Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction

Abstract

Significance During infection, the human pathogen Staphylococcus aureus expresses a surface-exposed receptor, Iron surface determinant B (IsdB), that captures free human hemoglobin (Hb) and removes heme to retrieve iron, an essential nutrient for bacterial proliferation inside the host. Using single-particle cryo-electron microscopy, we solved the structure of two complexes between Hb and IsdB that represent snapshots of the initial interaction, where heme is still bound to Hb, and the final complex after completion of heme extraction. The structural and dynamic details unlocked through these structures will boost the design of inhibitors of IsdB:Hb interaction that might work as innovative antimicrobials.

The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme–iron from human hemoglobin

“…The molecular strategy used by S. pyogenes to remove heme from Hb is distinct from previously characterized mechanisms used by other microbial pathogens. Three types of microbial Hb receptors have been identified: i) the surface displayed IsdB/IsdH receptors from S. aureus ( 51 – 56 ), ii) outer membrane-associated HpuA receptors in gram-negative bacteria such as Kingella denitrificans ( 57 , 58 ), and iii) surface displayed Hb–Hp receptors (HpHbR) present in the pathogenic trypanosomes Trypanosoma brucei and Trypanosoma congolense ( 59 – 61 ). These receptors are structurally distinct, but like Shr, the trypanosomal HpHbR receptors preferentially capture heme-loaded Hb by directly contacting its heme’s propionate groups using a combination of tyrosine and cationic residues ( 59 , 60 ).…”

Nanoscale dynamical investigation of the hemoglobin complex with the bacterial protein IsdB: is their interaction stabilized by catch bonds?

“…Hb with iron in the reduced Fe 2+ state, coordinated to O 2 or CO), and requires the heme iron to be in the ferric state. 22 Consistently, the binding of IsdB to HbCO, which occurs through a dense network of contacts, is not related to major conformational changes in the interaction partners. 22 On the contrary, even if high-resolution details are not available, many biochemical and biophysical techniques suggest a higher degree of flexibility of the IsdB : metHb interaction.…”

“…To further explore the pulling rate-enhanced binding trend found for the IsdB : metHb system, AFS experiments were carried out by using HbCO as the IsdB partner in the Hb : hemophore complex, where binding occurs normally but the extraction step does not take place. 22,31…”

“…Furthermore, a single-particle cryo-electron microscopy study has provided experimental evidence of key steps of the heme extraction by IsdB from Hb. 22…”

“…The equilibrium constant for metHb tetramer dissociation into dimers is in the low micromolar range; 21 IsdB binding further promotes tetramer dissociation as part of its mechanism of action leading to heme extraction. 22 Therefore, to prevent any interference from metHb tetramer-to-dimer dissociation in AFS experiments, we produced and tested cross-linked metHb ((ββ)XL–Hb), in which the two β-chains are covalently cross-linked (Fig. 1D), to exclude any interference from Hb tetramer dissociation on the measured unbinding behavior.…”