3VTM

Structure of heme transport protein IsdH-NEAT3 from S. aureus in complex with Indium-porphyrin

Summary for 3VTM

• Entry DOI: 10.2210/pdb3vtm/pdb
• Related: 2E7D 2Z6F 3QUG 3QUH
• Descriptor: Iron-regulated surface determinant protein H, PROTOPORPHYRIN IX CONTAINING INDIUM, GLYCEROL, ... (4 entities in total)
• Functional Keywords: indium, metalloporphyrin, metal selectivity, neat domain, heme binding, heme transport, hemin, ppix, cell wall, heme-binding protein
• Biological source: Staphylococcus aureus
• Cellular location: Secreted, cell wall ; Peptidoglycan-anchor : Q931P4
• Total number of polymer chains: 2
• Total formula weight: 27542.38

Authors

Vu, N.T.,Caaveiro, J.M.M.,Moriwaki, Y.,Tsumoto, K. (deposition date: 2012-05-31, release date: 2013-05-15, Last modification date: 2023-11-08)

Primary citation

Vu, N.T.,Moriwaki, Y.,Caaveiro, J.M.M.,Terada, T.,Tsutsumi, H.,Hamachi, I.,Shimizu, K.,Tsumoto, K.
Selective binding of antimicrobial porphyrins to the heme-receptor IsdH-NEAT3 of Staphylococcus aureus
Protein Sci., 22:942-953, 2013

PubMed Abstract: The Isd (iron-regulated surface determinant) system of the human pathogen Staphylococcus aureus is responsible for the acquisition of heme from the host organism. We recently reported that the extracellular heme receptor IsdH-NEAT3 captures and transfers noniron antimicrobial porphyrins containing metals in oxidation state (III). However, it is unclear if geometric factors such as the size of the metal (ionic radius) affect binding and transfer of metalloporphyrins. We carried out an ample structural, functional, and thermodynamic analysis of the binding properties of antimicrobial indium(III)-porphyrin, which bears a much larger metal ion than the iron(III) of the natural ligand heme. The results demonstrate that the NEAT3 receptor recognizes the In(III)-containing PPIX in a manner very similar to that of heme. Site-directed mutagenesis identifies Tyr642 as the central element in the recognition mechanism as suggested from the crystal structures. Importantly, the NEAT3 receptor possesses the remarkable ability to capture dimers of metalloporphyrin. Molecular dynamics simulations reveal that IsdH-NEAT3 does not require conformational changes, or large rearrangements of the residues within its binding site, to accommodate the much larger (heme)2 ligand. We discuss the implications of these findings for the design of potent inhibitors against this family of key receptors of S. aureus.

PubMed: 23649633
DOI: 10.1002/pro.2276

Experimental method

X-RAY DIFFRACTION (2.8 Å)