7B8R

Doxycycline bound structure of bacterial efflux pump.

Summary for 7B8R

• Entry DOI: 10.2210/pdb7b8r/pdb
• Descriptor: Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB, DARPin, DI(HYDROXYETHYL)ETHER, ... (5 entities in total)
• Functional Keywords: rnd transporter, multidrug resistance, efflux pump, antibiotics, transport protein
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 6
• Total formula weight: 254669.31

Authors

Wilhelm, J.,Sjuts, H.,Pos, K.M. (deposition date: 2020-12-13, release date: 2021-10-20, Last modification date: 2024-01-31)

Primary citation

Ornik-Cha, A.,Wilhelm, J.,Kobylka, J.,Sjuts, H.,Vargiu, A.V.,Malloci, G.,Reitz, J.,Seybert, A.,Frangakis, A.S.,Pos, K.M.
Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms.
Nat Commun, 12:6919-6919, 2021

PubMed Abstract: Upon antibiotic stress Gram-negative pathogens deploy resistance-nodulation-cell division-type tripartite efflux pumps. These include a H/drug antiporter module that recognizes structurally diverse substances, including antibiotics. Here, we show the 3.5 Å structure of subunit AdeB from the Acinetobacter baumannii AdeABC efflux pump solved by single-particle cryo-electron microscopy. The AdeB trimer adopts mainly a resting state with all protomers in a conformation devoid of transport channels or antibiotic binding sites. However, 10% of the protomers adopt a state where three transport channels lead to the closed substrate (deep) binding pocket. A comparison between drug binding of AdeB and Escherichia coli AcrB is made via activity analysis of 20 AdeB variants, selected on basis of side chain interactions with antibiotics observed in the AcrB periplasmic domain X-ray co-structures with fusidic acid (2.3 Å), doxycycline (2.1 Å) and levofloxacin (2.7 Å). AdeABC, compared to AcrAB-TolC, confers higher resistance to E. coli towards polyaromatic compounds and lower resistance towards antibiotic compounds.

PubMed: 34824229
DOI: 10.1038/s41467-021-27146-2

Experimental method

X-RAY DIFFRACTION (2.1 Å)