Paper Citing NAMD - Abstract
Osipiuk, Jerzy; Mulligan, Rory; Bargassa, Monireh; Hamilton, John E.; Cunningham, Mark A.; Joachimiak, Andrzej
Characterization of Member of DUF1888 Protein Family, Self-cleaving and Self-assembling Endopeptidase
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:19452-19461, JUN 1 2012
The crystal structure of SO1698 protein from Shewanella oneidensis was determined by a SAD method and refined to 1.57 angstrom. The structure is a beta sandwich that unexpectedly consists of two polypeptides; the N-terminal fragment includes residues 1-116, and the C-terminal one includes residues 117-125. Electron density also displayed the Lys-98 side chain covalently linked to Asp-116. The putative active site residues involved in self-cleavage were identified; point mutants were produced and characterized structurally and in a biochemical assay. Numerical simulations utilizing molecular dynamics and hybrid quantum/classical calculations suggest a mechanism involving activation of a water molecule coordinated by a catalytic aspartic acid.
