6ITZ

Peroxiredoxin from Thermococcus kodakaraensis

Summary for 6ITZ

• Entry DOI: 10.2210/pdb6itz/pdb
• Descriptor: Peroxiredoxin (1 entity in total)
• Functional Keywords: hydrogen peroxide, oxidoreductase, dodecamer
• Biological source: Thermococcus kodakarensis KOD1
• Total number of polymer chains: 2
• Total formula weight: 49354.73

Authors

Nakamura, T.,Himiyama, T. (deposition date: 2018-11-27, release date: 2019-03-06, Last modification date: 2024-10-23)

Primary citation

Himiyama, T.,Oshima, M.,Uegaki, K.,Nakamura, T.
Distinct molecular assembly of homologous peroxiredoxins from Pyrococcus horikoshii and Thermococcus kodakaraensis.
J.Biochem., 166:89-95, 2019

PubMed Abstract: Peroxiredoxins from Pyrococcus horikoshii (PhPrx) and Thermococcus kodakaraensis (TkPrx) are highly homologous proteins sharing 196 of the 216 residues. We previously reported a pentagonal ring-type decameric structure of PhPrx. Here, we present the crystal structure of TkPrx. Despite their homology, unlike PhPrx, the quaternary structure of TkPrx was found to be a dodecamer comprised of six homodimers arranged in a hexagonal ring-type assembly. The possibility of the redox-dependent conversion of the molecular assembly, which had been observed in PhPrx, was excluded for TkPrx based on the crystal structure of a mutant in which all of the cysteine residues were substituted with serine. The monomer structures of the dodecameric TkPrx and decameric PhPrx coincided well, but there was a slight difference in the relative orientation of the two domains. Molecular assembly of PhPrx and TkPrx in solution evaluated by gel-filtration chromatography was consistent with the crystallographic results. For both PhPrx and TkPrx, the gel-filtration elution volume slightly increased with a decrease in the protein concentration, suggesting the existence of an equilibrium state between the decameric/dodecameric ring and lower-order assembly. This structural assembly difference between highly homologous Prxs suggests a significant influence of quaternary structure on function, worthy of further exploration.

PubMed: 30796432
DOI: 10.1093/jb/mvz013

Experimental method

X-RAY DIFFRACTION (2.96 Å)