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TitleCryo-EM Structures of AcrD Illuminate a Mechanism for Capturing Aminoglycosides from Its Central Cavity.
Journal, issue, pagesmBio, Vol. 14, Issue 1, Page e0338322, Year 2023
Publish dateFeb 28, 2023
AuthorsZhemin Zhang / Christopher E Morgan / Meng Cui / Edward W Yu /
PubMed AbstractThe Escherichia coli acriflavine resistance protein D (AcrD) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. Its primary function is to provide resistance ...The Escherichia coli acriflavine resistance protein D (AcrD) is an efflux pump that belongs to the resistance-nodulation-cell division (RND) superfamily. Its primary function is to provide resistance to aminoglycoside-based drugs by actively extruding these noxious compounds out of E. coli cells. AcrD can also mediate resistance to a limited range of other amphiphilic agents, including bile acids, novobiocin, and fusidic acids. As there is no structural information available for any aminoglycoside-specific RND pump, here we describe cryo-electron microscopy (cryo-EM) structures of AcrD in the absence and presence of bound gentamicin. These structures provide new information about the RND superfamily of efflux pumps, specifically, that three negatively charged residues central to the aminoglycoside-binding site are located within the ceiling of the central cavity of the AcrD trimer. Thus, it is likely that AcrD is capable of picking up aminoglycosides via this central cavity. Through the combination of cryo-EM structural determination, mutagenesis analysis, and molecular simulation, we show that charged residues are critically important for this pump to shuttle drugs directly from the central cavity to the funnel of the AcrD trimer for extrusion. Here, we report cryo-EM structures of the AcrD aminoglycoside efflux pump in the absence and presence of bound gentamicin, posing the possibility that this pump is capable of capturing aminoglycosides from the central cavity of the AcrD trimer. The results indicate that AcrD utilizes charged residues to bind and export drugs, mediating resistance to these antibiotics.
External linksmBio / PubMed:36625574 / PubMed Central
MethodsEM (single particle)
Resolution2.95 - 3.09 Å
Structure data

28848

8f3e

EMDB-28848, PDB-8f3e:
Trimer of aminoglycoside efflux pump AcrD
Method: EM (single particle) / Resolution: 3.09 Å

28855

8f4n

EMDB-28855, PDB-8f4n:
Dimer of aminoglycoside efflux pump AcrD
Method: EM (single particle) / Resolution: 2.95 Å

28857

8f4r

EMDB-28857, PDB-8f4r:
Gentamicin bound aminoglycoside efflux pump AcrD
Method: EM (single particle) / Resolution: 3.06 Å

28861

8f56

EMDB-28861, PDB-8f56:
Dimer of aminoglycoside efflux pump AcrD treated with gentamicin
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-LLL:
(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR

Source
  • escherichia coli (E. coli)
KeywordsMEMBRANE PROTEIN / aminoglycoside efflux pump / AcrD / E.coli

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