1KMG

The Solution Structure Of Monomeric Copper-free Superoxide Dismutase

Summary for 1KMG

• Entry DOI: 10.2210/pdb1kmg/pdb
• Descriptor: Superoxide Dismutase, ZINC ION (2 entities in total)
• Functional Keywords: oxidoreductase, superoxide dismutase, copper-free protein, beta-barrel
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: P00441
• Total number of polymer chains: 1
• Total formula weight: 15897.86

Authors

Banci, L.,Bertini, I.,Cantini, F.,D'Onofrio, M.,Viezzoli, M.S. (deposition date: 2001-12-15, release date: 2002-10-02, Last modification date: 2024-11-13)

Primary citation

Banci, L.,Bertini, I.,Cantini, F.,D'Onofrio, M.,Viezzoli, M.S.
Structure and dynamics of copper-free SOD: The protein before binding copper.
Protein Sci., 11:2479-2492, 2002

PubMed Abstract: The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q). About 93% of carbon atoms, 95% of nitrogen atoms, and 96% of the protons were assigned. A total of 2467 meaningful NOEs and 170 dihedral angles provided a family of 35 conformers with RMSD values of 0.76 +/- 0.09 A for the backbone and 1.22 +/- 0.13 A for all heavy atoms. The secondary structure elements, connected by loops, produce the typical superoxide dismutase Greek key fold, formed by an eight-stranded beta-barrel. The comparison with the copper-bound monomeric and dimeric structures shows that the metal ligands have a conformation very close to that of the copper-bound forms. This feature indicates that the copper-binding site is preorganized and well ordered also in the absence of the copper ion. The active-site channel shows a sizable increase in width, achieving a suitable conformation to receive the copper ion. The histidines ring NH resonances that bind the copper ion and the region around the active-site channel experience, as found from (15)N relaxation studies, conformational exchange processes. The increased width of the channel and the higher mobility of the histidine rings of the copper site in the copper-free form with respect to the holoprotein is discussed in terms of the process of copper insertion.

PubMed: 12237469
DOI: 10.1110/ps.0210802

Experimental method

SOLUTION NMR