7YPP

Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.

Summary for 7YPP

• Entry DOI: 10.2210/pdb7ypp/pdb
• Descriptor: Superoxide dismutase [Cu-Zn], COPPER (II) ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: superoxide dismutase, sod, cuznsod, ramazzottius varieornatus, metal binding protein, oxidoreductase
• Biological source: Ramazzottius varieornatus
• Total number of polymer chains: 6
• Total formula weight: 121632.79

Authors

Sim, K.-S.,Fukuda, Y.,Inoue, T. (deposition date: 2022-08-04, release date: 2023-07-26, Last modification date: 2024-10-16)

Primary citation

Sim, K.S.,Inoue, T.
Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.
Acta Crystallogr.,Sect.F, 79:169-179, 2023

PubMed Abstract: Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.

PubMed: 37358501
DOI: 10.1107/S2053230X2300523X

Experimental method

X-RAY DIFFRACTION (2.2 Å)