9MHZ | pdb_00009mhz

Cryo-EM structure of S. aureus TarGH in complex with Targocil-II and ATP-gamma-S in a catalytically incompetent conformation

PDB DOI: https://doi.org/10.2210/pdb9MHZ/pdb
EM Map EMD-48282: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Lactococcus lactis
Mutation(s): No

Deposited: 2024-12-12 Released: 2025-04-23
Deposition Author(s): Peters, S.C., Worrall, L.J., Strynadka, N.C.J.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM analyses unveil details of mechanism and targocil-II mediated inhibition of S. aureus WTA transporter TarGH.

Li, F.K.K., Peters, S.C., Worrall, L.J., Sun, T., Hu, J., Vuckovic, M., Farha, M., Palacios, A., Caveney, N.A., Brown, E.D., Strynadka, N.C.J.

(2025) Nat Commun 16: 3224-3224

PubMed: 40185711 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-58202-w
Primary Citation Related Structures:
9CFL, 9CFP, 9MHD, 9MHU, 9MHZ

PubMed Abstract:
Wall teichoic acid (WTA) is a polyol phosphate polymer that covalently decorates peptidoglycan of gram-positive bacteria, including Staphylococcus aureus. Central to WTA biosynthesis is flipping of lipid-linked precursors across the cell membrane by TarGH, a type V ABC transporter. Here, we present cryo-EM structures of S. aureus TarGH in the presence of targocil-II, a promising small-molecule lead with β-lactam antibiotic synergistic action. Targocil-II binds to the extracellular dimerisation interface of TarG, we suggest mimicking flipped but not yet released substrate. In absence of targocil-II and in complex with ATP analogue ATPγS, determined at 2.3 Å resolution, the ATPase active site is allosterically inhibited. This is due to a so far undescribed D-loop conformation, potentially minimizing spurious ATP hydrolysis in the absence of substrate. Targocil-II binding comparatively causes local and remote conformational changes through to the TarH active site, with the D-loop now optimal for ATP hydrolysis. These structures suggest an ability to modulate ATP hydrolysis in a WTA substrate dependent manner and a jammed ATPase cycle as the basis of the observed inhibition by targocil-II. The molecular insights provide an unprecedented basis for development of TarGH targeted therapeutics for treatment of multidrug-resistant S. aureus and other gram-positive bacterial infections.

Organizational Affiliation

Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.

Macromolecule Content

Total Structure Weight: 132.16 kDa
Atom Count: 8,924
Modeled Residue Count: 1,068
Deposited Residue Count: 1,116
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transport permease protein	A, D [auth C]	294	Staphylococcus aureus	Mutation(s): 0 Gene Names: tagG, SAUSA300_0625
UniProt
Find proteins for Q2G2X5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G2X5 Go to UniProtKB: Q2G2X5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G2X5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Teichoic acids export ATP-binding protein TagH	B, C [auth D]	264	Staphylococcus aureus	Mutation(s): 0 Gene Names: tagH, SAUSA300_0624 EC: 7.5.2.4
UniProt
Find proteins for Q2G2L1 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G2L1 Go to UniProtKB: Q2G2L1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G2L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV0 (Subject of Investigation/LOI) Query on AV0 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C]	E [auth A], K [auth C]	Lauryl Maltose Neopentyl Glycol C₄₇ H₈₈ O₂₂ MADJBYLAYPCCOO-VWHTXWAPSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth D] MOL2 format, chain G [auth B] MOL2 format, chain I [auth D] mmCIF format, chain G [auth B] mmCIF format, chain I [auth D]	G [auth B], I [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain G [auth B] Focus chain I [auth D] Interactions & Density Focus chain G [auth B] Focus chain I [auth D]
A1AV9 (Subject of Investigation/LOI) Query on A1AV9 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C]	F [auth A], L [auth C]	Targocil-II C₂₆ H₂₂ Cl N O₆ AKQCCBGXRNNPLS-OAQYLSRUSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain J [auth D] MOL2 format, chain H [auth B] MOL2 format, chain J [auth D] mmCIF format, chain H [auth B] mmCIF format, chain J [auth D]	H [auth B], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain J [auth D] Interactions & Density Focus chain H [auth B] Focus chain J [auth D]