Structural insights into Escherichia coli polymyxin B resistance protein D with X-ray crystallography and small-angle X-ray scattering

Hang-Hyun Jo ,Changill Ban,Jinseong Jeon ,Eui Young Jeong

doi:10.1186/preaccept-1347178600140830

Hang-Hyun Jo , Changill Ban

Open Access

https://doi.org/10.1186/preaccept-1347178600140830

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Abstract

BackgroundPolymyxin B resistance protein D (PmrD) plays a key role in the polymyxin B-resistance pathway, as it is the signaling protein that can act as a specific connecter between PmrA/PmrB and PhoP/PhoQ. We conducted structural analysis to characterize Escherichia coli (E. coli) PmrD, which exhibits different features compared with PmrD in other bacteria.ResultsThe X-ray crystal structure of E. coli PmrD was determined at a 2.00 Å resolution, revealing novel information such as the unambiguous secondary structures of the protein and the presence of a disulfide bond. Furthermore, various assays such as native gel electrophoresis, surface plasmon resonance (SPR), size-exclusion chromatography, dynamic light scattering (DLS), and small-angle X-ray scattering (SAXS) measurements, were performed to elucidate the structural and functional role of the internal disulfide bond in E. coli PmrD.ConclusionsThe structural characteristics of E. coli PmrD were clearly identified via diverse techniques. The findings help explain the different protective mechanism of E. coli compared to other Gram-negative bacteria.

Highlights

Polymyxin B resistance protein D (PmrD) plays a key role in the polymyxin B-resistance pathway, as it is the signaling protein that can act as a specific connecter between PmrA/PmrB and PhoP/PhoQ
The findings reveal the crystal structure of E. coli PmrD in high resolution, and the structural traits are described in detail
The crystal structure of E. coli PmrD was initially solved using the molecular-replacement method with the starting model, the NMR structure of E. coli PmrD [Protein Data Bank (PDB): 2JSO]

Summary

Introduction

Polymyxin B resistance protein D (PmrD) plays a key role in the polymyxin B-resistance pathway, as it is the signaling protein that can act as a specific connecter between PmrA/PmrB and PhoP/PhoQ. Polymyxin B, isolated from the bacterium Paenibacillus polymyxa, is one of the most potent antibiotics It binds to lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria [1]. Because Gram-negative bacteria display the negatively charged LPS on the surface of the outer membrane, the cationic polymyxin B can interact with phospholipids to make the membrane permeable, resulting in the acceleration of water uptake, membrane disruption, and endotoxin release. It acts as a detergent against most Gram-negative bacteria, with the exception of the Proteus group [2,3,4]. The study of E. coli PmrD has been considered a decisive factor for determining discrepancies among several species [9,10,11,12]

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