4FFN

PylC in complex with D-ornithine and AMPPNP

Summary for 4FFN

• Entry DOI: 10.2210/pdb4ffn/pdb
• Related: 2YZG 3OUZ 4FFL 4FFM 4FFO 4FFP 4FFR
• Descriptor: PylC, D-ORNITHINE, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (6 entities in total)
• Functional Keywords: amino acid, biosynthesis of pyrrolysine, isopeptide bond formation, atp-grasp fold, ligase, atp-binding, l-lysine and 3r-methyl-d-ornithine, cytosol, ligase-substrate complex, ligase/substrate
• Biological source: Methanosarcina barkeri
• Total number of polymer chains: 1
• Total formula weight: 42058.18

Authors

Quitterer, F.,List, A.,Beck, P.,Bacher, A.,Groll, M. (deposition date: 2012-06-01, release date: 2012-09-19, Last modification date: 2024-02-28)

Primary citation

Quitterer, F.,List, A.,Beck, P.,Bacher, A.,Groll, M.
Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
J.Mol.Biol., 424:270-282, 2012

PubMed 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.

PubMed: 22985965
DOI: 10.1016/j.jmb.2012.09.007

Experimental method

X-RAY DIFFRACTION (2.4 Å)