The 1.23 Å structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link

The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Å resolution. PPLO, a copper amine oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor, differs from most other members of the CuAO enzyme family in having the ability to oxidize the side chain of lysine residues in a polypeptide. In the asymmetric unit of the crystals, the structure analysis has located residues 43-779 of the polypeptide chain, seven carbohydrate residues, the active-site Cu atom, an imidazole molecule bound at the active site, two buried Ca²⁺ ions, five surface Mg²⁺ ions, five surface Cl^- ions and 1045 water molecules. The crystallographic residuals are R = 0.112 and R_free = 0.146. The TPQ cofactor and several other active-site residues are poorly ordered, in contrast to the surrounding well ordered structure. A covalent cross-link is observed between two lysine residues, Lys778 and Lys66. The cross-link is likely to have been formed by the oxidation of Lys778 followed by a spontaneous reaction with Lys66. The link is modelled as dehydrolysinonorleucine.