Abstract
Iron is an essential cofactor for fundamental biological processes. However, Fe(III) is poorly soluble under aerobic conditions, limiting its bioavailability. To secure this essential nutrient, bacteria release high-affinity siderophores that capture environmental Fe(III) and are subsequently imported into the cell as ferric siderophore complexes. While biochemical studies have characterized siderophore uptake in Bacillus species, atomic-level mechanisms of recognition and coordination remain unclear. Here, we investigate the siderophore-binding protein FatB from Bacillus cereus and its interactions with its siderophore, petrobactin (PB), as well as with ferric petrobactin (FePB) and its ferric photoproduct (FePBν). Crystal structures of apo- and ferric-ligand-bound FatB, supported by biophysical and mutational analyses, reveal that ferric-siderophore binding induces substantial domain closure of FatB. This conformational transition involves an extensive ~29-Å reorganization of a flexible loop, which positions His252 alongside Tyr317 to directly coordinate the Fe(III) center in the FePB-FatB complex. This protein-derived coordination mode is maintained in the FePBν-FatB complex, where a structured water network preserves interfacial complementarity and functional recognition. These findings provide a structural framework for siderophore recognition and iron acquisition and illustrate how active-site coordination and domain reorganization facilitate robust capture of chemically labile ligands, offering insights for antimicrobial development targeting bacterial iron uptake.
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Data availability
All crystallographic coordinates and associated structure-factor data have been deposited into the Protein Data Bank (PDB) under accession codes 21ZD (apo-FatB), 21ZE (FePB-FatB), 21ZF (FePBν-FatB), and 21ZG (Fe(3,4-DHB)2-FatB). Previously published structures used in this study are available in the PDB under accession codes 8BNW (apo-Pth), 3GFV (apo-YclQ), and 7SF6 (Desulfitobacterium hafniense FatB). The SAXS data have been deposited in the SASBDB database under accession codes SASDYB7 (apo-FatB), SASDYC7 (PB-FatB), SASDYD7 (FePB-FatB), SASDYE7 (FePBν-FatB), SASDYF7 (Fe(3,4-DHB)2-FatB). MD simulation parameter and coordinate files are provided as Supplementary Data 1. Source data are provided as a Source data file. Source data are provided with this paper.
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Acknowledgements
We thank the beamline staff at the Pohang Light Source-II (PLS-II), Pohang Accelerator Laboratory (PAL, Korea), for their kind assistance during data collection. Small-angle X-ray scattering (SAXS) experiments were performed at beamline 4 C, and X-ray diffraction data were collected at beamline 11 C. This work was supported by the Institute for Basic Science (IBS-R033; H.I.).
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H.L., S.O.K., and H.I. conceived the research and developed the methodology. H.L., S.O.K. selected the target samples. H.L., S.O.K., and S.Y. prepared the target samples. H.L., S.O.K., S.Y., and T.N. collected the experimental data. H.L., S.Y. performed the data processing, and H.L. analyzed the data. A.S. carried out the ab initio simulations of the ground and excited states, along with the corresponding spectral analysis. H.L., S.O.K., A.S., and H.I. wrote and revised the manuscript. H.I. supervised the overall project. All authors discussed the results and approved the final version of the manuscript.
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Lee, H., Kim, S.O., You, S. et al. Structural basis of FatB-mediated iron uptake via tyrosine/histidine direct coordination accompanying long-distance domain reorganization. Nat Commun (2026). https://doi.org/10.1038/s41467-026-72127-y
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DOI: https://doi.org/10.1038/s41467-026-72127-y
