9NR0

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

Summary for 9NR0

• Entry DOI: 10.2210/pdb9nr0/pdb
• Descriptor: Superoxide dismutase [Mn], mitochondrial, POTASSIUM ION, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: manganese superoxide dismutase, metalloenzyme, peroxide, metal binding protein, oxidoreductase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 45972.41

Authors

Dasgupta, M.,Borgstahl, G.E.O. (deposition date: 2025-03-13, release date: 2025-08-27, Last modification date: 2025-11-12)

Primary citation

Dasgupta, M.,Slobodnik, K.,Cone, E.A.,Azadmanesh, J.,Kroll, T.,Borgstahl, G.E.O.
High-resolution X-ray structure of Gln143Asn manganese superoxide dismutase captures multiple hydrogen peroxide-binding sites.
Acta Crystallogr.,Sect.F, 81:467-477, 2025

PubMed Abstract: Human mitochondrial manganese superoxide dismutase (MnSOD) converts superoxide into hydrogen peroxide and molecular oxygen, serving as a key defence against oxidative damage. Despite extensive studies, the full structural characterization of HO-binding sites in MnSOD remains largely unexplored. Previous HO-soaked MnSOD structures have identified two distinct HO-binding sites: one directly ligated to the catalytic manganese (LIG position) and another at the active-site gateway (PEO position) between the second-shell residues Tyr34 and His30. In this study, a kinetically impaired Gln143Asn MnSOD variant is used to trap and explore additional HO-binding sites beyond the second-shell solvent gate. In the wild-type enzyme, Gln143 mediates proton transfers with the manganese-bound solvent (WAT1) to drive redox cycling of the metal, which is necessary for effective superoxide dismutation. Substitution with Asn stalls catalysis because the increased distance from WAT1 disrupts critical proton-coupled electron-transfer (PCET) events, and the redox cycling of the active-site metal is impaired. This, in turn, stalls the electrostatic cycling of positive charge on the enzyme surface and enhances the likelihood of trapping transient HO-bound states in this variant. The results reveal several HO molecules leading up to the active site, in addition to the canonical LIG and PEO positions.

PubMed: 41128288
DOI: 10.1107/S2053230X25009045

Experimental method

X-RAY DIFFRACTION (1.55 Å)