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TitleStructure and mechanism of a mycobacterial isoniazid efflux pump MsRv1273c/72c with a degenerate nucleotide-binding site.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 3969, Year 2025
Publish dateApr 28, 2025
AuthorsJing Yu / Yuhui Lan / Chen Zhu / Zhendong Chen / Junyi Pan / Yanfeng Shi / Lan Yang / Tianyu Hu / Yan Gao / Yao Zhao / Xiaobo Chen / Xiuna Yang / Shuihua Lu / Luke W Guddat / Haitao Yang / Zihe Rao / Jun Li /
PubMed AbstractHeterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. ...Heterodimeric ATP-binding cassette (ABC) transporters containing one catalytically impaired degenerate nucleotide-binding site (NBS) have a mechanism different from those with two active NBSs. However, the structural basis of their transport mechanism remains to be explained. Here, we determine mycobacterial MsRv1273c/72c to be an isoniazid efflux pump and determine several structures by cryo-electron microscopy showing specific asymmetrical features including an N-terminal extending loop and a periplasmic helical hairpin only found in MsRv1272c. In addition, we capture three distinct asymmetric states where the nucleotide-binding domains are partially dimerized at the degenerate site. Using these intermediate states, the D-WalkerB loop and X-signature loop of MsRv1272c modulate and couple the function of both NBSs through conformational changes. Thus, these data provide insights into the mechanism of this heterodimeric ABC transporter containing a degenerate NBS. The structures also provide a framework for the rational design of anti-tuberculosis drugs targeting this drug-efflux pump.
External linksNat Commun / PubMed:40295516 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 4.01 Å
Structure data

37450

8wcw

EMDB-37450, PDB-8wcw:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the IFapo state
Method: EM (single particle) / Resolution: 3.11 Å

37451

8wcx

EMDB-37451, PDB-8wcx:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the AMPPNP-bound IFasym-1 state
Method: EM (single particle) / Resolution: 3.09 Å

38626

8xsr

EMDB-38626, PDB-8xsr:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ATP|ADP-bound IFasym-2 state
Method: EM (single particle) / Resolution: 2.93 Å

38627

8xss

EMDB-38627, PDB-8xss:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ADP-bound IFasym-3 state (ATP 37 degrees C treated
Method: EM (single particle) / Resolution: 3.33 Å

38628

8xst

EMDB-38628, PDB-8xst:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ADP-bound IFasym-3 state (ADP 4 degrees C treated)
Method: EM (single particle) / Resolution: 3.1 Å

60789

9iqe

EMDB-60789, PDB-9iqe:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ADP-bound IFasym-3 (peptidisc) state (ATP 37degrees C treated)
Method: EM (single particle) / Resolution: 3.78 Å

60790

9iqf

EMDB-60790, PDB-9iqf:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ADP-bound IFasym-3 (peptidisc) state (ADP 4degrees C treated)
Method: EM (single particle) / Resolution: 4.01 Å

60791

9iqg

EMDB-60791, PDB-9iqg:
Cryo-EM structure of MsRv1273c/72c from Mycobacterium smegmatis in the ATP|ADP+Vi-bound Occ (Vi) state
Method: EM (single particle) / Resolution: 2.7 Å

62611

9kwi

EMDB-62611, PDB-9kwi:
Cryo-EM structure of MsRv1273c/72c(E553Q) mutant from Mycobacterium smegmatis in the ATP-bound Occ state
Method: EM (single particle) / Resolution: 3.19 Å

Chemicals

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

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-VO4:
VANADATE ION

Source
  • mycolicibacterium smegmatis mc2 155 (bacteria)
KeywordsTRANSPORT PROTEIN / ABC transporter / exporter

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