9O9X

ytrEF nucleotide-free conformation

Summary for 9O9X

• Entry DOI: 10.2210/pdb9o9x/pdb
• EMDB information: 70265
• Descriptor: ABC transporter ATP-binding protein YtrE, ABC transporter permease YtrF (2 entities in total)
• Functional Keywords: abc transporter, transporter, membrane protein
• Biological source: Bacillus subtilis subsp. subtilis str. 168; More
• Total number of polymer chains: 4
• Total formula weight: 152284.77

Authors

Yu, P.,Krah, B.S.,Orlando, M.A.,Orlando, B.J. (deposition date: 2025-04-18, release date: 2025-10-15, Last modification date: 2026-01-21)

Primary citation

Yu, P.,Krah, B.S.,Orlando, M.A.,Subramanian, S.,Orlando, B.J.
Structural analysis of a Gram-positive type VII ABC transporter induced by cell wall-targeting antibiotics.
Structure, 34:145-156.e4, 2026

PubMed Abstract: Bacteria utilize a variety of mechanisms to remodel the cell wall in response to environmental and antimicrobial stress. In the model organism Bacillus subtilis, the ytr operon encoding putative ATP-binding cassette (ABC) transporter(s) is highly upregulated in response to cell wall-targeting antibiotics. Here we show that the ytr operon encodes two distinct ABC transporters: YtrBCD and YtrEF. Using cryo-electron microscopy(cryo-EM), we determined the structures of YtrEF in nucleotide-free and ADP-vanadate bound states. The structures demonstrate that YtrEF adopts a type VII ABC transporter fold. Nucleotide binding induced conformational changes that propagate from the cytosolic region through the transmembrane helices to ultimately reorient the extracellular domains. Extended bacterial growth assays and suppressor mutation identification indicated that YtrEF contributes to alteration of colony morphology. These findings establish YtrEF as a type VII ABC transporter that is induced by cell wall-targeting antibiotics and a new avenue to phenotypically assess the ytr operon.

PubMed: 41161309
DOI: 10.1016/j.str.2025.10.004

Experimental method

ELECTRON MICROSCOPY (3.4 Å)