Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb9kbe/pdb

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb8z1u/pdb

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb8zxs/pdb

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Language：English   Publisher：Cold Spring Harbor Laboratory  

Summary

Antibiotic efflux plays a key role for the multidrug resistance in Gram-negative bacteria^1–3. Multidrug efflux pumps of the resistance nodulation and cell division (RND) superfamily function as part of cell envelope spanning systems and provide resistance to diverse antibiotics 4,5. Here, we identify two phylogenetic clusters of RND proteins with conserved binding pocket residues. Based on the characterisation of one representative of each cluster,K. pneumoniaeOqxB andE. coliAcrB, we show that the transfer of a single conserved residue between both clusters alters the resistance against a panel of structurally unrelated drugs. The substitution is not only associated with changes in the binding pocket architecture, but also alters the equilibrium between the conformational states of the transport cycle. We show that AcrB and OqxB adopt fundamentally different apo states that suggest different mechanisms of initial substrate binding and might determine the differences between the substrate preferences of both pumps. The observed conformational heterogeneity between different RND clusters is suggested to be phylogenetically conserved and might play a role for the diversification of the resistance phenotype between homologous RND multidrug efflux pumps.

DOI： 10.1101/2024.11.22.624703

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.2142/biophys.64.185

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

Abstract

The envelope of Escherichia coli contains approximately 100 different species of lipoproteins, most of which are localized to the inner leaflet of the outer membrane. The Lol (localization of lipoprotein) system, consisting of five Lol proteins, is responsible for the trafficking of lipoproteins to the outer membrane. LolCDE binds to lipoproteins destined for the outer membrane and transfers them to the periplasmic chaperone LolA. Although the cryo-EM structures of Escherichia coli LolCDE have been reported, the mechanisms by which outer membrane lipoproteins are transferred to LolA remain elusive. In this study, we investigated the interaction between LolCDE and lipoproteins using site-specific photo-crosslinking. We introduced a photo-crosslinkable amino acid into different locations across the four helices which form the central lipoprotein-binding cavity, and identified domains that crosslink with peptidoglycan-associated lipoprotein (Pal) in vivo. Using one of the derivatives containing the photo-crosslinkable amino acid, we developed an in vitro system to analyze the binding of lipoproteins to LolCDE. Our results indicate that compound 2, a LolCDE inhibitor, does not inhibit the binding of lipoproteins to LolCDE, but rather promotes the dissociation of bound lipoproteins from LolCDE.

DOI： 10.1093/jb/mvad118

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb7wlv/pdb

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb7wls/pdb

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1073/pnas.2215072120

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Microbiology Society  

ATP-binding cassette (ABC) transporters are one of the largest protein superfamilies and are found in all living organisms. These transporters use the energy from ATP binding and hydrolysis to transport various substrates. In this review, we focus on the structural and functional aspects of ABC transporters, with special emphasis on type VII ABC transporters, a newly defined class possessing characteristic structures. A notable feature of type VII ABC transporters is that they assemble into tripartite complexes that span both the inner and outer membranes of Gram-negative bacteria. One of the original type VII ABC transporters, which possesses all characteristic features of this class, is the macrolide efflux transporter MacB. Recent structural analyses of MacB and homologue proteins revealed the unique mechanisms of substrate translocation by type VII ABC transporters.

DOI： 10.1099/mic.0.001257

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Authorship：Lead author   Publishing type：Research paper (scientific journal)  

DOI： 10.1142/9789811254796_0001

Scopus

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media {LLC}  

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.

DOI： 10.1038/s41467-021-25679-0

PubMed

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb7cz9/pdb

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Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/1873-3468.13929

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Authorship：Lead author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：公益社団法人 日本薬学会  

MacBは、外膜貫通チャネルTolCと膜融合蛋白質MacAと共に三者複合体を形成し、2重の膜構造を持つグラム陰性菌において、マクロライドなどの基質を細胞外へと排出するABCトランスポーターである。MacBは、細胞質膜において単独で働くABCトランスポーターとは異なり、同じく三者複合体として働くRND型トランスポーターと同様に、ペリプラズムから基質を取り込み、排出を行う新たな機構が提案された。

DOI： 10.14894/faruawpsj.56.6_499

CiNii Research

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Other Link： https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18H02386/

Publishing type：Research paper (scientific journal)   Publisher：International Union of Crystallography ({IUCr})  

DOI： 10.1107/S2053230X18013547

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb5gko/pdb

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb5ws4/pdb

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/s41467-017-01399-2

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1038/nmicrobiol.2017.70

Web of Science

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb5nil/pdb

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Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb5nik/pdb

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.febslet.2014.09.037

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.jmb.2013.06.013

Web of Science

Scopus

PubMed

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Authorship：Lead author   Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb2zcx/pdb

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Doctoral thesis  

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1107/S0907444907059835

Web of Science

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Authorship：Lead author   Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb2zb9/pdb

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1002/prot.20913

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1074/jbc.M505999200

Web of Science

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Publishing type：Research paper (scientific journal)  

DOI： 10.1107/S0108767305088951

Web of Science

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Authorship：Lead author   Publisher：Worldwide Protein Data Bank  

DOI： 10.2210/pdb1ub9/pdb

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Authorship：Lead author   Publishing type：Research paper, summary (international conference)  

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Presentation type：Poster presentation  

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Presentation type：Poster presentation  

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Presentation type：Oral presentation (general)  

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Presentation type：Poster presentation  

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