonance (NMR) data analysis of PM1 ferredoxin domain interaction with FusA.
- Molecular docking modeling.
Main Results:
- The X-ray structure of full-length PM1, comprising N-terminal ferredoxin and C-terminal catalytic domains linked by a helix, was determined.
- Docking models of the PM1 ferredoxin domain with FusA were generated.
- A mechanism for PM1 translocation involving dynamic domain rearrangement was proposed.
Conclusions:
- PM1 utilizes its ferredoxin domain to engage with the plant ferredoxin uptake system (FusA).
- Structural and modeling data provide insights into PM1's mechanism of outer membrane translocation.
- Understanding PM1 uptake may inform strategies against Pectobacterium-mediated plant diseases.
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