3RUR

Staphylococcus aureus heme-bound selenomethionine-labeled IsdB-N2

Summary for 3RUR

• Entry DOI: 10.2210/pdb3rur/pdb
• Descriptor: Iron-regulated surface determinant protein B, PROTOPORPHYRIN IX CONTAINING FE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: heme protein, heme uptake, neat domain, heme binding, cell wall, metal transport
• Biological source: Staphylococcus aureus subsp. aureus
• Cellular location: Secreted, cell wall ; Peptidoglycan-anchor : Q7A656
• Total number of polymer chains: 4
• Total formula weight: 60400.84

Authors

Gaudin, C.F.M.,Grigg, J.C.,Arrieta, A.L.,Murphy, M.E.P. (deposition date: 2011-05-05, release date: 2011-05-18, Last modification date: 2023-12-06)

Primary citation

Gaudin, C.F.,Grigg, J.C.,Arrieta, A.L.,Murphy, M.E.
Unique Heme-Iron Coordination by the Hemoglobin Receptor IsdB of Staphylococcus aureus.
Biochemistry, 50:5443-5452, 2011

PubMed Abstract: Iron is an essential requirement for life for nearly all organisms. The human pathogen Staphylococcus aureus is able to acquire iron from the heme cofactor of hemoglobin (Hb) released from lysed erythrocytes. IsdB, the predominant Hb receptor of S. aureus, is a cell wall-anchored protein that is composed of two NEAT domains. The N-terminal NEAT domain (IsdB-N1) binds Hb, and the C-terminal NEAT domain (IsdB-N2) relays heme to IsdA for transport into the cell. Here we present the 1.45 Å resolution X-ray crystal structure of the IsdB-N2-heme complex. While the structure largely conforms to the eight-strand β-sandwich fold seen in other NEAT domains such as IsdA-N and uses a conserved Tyr residue to coordinate heme-iron, a Met residue is also involved in iron coordination, resulting in a novel Tyr-Met hexacoordinate heme-iron state. The kinetics of the transfer of heme from IsdB-N2 to IsdA-N can be modeled as a two-step process. The rate of transfer of heme between the isolated NEAT domains (82 s(-1)) was found to be similar to that measured for the full-length proteins. Replacing the iron coordinating Met with Leu did not abrogate high-affinity heme binding but did reduce the heme transfer rate constant by more than half. This unusual Met-Tyr heme coordination may also bestow properties on IsdB that help it to bind heme in different oxidation states or extract heme from hemoglobin.

PubMed: 21574663
DOI: 10.1021/bi200369p

Experimental method

X-RAY DIFFRACTION (1.7 Å)