9QE3
Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate at pH 5.5
Summary for 9QE3
| Entry DOI | 10.2210/pdb9qe3/pdb |
| Descriptor | Myeloperoxidase inhibitor SPIN, Myeloperoxidase light chain, Myeloperoxidase heavy chain, ... (9 entities in total) |
| Functional Keywords | innate immunity, enzyme substrate complex, inhibitor, oxidoreductase |
| Biological source | Staphylococcus aureus More |
| Total number of polymer chains | 6 |
| Total formula weight | 153623.78 |
| Authors | |
| Primary citation | Leitgeb, U.,Crha, R.,Fegerl, I.,Furtmuller, P.G.,Oostenbrink, C.,Pfanzagl, V. Halide binding by myeloperoxidase is regulated by access channel dynamics and charge interactions. Int.J.Biol.Macromol., :148038-148038, 2025 Cited by PubMed Abstract: The heme enzyme myeloperoxidase is a key player in the innate immune defense. It uses hydrogen peroxide to produce bactericidal hypohalous acids from (pseudo)halides, foremost chloride, and thiocyanate in the neutrophil phagosome. However, the available structural data on the halide-binding site, the marked pH dependence of halide oxidation, and the atypical pK of an active-site histidine 261 fail to fully account for the mechanism of halide oxidation by myeloperoxidase. In the present study, crystal structures of myeloperoxidase-halide complexes show that halides can integrate into the hydrogen-bonding network formed by conserved water molecules, without directly interacting with the deprotonated histidine at both acidic and neutral pH. Molecular dynamics simulations reveal that protonation of histidine 261 decreases active site rigidity and increases the flexibility of arginine 405. Together with the terminal residues of the myeloperoxidase heavy and light chains, arginine 405 contributes to halide transport into the active site. Kinetic analyses and simulations further demonstrate that sodium ions play a critical role as charge shields, enabling halides to traverse the negatively charged access channel, which represents a key bottleneck for halide binding. Thus, halide access to the active site is governed by a complex interplay of electrostatic interactions involving both solvent ions and charged amino acid residues. PubMed: 41043752DOI: 10.1016/j.ijbiomac.2025.148038 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.06 Å) |
Structure validation
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