5YU3

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

Summary for 5YU3

• Entry DOI: 10.2210/pdb5yu3/pdb
• Descriptor: Lysine cyclodeaminase, SODIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (5 entities in total)
• Functional Keywords: l-lysine cyclodeaminase, streptomyces pristinaespiralis, lyase
• Biological source: Streptomyces pristinaespiralis
• Total number of polymer chains: 4
• Total formula weight: 149555.63

Authors

Min, K.J.,Yoon, H.J.,Matsuura, A.,Kim, Y.H.,Lee, H.H. (deposition date: 2017-11-20, release date: 2018-05-02, Last modification date: 2024-03-27)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.79 Å)