21ZE

Crystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric petrobactin

Summary for 21ZE

• Entry DOI: 10.2210/pdb21ze/pdb
• Descriptor: Ferric anguibactin-binding protein, 4-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-2-[2-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-2-oxidanylidene-ethyl]-2-oxidanyl-4-oxidanylidene-butanoic acid, FE (III) ION, ... (5 entities in total)
• Functional Keywords: siderophore-binding protein, substrate-binding protein, abc transporter, metal transport protein
• Biological source: Bacillus cereus ATCC 14579
• Total number of polymer chains: 1
• Total formula weight: 33762.81

Authors

Lee, H.,Kim, S.O.,You, S.,Noh, T.,Ihee, H. (deposition date: 2026-01-04, release date: 2026-04-22, Last modification date: 2026-04-29)

Primary citation

Lee, H.,Kim, S.O.,You, S.,Segalina, A.,Noh, T.,Ihee, H.
Structural basis of FatB-mediated iron uptake via tyrosine/histidine direct coordination accompanying long-distance domain reorganization.
Nat Commun, 2026

PubMed 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 (FePB). 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 FePB-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.

PubMed: 42000734
DOI: 10.1038/s41467-026-72127-y

Experimental method

X-RAY DIFFRACTION (1.78 Å)