title: Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5Å resolution.
abstract: The second step in the biosynthesis of the 22nd genetically encoded amino acid pyrrolysine (Pyl) is catalyzed by PylC that forms the pseudopeptide L-lysine-N(ε)-3R-methyl-D-ornithine. Here, we present six crystal structures of the monomeric active ligase in complex with substrates, reaction intermediates, and products including ATP, the non-hydrolyzable ATP analogue 5'-adenylyl-β-γ-imidodiphosphate, ADP, D-ornithine (D-Orn), L-lysine (Lys), phosphorylated D-Orn, L-lysine-N(ε)-D-ornithine, inorganic phosphate, carbonate, and Mg(2+). The overall structure of PylC reveals similarities to the superfamily of ATP-grasp enzymes; however, there exist unique structural and functional features for a topological control of successive substrate entry and product release. Furthermore, the presented high-resolution structures provide detailed insights into the reaction mechanism of isopeptide bond formation starting with phosphorylation of D-Orn by transfer of a phosphate moiety from activated ATP. The binding of Lys to the enzyme complex is then followed by an S(N)2 reaction resulting in L-lysine-N(ε)-D-ornithine and inorganic phosphate. Surprisingly, PylC harbors two adenine nucleotides bound at the active site, what has not been observed in any ATP-grasp protein analyzed to date. Whereas one ATP molecule is involved in catalysis, the second adenine nucleotide functions as a selective anchor for the C- and N-terminus of the Lys substrate and is responsible for protein stability as shown by mutagenesis.
authors.affiliation: Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany.
authors.forename: Felix
authors.initials: F
authors.lastname: Quitterer
authors.forename: Anja
authors.initials: A
authors.lastname: List
authors.forename: Philipp
authors.initials: P
authors.lastname: Beck
authors.forename: Adelbert
authors.initials: A
authors.lastname: Bacher
authors.forename: Michael
authors.initials: M
authors.lastname: Groll
mesh_terms: D000595:Amino Acid Sequence; D053898:Biosynthetic Pathways; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D008239:Lysine / Q000031:analogs & derivatives* / Q000096:biosynthesis; D017021:Methanosarcina barkeri / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010770:Phosphotransferases / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D010770:Phosphotransferases; C456839:pyrrolysine; D008239:Lysine