Evidence map›Paper›PMID 38802368›Full record

ArticleNature communications2024

Proton-coupled transport mechanism of the efflux pump NorA.

Jianping Li, Yan Li, Akiko Koide, Huihui Kuang, Victor J Torres, Shohei Koide, Da-Neng Wang, Nathaniel J Traaseth

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
  5. Miniprotein inhibitors of thebioRxiv : the preprint server for biology · 2026
    Article
  6. Review
  7. Energetic and structural control of polyspecificity in a multidrug transporter.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
  15. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Jianping LiDepartment of Chemistry, New York University, New York, NY, USA.
Yan LiDepartment of Cell Biology, New York University School of Medicine, New York, NY, USA.
Akiko KoidePerlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0003-1796-7077
Huihui KuangSimons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
Victor J TorresDepartment of Microbiology, New York University School of Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0002-7126-0489
Shohei KoidePerlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.ORCID http://orcid.org/0000-0001-5473-4358
Da-Neng WangDepartment of Cell Biology, New York University School of Medicine, New York, NY, USA. da-neng.wang@med.nyu.edu.ORCID http://orcid.org/0000-0002-6496-4699
Nathaniel J TraasethDepartment of Chemistry, New York University, New York, NY, USA. traaseth@nyu.edu.ORCID http://orcid.org/0000-0002-1185-6088

Funding

Vaccine FacilityP30CA016087 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI MARK Reid PHILIPS · 1985 to 2026
$83.1M
NCCAT: National Center for CryoEM Access and Training- Supplement for Windows 10 and FFIU24GM129539 · NIGMS · NEW YORK STRUCTURAL BIOLOGY CENTER · PI DE MARCO, ALEX, KIEFT, JEFFREY S · 2018 to 2023
$53.9M
Mechanisms of Allostery and Molecular Recognition in the Small Multidrug Resistance FamilyR01AI108889 · NIAID · NEW YORK UNIVERSITY · PI Nathaniel J. Traaseth · 2014 to 2026
$5.4M
Transport Cycle and Inhibition of Human Na+-dicarboxylate Cotransporter NaDC3R01NS108151 · NINDS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI DANENG WANG · 2018 to 2026
$4.1M
Transport Mechanisms and Inhibition of Efflux Pumps in Pathogenic OrganismsR01AI165782 · NIAID · NEW YORK UNIVERSITY · PI SHOHEI KOIDE, Nathaniel J. Traaseth · 2022 to 2026
$4.0M
Dynamics and mechanism of sodium-dependent carboxylate transportersR01DK135088 · NIDDK · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI Ruben L Gonzalez, Emad Tajkhorshid · 2023 to 2026
$2.6M
Structural basis of the Ragulator-Rag GTPase complex as a platform for mTOR activation on the lysosomal surfaceR01GM121994 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI WANG, DANENG · 2017 to 2020
$1.5M
Structural and mechanistic studies of INDY proteinsR01DK099023 · NIDDK · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI WANG, DANENG · 2013 to 2016
$1.5M
Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID) AI165782National Science Foundation (NSF) MCB1506420NCI NIH HHS P30 CA016087NIAID NIH HHS R01 AI108889NIAID NIH HHS R01 AI165782NIDDK NIH HHS R01 DK135088NIGMS NIH HHS R01 GM121994NIGMS NIH HHS U24 GM129539NINDS NIH HHS R01 NS108151U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) AI108889U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID) AI165782U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases) DK135088U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) GM121994U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS) NS108151
6 · The paper itself

Abstract

Efflux pump antiporters confer drug resistance to bacteria by coupling proton import with the expulsion of antibiotics from the cytoplasm. Despite efforts there remains a lack of understanding as to how acid/base chemistry drives drug efflux. Here, we uncover the proton-coupling mechanism of the Staphylococcus aureus efflux pump NorA by elucidating structures in various protonation states of two essential acidic residues using cryo-EM. Protonation of Glu222 and Asp307 within the C-terminal domain stabilized the inward-occluded conformation by forming hydrogen bonds between the acidic residues and a single helix within the N-terminal domain responsible for occluding the substrate binding pocket. Remarkably, deprotonation of both Glu222 and Asp307 is needed to release interdomain tethering interactions, leading to opening of the pocket for antibiotic entry. Hence, the two acidic residues serve as a "belt and suspenders" protection mechanism to prevent simultaneous binding of protons and drug that enforce NorA coupling stoichiometry and confer antibiotic resistance.

Indexed as

ATP-Binding Cassette, Sub-Family C ProteinsBacterial ProteinsCryoelectron MicroscopyProtonsStaphylococcus aureusAnti-Bacterial AgentsBinding SitesBiological TransportHydrogen BondingModels, MolecularProtein ConformationAnti-Bacterial AgentsATP-Binding Cassette, Sub-Family C ProteinsBacterial ProteinsNorA protein, StaphylococcusProtons

Identifiers

PMID38802368
PMCPMC11130294

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.