The mycobacterial ABC transporter IrtAB employs a membrane-facing crevice for siderophore-mediated iron uptake

Nat Commun. 2025 Jan 29;16(1):1133. doi: 10.1038/s41467-024-55136-7.

Abstract

The mycobacterial ABC transporter IrtAB features an ABC exporter fold, yet it imports iron-charged siderophores called mycobactins. Here, we present extensive cryo-EM analyses and DEER measurements, revealing that IrtAB alternates between an inward-facing and an outward-occluded conformation, but does not sample an outward-facing conformation. When IrtAB is locked in its outward-occluded conformation in nanodiscs, mycobactin is bound in the middle of the lipid bilayer at a membrane-facing crevice opening at the heterodimeric interface. Mutations introduced at the crevice abrogate mycobactin import and in corresponding structures, the crevice is collapsed. A conserved triple histidine motif coordinating a zinc ion is present below the mycobactin binding site. Substitution of these histidine residues with alanine results in a decoupled transporter, which hydrolyzes ATP, but lost its capacity to import mycobactins. Our data suggest that IrtAB imports mycobactin via a credit-card mechanism in a transport cycle that is coupled to the presence of zinc.

MeSH terms

  • ATP-Binding Cassette Transporters* / chemistry
  • ATP-Binding Cassette Transporters* / genetics
  • ATP-Binding Cassette Transporters* / metabolism
  • Bacterial Proteins* / genetics
  • Bacterial Proteins* / metabolism
  • Binding Sites
  • Biological Transport
  • Cryoelectron Microscopy
  • Histidine / metabolism
  • Iron* / metabolism
  • Models, Molecular
  • Mutation
  • Mycobacterium smegmatis / genetics
  • Mycobacterium smegmatis / metabolism
  • Oxazoles / metabolism
  • Protein Conformation
  • Siderophores* / metabolism
  • Zinc / metabolism

Substances

  • ATP-Binding Cassette Transporters
  • Iron
  • Siderophores
  • Bacterial Proteins
  • mycobactins
  • Oxazoles
  • Zinc
  • Histidine