Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains

Post-translational modification of proteins by covalent attachment of ubiquitin regulates diverse cellular events. A Lys48-linked polyubiquitin chain is formed via an isopeptide bond between Lys48 and the C-terminal Gly76 of different ubiquitin molecules. The chain is attached to a lysine residue of a substrate protein, which leads to proteolytic degradation of the protein by the 26S proteasome. In order to reveal the chain-length-dependent higher order structures of polyubiquitin chains, Lys48-linked polyubiquitin chains were synthesized enzymatically on a large scale and the chains were separated according to chain length by cation-exchange column chromatography. Subsequently, crystallization screening was performed using the hanging-drop vapour-diffusion method, from which crystals of tetraubiquitin, hexaubiquitin and octaubiquitin chains were obtained. The crystals of the tetraubiquitin and hexaubiquitin chains diffracted to 1.6 and 1.8 angstrom resolution, respectively. The tetraubiquitin crystals belonged to space group C222(1), with unit-cell parameters a = 58.795, b = 76.966, c = 135.145 angstrom. The hexaubiquitin crystals belonged to space group P2(1), with unit-cell parameters a = 51.248, b = 102.668, c = 51.161 angstrom. Structural analysis by molecular replacement is in progress.