Selective binding of antimicrobial porphyrins to the heme‐receptor IsdH‐NEAT3 of Staphylococcus aureus

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.

Novel Mechanism of Hemin Capture by Hbp2, the Hemoglobin-binding Hemophore from Listeria monocytogenes

“…The first tyrosine directly coordinates the metal in hemin, whereas the second tyrosine stabilizes the positioning of the coordinating tyrosine through side chain-side chain hydrogen bonding. Both of these interactions are important as tyrosine mutation significantly reduces affinity (37). Interestingly, our hemin binding measurements indicate that the central NEAT domain within Hbp2 (Hbp2 N2 ) interacts with hemin with high affinity even though it lacks the second tyrosine in the YXXXY motif (in Hbp2 N2 the motif is replaced with YXXXA).…”

The structure of haemoglobin bound to the haemoglobin receptor IsdH fromStaphylococcus aureusshows disruption of the native α-globin haem pocket

“…Other contacts between IsdH N3 or IsdH Linker and Hb involve regions of with native structure; these contacts may brace the IsdH N3 domain against stable regions of to facilitate conformational exchange of residues surrounding the haem. Structures of the free IsdH N3 domain in the apo and haem-bound states show that the Tyr642 -hairpin also undergoes a small movement upon haem ligation (Vu et al, 2013;Moriwaki et al, 2011;Watanabe et al, 2008), suggesting that concerted changes in the structure of the IsdH N3 Tyr642 -hairpin and the Hb F helix/FG corner could accompany haem transfer.…”

“…IsdA/B/C/H proteins are all anchored via a C-terminal amide linkage to the peptide cross-bridge of the cell-wall peptidoglycan (Mazmanian et al, 2002), and all bind haem via a near iron transporter (NEAT) domain, which is an antiparallel -barrel domain of 15-20 kDa with an immunoglobulin-like topology (Vu et al, 2013;Moriwaki et al, 2011;Watanabe et al, 2008;Pilpa et al, 2006;Grigg et al, 2007bGrigg et al, , 2011Villareal et al, 2008;Sharp et al, 2007;Gaudin et al, 2011). Related NEAT domains that function in haem acquisition have been described in Streptococcus pyogenes (Aranda et al, 2007), Listeria monocytogenes (Malmirchegini et al, 2014) and Bacillus anthracis (Ekworomadu et al, 2012;Honsa et al, 2013), highlighting the importance of NEAT domains for iron uptake in Gram-positive pathogens.…”

Rapid Heme Transfer Reactions between NEAr Transporter Domains of Staphylococcus aureus: A Theoretical Study Using QM/MM and MD Simulations

“…The primary tyrosine residues IsdH–Tyr642, IsdA–Tyr166, and IsdC–Tyr132 were deprotonated. The force field parameters for heme and the primary tyrosine residues of the donor proteins (IsdH-N3 in the IsdH-N3•heme•IsdA-N system and IsdA-N in the IsdA-N•heme•IsdC-N system) that coordinate heme iron are described in our previous report [ 36 ]. However, the primary tyrosine residues of the acceptor proteins (IsdA-N in the IsdH-N3•heme•IsdA-N system and IsdC-N in the IsdA-N•heme•IsdC-N system) were not coordinated with heme iron during MD simulations, and alternative partial charges were prepared for these residues.…”