Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae

Nagakumar Bharatham,Maitrayee Sarma,Vasanthi Ramachandran,Anirudh P Shanbhag,Maho Aoki,Savitha Nagaraj,Riya Narjari,Nainesh Katagihallimath,Eiki Yamashita,Ui Okada,Satoshi Murakami,Teby Thomas,Sreevalli Sharma,Santanu Datta,Sreenath Rajagopal,Purnendu Bhowmik

doi:10.1038/s41467-021-25679-0

Abstract

OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.

Highlights

OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae
Besides being on the bacterial chromosome, it is present on mobile insertion elements like IS26 or plasmids in E. coli and E. cloacae showing its potential to spread to other bacteria[27]
OqxB from K. pneumoniae was purified and its crystal structure was solved at 1.85 Å resolution. (PDB ID: 7CZ9, Supplementary Table S1)

Summary

Introduction

OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. Protein crystal structures play a definitive role in elucidating complex biological mechanisms involving substrate/inhibitor binding They offer atomic insights related to its biological activity, thereby facilitating drug development to manipulate protein function[29]. Recent observations indicate that OqxB seems to play a decisive role in other Gram-negative bacteria like E. coli, Enterobacter cloacae and Salmonella spp. due to its mobilization through horizontal gene transfer[26]. This qualifies it as a prime candidate for a detailed structural-functional analysis and studies its role in efflux

Objectives

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Results

Conclusion