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Structure paper

TitleCryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 119, Issue 14, Page e2116708119, Year 2022
Publish dateApr 5, 2022
AuthorsOmar De Bei / Marialaura Marchetti / Luca Ronda / Eleonora Gianquinto / Loretta Lazzarato / Dimitri Y Chirgadze / Steven W Hardwick / Lee R Cooper / Francesca Spyrakis / Ben F Luisi / Barbara Campanini / Stefano Bettati /
PubMed AbstractIron surface determinant B (IsdB) is a hemoglobin (Hb) receptor essential for hemic iron acquisition by Staphylococcus aureus. Heme transfer to IsdB is possible from oxidized Hb (metHb), but ...Iron surface determinant B (IsdB) is a hemoglobin (Hb) receptor essential for hemic iron acquisition by Staphylococcus aureus. Heme transfer to IsdB is possible from oxidized Hb (metHb), but inefficient from Hb either bound to oxygen (oxyHb) or bound to carbon monoxide (HbCO), and encompasses a sequence of structural events that are currently poorly understood. By single-particle cryo-electron microscopy, we determined the structure of two IsdB:Hb complexes, representing key species along the heme extraction pathway. The IsdB:HbCO structure, at 2.9-Å resolution, provides a snapshot of the preextraction complex. In this early stage of IsdB:Hb interaction, the hemophore binds to the β-subunits of the Hb tetramer, exploiting a folding-upon-binding mechanism that is likely triggered by a cis/trans isomerization of Pro173. Binding of IsdB to α-subunits occurs upon dissociation of the Hb tetramer into α/β dimers. The structure of the IsdB:metHb complex reveals the final step of the extraction process, where heme transfer to IsdB is completed. The stability of the complex, both before and after heme transfer from Hb to IsdB, is influenced by isomerization of Pro173. These results greatly enhance current understanding of structural and dynamic aspects of the heme extraction mechanism by IsdB and provide insight into the interactions that stabilize the complex before the heme transfer event. This information will support future efforts to identify inhibitors of heme acquisition by S. aureus by interfering with IsdB:Hb complex formation.
External linksProc Natl Acad Sci U S A / PubMed:35357971 / PubMed Central
MethodsEM (single particle)
Resolution2.89 - 5.82 Å
Structure data

13319

7pcf

EMDB-13319, PDB-7pcf:
Human methemoglobin bound to Staphylococcus aureus hemophore IsdB
Method: EM (single particle) / Resolution: 5.82 Å

13320

7pch

EMDB-13320, PDB-7pch:
Human carboxyhemoglobin bound to Staphylococcus aureus hemophore IsdB - 1:2 complex
Method: EM (single particle) / Resolution: 2.89 Å

13325

7pcq

EMDB-13325, PDB-7pcq:
Human carboxyhemoglobin bound to Staphylococcus aureus hemophore IsdB - 1:1 complex
Method: EM (single particle) / Resolution: 3.62 Å

Chemicals

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
  • staphylococcus aureus subsp. aureus mw2 (bacteria)
  • Human (human)
KeywordsMETAL TRANSPORT / Iron acquisition / Hemophore / Hemoglobin / NEAT domain

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