9M59

Cu/Zn-superoxide dismutase from Deinococcus radiodurans (Calcium-bound)

Summary for 9M59

• Entry DOI: 10.2210/pdb9m59/pdb
• Descriptor: Superoxide dismutase (SodC), Cu-Zn family, ZINC ION, COPPER (II) ION, ... (7 entities in total)
• Functional Keywords: superoxide dismutase, beta-propeller lactonase, metal binding protein
• Biological source: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Total number of polymer chains: 2
• Total formula weight: 93580.00

Authors

Muraki, N.,Megata, M.,Furukawa, Y. (deposition date: 2025-03-05, release date: 2025-09-24)

Primary citation

Furukawa, Y.,Megata, M.,Shintani, A.,Sue, K.,Morohoshi, T.,Akutsu, M.,Muraki, N.
Cu/Zn-superoxide dismutase naturally fused with a beta-propeller lactonase in Deinococcus radiodurans.
J.Biol.Chem., 301:110499-110499, 2025

PubMed Abstract: Cu/Zn-superoxide dismutase (Cu/Zn-SOD) is an antioxidant enzyme widely present across species; however, the structural diversity and physiological roles of Cu/Zn-SOD are yet to be fully uncovered. Here, we show a unique type of Cu/Zn-SOD from Deinococcus radiodurans (DrSOD) with an additional β-propeller domain. Our structural analysis of DrSOD revealed a typical bacterial Cu/Zn-SOD domain, binding both a copper and zinc ion, alongside a six-bladed β-propeller domain coordinating a calcium ion. DrSOD was indeed expressed in D. radiodurans, but its deletion did not lead to any noticeable changes in resistance to DNA-damaging stresses, a characteristic trait of D. radiodurans. Despite this, the Cu/Zn-SOD domain retained superoxide dismutase activity, and the β-propeller domain was found to exhibit a lactonase activity specifically for hydrolyzing 2-coumaranone. Taken together, while the precise physiological role of DrSOD needs to be further investigated, our findings here reveal a unique multi-functional enzyme architecture, expanding the known structural diversity of Cu/Zn-SODs.

PubMed: 40684944
DOI: 10.1016/j.jbc.2025.110499

Experimental method

X-RAY DIFFRACTION (1.9 Å)