3F7K

X-ray Crystal Structure of an Alvinella pompejana Cu,Zn Superoxide Dismutase- Hydrogen Peroxide Complex

Summary for 3F7K

• Entry DOI: 10.2210/pdb3f7k/pdb
• Related: 3F7L
• Descriptor: Copper,Zinc Superoxide Dismutase, COPPER (I) ION, COPPER (II) ION, ... (8 entities in total)
• Functional Keywords: oxidoreductase (superoxide acceptor), superoxide dismutase, greek key beta-barrel, amyloid filaments, als, fals, lou gehrig's disease, amyotrophic lateral sclerosis, alvinella pompejana, pompeii worm, eukaryotic thermophile, thermostable protein, hydrogen peroxide product complex, oxidoreductase
• Biological source: Alvinella pompejana
• Total number of polymer chains: 1
• Total formula weight: 16356.25

Authors

Shin, D.S.,DiDonato, M.,Barondeau, D.P.,Getzoff, E.D.,Tainer, J.A. (deposition date: 2008-11-09, release date: 2009-02-10, Last modification date: 2024-10-30)

Primary citation

Shin, D.S.,Didonato, M.,Barondeau, D.P.,Hura, G.L.,Hitomi, C.,Berglund, J.A.,Getzoff, E.D.,Cary, S.C.,Tainer, J.A.
Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis.
J.Mol.Biol., 385:1534-1555, 2009

PubMed Abstract: Prokaryotic thermophiles supply stable human protein homologs for structural biology; yet, eukaryotic thermophiles would provide more similar macromolecules plus those missing in microbes. Alvinella pompejana is a deep-sea hydrothermal-vent worm that has been found in temperatures averaging as high as 68 degrees C, with spikes up to 84 degrees C. Here, we used Cu,Zn superoxide dismutase (SOD) to test if this eukaryotic thermophile can provide insights into macromolecular mechanisms and stability by supplying better stable mammalian homologs for structural biology and other biophysical characterizations than those from prokaryotic thermophiles. Identification, cloning, characterization, X-ray scattering (small-angle X-ray scattering, SAXS), and crystal structure determinations show that A. pompejana SOD (ApSOD) is superstable, homologous, and informative. SAXS solution analyses identify the human-like ApSOD dimer. The crystal structure shows the active site at 0.99 A resolution plus anchoring interaction motifs in loops and termini accounting for enhanced stability of ApSOD versus human SOD. Such stabilizing features may reduce movements that promote inappropriate intermolecular interactions, such as amyloid-like filaments found in SOD mutants causing the neurodegenerative disease familial amyotrophic lateral sclerosis or Lou Gehrig's disease. ApSOD further provides the structure of a long-sought SOD product complex at 1.35 A resolution, suggesting a unified inner-sphere mechanism for catalysis involving metal ion movement. Notably, this proposed mechanism resolves apparent paradoxes regarding electron transfer. These results extend knowledge of SOD stability and catalysis and suggest that the eukaryote A. pompejana provides macromolecules highly similar to those from humans, but with enhanced stability more suitable for scientific and medical applications.

PubMed: 19063897
DOI: 10.1016/j.jmb.2008.11.031

Experimental method

X-RAY DIFFRACTION (1.35 Å)