2K78 image
Entry Detail
PDB ID:
2K78
Title:
Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2008-08-06
Release Date:
2008-08-19
Method Details:
Experimental Method:
Conformers Calculated:
200
Conformers Submitted:
30
Selection Criteria:
structures with the lowest energy
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Iron-regulated surface determinant protein C
Chain IDs:A
Chain Length:147
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain MW2)
Ligand Molecules
Primary Citation
The IsdC Protein from Staphylococcus aureus Uses a Flexible Binding Pocket to Capture Heme.
J.Biol.Chem. 283 31591 31600 (2008)
PMID: 18715872 DOI: 10.1074/jbc.M801126200

Abstact

Staphylococcus aureus scavenges heme-iron from host hemoproteins using iron-regulated surface determinant (Isd) proteins. IsdC is the central conduit through which heme is passed across the cell wall and binds this molecule using a NEAr Transporter (NEAT) domain. NMR spectroscopy was used to determine the structure of IsdC in complex with a heme analog, zinc-substituted protoporphyrin IX (ZnPPIX). The backbone coordinates of the ensemble of conformers representing the structure exhibit a root mean square deviation to the mean structure of 0.53 +/- 0.11 angstroms. IsdC partially buries protoporphyrin within a large hydrophobic pocket that is located at the end of its beta-barrel structure. The central metal ion of the analog adopts a pentacoordinate geometry in which a highly conserved tyrosine residue serves as a proximal ligand. Consistent with the structure and its role in heme transfer across the cell wall, we show that IsdC weakly binds heme (K(D) = 0.34 +/- 0.12 microm) and that ZnPPIX rapidly dissociates from the protein at a rate of 126 +/- 30 s(-1). NMR studies of the apo-form of IsdC reveal that a 3(10) helix within the binding pocket undergoes a flexible to rigid transition as heme is captured. This structural plasticity may increase the efficiency of heme transfer across the cell wall by facilitating protein-protein interactions between apoIsdC and upstream hemoproteins.

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