Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae

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

doi:10.1038/s41467-021-25679-0

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae

Nat Commun. 2021 Sep 13;12(1):5400. doi: 10.1038/s41467-021-25679-0.

Authors

Nagakumar Bharatham^{1

2}, Purnendu Bhowmik^{1

2}, Maho Aoki³, Ui Okada³, Sreevalli Sharma^{1

2}, Eiki Yamashita⁴, Anirudh P Shanbhag¹, Sreenath Rajagopal¹, Teby Thomas⁵, Maitrayee Sarma¹, Riya Narjari¹, Savitha Nagaraj⁶, Vasanthi Ramachandran^{1

2}, Nainesh Katagihallimath^{1

2}, Santanu Datta¹, Satoshi Murakami⁷

Affiliations

¹ Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka, India.
² The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka, India.
³ Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
⁴ Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
⁵ St. John's Research Institute, Bengaluru, Karnataka, India.
⁶ St. John's Medical Hospital, Bengaluru, Karnataka, India.
⁷ Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan. [email protected].

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Anti-Bacterial Agents / pharmacology*
Bacterial Proteins / chemistry
Bacterial Proteins / genetics*
Bacterial Proteins / metabolism
Binding Sites / genetics
Crystallography, X-Ray
Drug Resistance, Multiple, Bacterial / genetics*
Klebsiella pneumoniae / genetics*
Klebsiella pneumoniae / metabolism
Membrane Transport Proteins / chemistry
Membrane Transport Proteins / genetics*
Membrane Transport Proteins / metabolism
Microbial Sensitivity Tests
Molecular Docking Simulation
Molecular Dynamics Simulation
Protein Binding
Protein Conformation
Protein Multimerization
Structure-Activity Relationship

Substances

Anti-Bacterial Agents
Bacterial Proteins
Membrane Transport Proteins

Associated data

figshare/10.6084/m9.figshare.15089934.v1
figshare/10.6084/m9.figshare.15090153.v1
figshare/10.6084/m9.figshare.15090162.v1
figshare/10.6084/m9.figshare.15090189.v1
figshare/10.6084/m9.figshare.15090249.v1
figshare/10.6084/m9.figshare.15090210.v1

Grants and funding

R01 AI136803/AI/NIAID NIH HHS/United States