9nsj | pdb_00009nsj

Finding the exit route of hydrogen peroxide from the manganese superoxide dismutase (MnSOD) active site

spinqualitylabelsall models 9nsj, resolution 1.33Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9nsj is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.33Å Ligands: K, MN, PEO, PO4 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Disease SODM_HUMAN Genetic variation in SOD2 is associated with susceptibility to microvascular complications of diabetes type 6 (MVCD6) [MIM:612634. These are pathological conditions that develop in numerous tissues and organs as a consequence of diabetes mellitus. They include diabetic retinopathy, diabetic nephropathy leading to end-stage renal disease, and diabetic neuropathy. Diabetic retinopathy remains the major cause of new-onset blindness among diabetic adults. It is characterized by vascular permeability and increased tissue ischemia and angiogenesis. Function SODM_HUMAN Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems. Publication Abstract from PubMed Mitochondrial manganese superoxide dismutase (MnSOD) converts superoxide (O(2) (●-)) into hydrogen peroxide (H(2)O(2)) and molecular oxygen (O(2)), serving as a key defense against oxidative damage. Despite decades of research, the product exit pathway in MnSOD remains understudied, due to the enzyme's rapid, diffusion-limited catalysis. Here, we structurally characterize the H(2)O(2) exit route in MnSOD, using a kinetically impaired Gln143Asn variant. In the wild-type enzyme, Gln143 participates in proton transfer reactions with the Mn(3+)-bound solvent (WAT1) to drive redox cycling of the metal for effective O(2) (●-) dismutation. Substitution with Asn disrupts the proton transfer, as Asn is too far away from WAT1, and stalls redox transitions in the Gln143Asn variant. This generates a "slow-motion" version of catalysis that maximizes the likelihood of trapping and visualizing the H(2)O(2) exit process with improved experimental control. Results reveal that the Gln143Asn substitution introduces a cavity, which permits conformational flexibility of Tyr34, that would be sterically disallowed in the wild-type. This flexibility of Tyr34 narrows the gateway between the second-shell residues Tyr34 and His30 and restricts diffusion of the Mn(2+)-bound peroxide out of the metal's primary coordination sphere. Also, peroxide occupies a secondary binding site between Tyr34 and His30. The combination of Tyr34 flexibility and the enzyme's inability to redox cycle causes a "traffic jam" of peroxide at the mouth of the blocked gateway. Overall, our findings provide novel structural insight into the mechanism of product trafficking in MnSOD and underscore the utility of rational mutagenesis in accessing elusive mechanistic states. Mapping the Exit Route of Hydrogen Peroxide From the Manganese Superoxide Dismutase (MnSOD) Active Site.,Dasgupta M, Slobodnik K, Cone EA, Azadmanesh J, Kroll T, Borgstahl GEO bioRxiv [Preprint]. 2025 Jul 19:2025.07.17.665311. doi: , 10.1101/2025.07.17.665311. PMID:40791321 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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