The structure of the Caenorhabditis elegans manganese superoxide dismutase MnSOD‐3‐azide complex

Abstract

C. elegans MnSOD-3 has been implicated in the longevity pathway and its mechanism of catalysis is relevant to the aging process and carcinogenesis. The structures of MnSOD-3 provide unique crystallographic evidence of a dynamic region of the tetrameric interface (residues 41-54). We have determined the structure of the MnSOD-3-azide complex to 1.77-Å resolution. Analysis of this complex shows that the substrate analog, azide, binds end-on to the manganese center as a sixth ligand and that it ligates directly to a third and new solvent molecule also positioned within interacting distance to the His30 and Tyr34 residues of the substrate access funnel. This is the first structure of a eukaryotic MnSOD-azide complex that demonstrates the extended, uninterrupted hydrogen-bonded network that forms a proton relay incorporating three outer sphere solvent molecules, the substrate analog, the gateway residues, Gln142, and the solvent ligand. This configuration supports the formation and release of the hydrogen peroxide product in agreement with the 5-6-5 catalytic mechanism for MnSOD. The high product dissociation constant k 4 of MnSOD-3 reflects low product inhibition making this enzyme efficient even at high levels of superoxide.

A Single Mutation is Sufficient to Modify the Metal Selectivity and Specificity of a Eukaryotic Manganese Superoxide Dismutase to Encompass Iron

“…As previously reported, there is evidence from the electron density maps of some flexibility in the region of chain A Q40‐A59 with the structure occupying two alternate conformations 11. The predominant density observed was similar to the configuration of 4X9Q.…”

“…We have previously reported the structure of the wild‐type MnSOD‐3 from C.elegans (PDB: 3DC5 and 4X9Q) and its complex with the substrate analogue, azide (PDB: 5AG2) 10, 11. These data have reinforced our understanding and the importance of the extensive hydrogen bonded network formed between the external solvent, a number of significant residues and the metal in the active site of the enzyme.…”

Substrate-analog binding and electrostatic surfaces of human manganese superoxide dismutase

“…WAT2 of both structures and both chains has a B value near 30 Å 2 compared to the average solvent values of 26 and 24 Å 2 of the native and azide structures, respectively. While WAT2 is the least-defined atom of the hydrogen bond network in our structures, its higher B factor may be reflective of a dynamic nature during catalysis, and the same feature has been observed in the 100 K MnSOD structure from C. elegans (Hunter et al, 2015). The 100 K structure from E. coli reveals a well-defined WAT2, with an average B value of 18 Å 2 between the four chains among an average solvent value of 28 Å 2 (Borgstahl et al, 2000).…”

“…The azide ion is a potent competitive inhibitor and is frequently assumed to act as a substrate analog to superoxide (Bull and Fee, 1985b; Misra and Fridovich, 1978). Published structures of azide in complex with MnSOD have been solved at room temperature for Thermus thermophilus (PDB entry 1MNG ) and cryocooled for Caenorhabditis elegans (PDB entry 5AG2 ) (Hunter et al, 2015; Lah et al, 1995). Both show the azide binding end-on to the manganese ion at the sixth coordinate.…”

Antioxidation and anti-ageing activities of different stereoisomeric astaxanthin in vitro and in vivo

“…Effects of different stereoisomers of AST on enzyme activity and SOD-3 expression SOD and CAT play important roles for detoxification of ROS in C. elegans (Hunter et al, 2015;Taub, Lau, & Ma, 1999). We propose that AST may either directly scavenge free radicals, similar to several key antioxidant enzymes (SOD and CAT), or exert positive regulatory effect on these enzymes.…”