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Structure paper

TitleCryo-EM structures of a mycobacterial ABC transporter that mediates rifampicin resistance.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 37, Page e2403421121, Year 2024
Publish dateSep 10, 2024
AuthorsYinan Wang / Shan Gao / Fangyu Wu / Yicheng Gong / Nengjiang Mu / Chuancun Wei / Chengyao Wu / Jun Wang / Ning Yan / Huifang Yang / Yifan Zhang / Jiayi Liu / Zeyu Wang / Xiuna Yang / Sin Man Lam / Guanghou Shui / Siyuan Li / Lintai Da / Luke W Guddat / Zihe Rao / Lu Zhang /
PubMed AbstractDrug-resistant Tuberculosis (TB) is a global public health problem. Resistance to rifampicin, the most effective drug for TB treatment, is a major growing concern. The etiological agent, (), has a ...Drug-resistant Tuberculosis (TB) is a global public health problem. Resistance to rifampicin, the most effective drug for TB treatment, is a major growing concern. The etiological agent, (), has a cluster of ATP-binding cassette (ABC) transporters which are responsible for drug resistance through active export. Here, we describe studies characterizing Rv1217c-1218c as an ABC transporter that can mediate mycobacterial resistance to rifampicin and have determined the cryo-electron microscopy structures of Rv1217c-1218c. The structures show Rv1217c-1218c has a type V exporter fold. In the absence of ATP, Rv1217c-1218c forms a periplasmic gate by two juxtaposed-membrane helices from each transmembrane domain (TMD), while the nucleotide-binding domains (NBDs) form a partially closed dimer which is held together by four salt-bridges. Adenylyl-imidodiphosphate (AMPPNP) binding induces a structural change where the NBDs become further closed to each other, which downstream translates to a closed conformation for the TMDs. AMPPNP binding results in the collapse of the outer leaflet cavity and the opening of the periplasmic gate, which was proposed to play a role in substrate export. The rifampicin-bound structure shows a hydrophobic and periplasm-facing cavity is involved in rifampicin binding. Phospholipid molecules are observed in all determined structures and form an integral part of the Rv1217c-1218c transporter system. Our results provide a structural basis for a mycobacterial ABC exporter that mediates rifampicin resistance, which can lead to different insights into combating rifampicin resistance.
External linksProc Natl Acad Sci U S A / PubMed:39226350 / PubMed Central
MethodsEM (single particle)
Resolution2.9 - 3.0 Å
Structure data

36795

8k1m

EMDB-36795, PDB-8k1m:
mycobacterial efflux pump, apo state
Method: EM (single particle) / Resolution: 2.9 Å

36796

8k1n

EMDB-36796, PDB-8k1n:
mycobacterial efflux pump, substrate-bound state
Method: EM (single particle) / Resolution: 3.0 Å

36797

8k1o

EMDB-36797, PDB-8k1o:
mycobacterial efflux pump, AMPPNP bound state
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-L9Q:
(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

ChemComp-RFP:
RIFAMPICIN

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria)
KeywordsTRANSPORT PROTEIN / ABC transporter / efflux pump

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