title: The 1.23 Angstrom structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link.
abstract: The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Angstrom 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 Ca(2+) ions, five surface Mg(2+) 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.
authors.affiliation: School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.
authors.forename: Anthony P
authors.initials: AP
authors.lastname: Duff
authors.forename: Aina E
authors.initials: AE
authors.lastname: Cohen
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Ellis
authors.forename: Kim
authors.initials: K
authors.lastname: Hilmer
authors.forename: David B
authors.initials: DB
authors.lastname: Langley
authors.forename: David M
authors.initials: DM
authors.lastname: Dooley
authors.forename: Hans C
authors.initials: HC
authors.lastname: Freeman
authors.forename: J Mitchell
authors.initials: JM
authors.lastname: Guss
mesh_terms: D001665:Binding Sites; D003300:Copper / Q000737:chemistry; D003432:Cross-Linking Reagents / Q000494:pharmacology; D018360:Crystallography, X-Ray / Q000379:methods*; D004151:Dipeptides / Q000737:chemistry; D006031:Glycosylation; D007477:Ions; D008239:Lysine / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D010843:Pichia / Q000201:enzymology*; D011487:Protein Conformation; D008249:Protein-Lysine 6-Oxidase / Q000737:chemistry*
chemical_list: D003432:Cross-Linking Reagents; D004151:Dipeptides; D007477:Ions; C007238:dehydrolysylnorleucine; D003300:Copper; D008249:Protein-Lysine 6-Oxidase; D008239:Lysine