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Structure paper

TitleStructural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms.
Journal, issue, pagesNat Commun, Vol. 12, Issue 1, Page 6919, Year 2021
Publish dateNov 25, 2021
AuthorsAlina Ornik-Cha / Julia Wilhelm / Jessica Kobylka / Hanno Sjuts / Attilio V Vargiu / Giuliano Malloci / Julian Reitz / Anja Seybert / Achilleas S Frangakis / Klaas M Pos /
PubMed AbstractUpon 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 ...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.
External linksNat Commun / PubMed:34824229 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.1 - 3.84 Å
Structure data

12088

7b8p

EMDB-12088, PDB-7b8p:
Acinetobacter baumannii multidrug transporter AdeB in OOO state
Method: EM (single particle) / Resolution: 3.54 Å

12089

7b8q

EMDB-12089, PDB-7b8q:
Acinetobacter baumannii multidrug transporter AdeB in L*OO state
Method: EM (single particle) / Resolution: 3.84 Å

PDB-7b8r:
Doxycycline bound structure of bacterial efflux pump.
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-7b8s:
Fusidic acid bound structure of bacterial efflux pump.
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-7b8t:
Levofloxacin bound structure of bacterial efflux pump.
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

Chemicals

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-DXT:
(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / antibiotic*YM

ChemComp-HOH:
WATER

ChemComp-FUA:
FUSIDIC ACID / antibiotic, Antimicrobial*YM

ChemComp-LFX:
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid / medication, antibiotic*YM

Source
  • Acinetobacter baumannii AYE (bacteria)
  • acinetobacter baumannii (strain aye) (bacteria)
  • escherichia coli (strain k12) (bacteria)
  • synthetic construct (others)
KeywordsTRANSPORT PROTEIN / RND-transporter / multidrug transporter / antibiotic resistance / membrane protein / RND transporter / multidrug resistance / efflux pump / antibiotics

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