5YU4

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

5YU4 の概要

• エントリーDOI: 10.2210/pdb5yu4/pdb
• 分子名称: Lysine cyclodeaminase, SODIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• 機能のキーワード: l-lysine cyclodeaminase, streptomyces pristinaespiralis, lyase
• 由来する生物種: Streptomyces pristinaespiralis
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 149567.65

構造登録者

Min, K.J.,Yoon, H.J.,Matsuura, A.,Kim, Y.H.,Lee, H.H. (登録日: 2017-11-20, 公開日: 2018-05-02, 最終更新日: 2024-03-27)

主引用文献

Min, K.,Yoon, H.J.,Matsuura, A.,Kim, Y.H.,Lee, H.H.
Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
Mol. Cells, 41:331-341, 2018

PubMed Abstract: L-pipecolic acid is a non-protein amino acid commonly found in plants, animals, and microorganisms. It is a well-known precursor to numerous microbial secondary metabolites and pharmaceuticals, including anticancer agents, immunosuppressants, and several antibiotics. Lysine cyclodeaminase (LCD) catalyzes β-deamination of L-lysine into L-pipecolic acid using β-nicotinamide adenine dinucleotide as a cofactor. Expression of a human homolog of LCD, μ-crystallin, is elevated in prostate cancer patients. To understand the structural features and catalytic mechanisms of LCD, we determined the crystal structures of LCD (SpLCD) in (i) a binary complex with NAD, (ii) a ternary complex with NAD and L-pipecolic acid, (iii) a ternary complex with NAD and L-proline, and (iv) a ternary complex with NAD and L-2,4-diamino butyric acid. The overall structure of SpLCD was similar to that of ornithine cyclodeaminase from . In addition, SpLCD recognized L-lysine, L-ornithine, and L-2,4-diamino butyric acid despite differences in the active site, including differences in hydrogen bonding by Asp236, which corresponds with Asp228 from ornithine cyclodeaminase. The substrate binding pocket of SpLCD allowed substrates smaller than lysine to bind, thus enabling binding to ornithine and L-2,4-diamino butyric acid. Our structural and biochemical data facilitate a detailed understanding of substrate and product recognition, thus providing evidence for a reaction mechanism for SpLCD. The proposed mechanism is unusual in that NAD is initially converted into NADH and then reverted back into NAD at a late stage of the reaction.

PubMed: 29629557
DOI: 10.14348/molcells.2018.2313

実験手法

X-RAY DIFFRACTION (2.144 Å)