1Q0D

Crystal structure of Ni-containing superoxide dismutase with Ni-ligation corresponding to the oxidized state

Summary for 1Q0D

• Entry DOI: 10.2210/pdb1q0d/pdb
• Related: 1Q0F 1Q0G 1Q0K 1Q0M
• Descriptor: Superoxide dismutase [Ni], SULFATE ION, NICKEL (III) ION, ... (4 entities in total)
• Functional Keywords: homohexamer of four-helix bundles, oxidoreductase
• Biological source: Streptomyces seoulensis
• Cellular location: Cytoplasm: P80734
• Total number of polymer chains: 12
• Total formula weight: 160736.70

Authors

Wuerges, J.,Lee, J.-W.,Yim, Y.-I.,Yim, H.-S.,Kang, S.-O.,Djinovic Carugo, K. (deposition date: 2003-07-16, release date: 2004-05-18, Last modification date: 2024-02-14)

Primary citation

Wuerges, J.,Lee, J.-W.,Yim, Y.-I.,Yim, H.-S.,Kang, S.-O.,Djinovic Carugo, K.
Crystal structure of nickel-containing superoxide dismutase reveals another type of active site
Proc.Natl.Acad.Sci.USA, 101:8569-8574, 2004

PubMed Abstract: Superoxide dismutases (SODs, EC 1.15.1.1) are ubiquitous enzymes that efficiently catalyze the dismutation of superoxide radical anions to protect biological molecules from oxidative damage. The crystal structure of nickel-containing SOD (NiSOD) from Streptomyces seoulensis was determined for the resting, x-ray-reduced, and thiosulfate-reduced enzyme state. NiSOD is a homohexamer consisting of four-helix-bundle subunits. The catalytic center resides in the N-terminal active-site loop, where a Ni(III) ion is coordinated by the amino group of His-1, the amide group of Cys-2, two thiolate groups of Cys-2 and Cys-6, and the imidazolate of His-1 as axial ligand that is lost in the chemically reduced state as well as after x-ray-induced reduction. This structure represents a third class of SODs concerning the catalytic metal species, subunit structure, and oligomeric organization. It adds a member to the small number of Ni-metalloenzymes and contributes with its Ni(III) active site to the general understanding of Ni-related biochemistry. NiSOD is shown to occur also in bacteria other than Streptomyces and is predicted to be present in some cyanobacteria.

PubMed: 15173586
DOI: 10.1073/pnas.0308514101

Experimental method

X-RAY DIFFRACTION (2.2 Å)