8KDL

Crystal structure of LmbF in complex with PLP

8KDL の概要

• エントリーDOI: 10.2210/pdb8kdl/pdb
• 分子名称: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme, GLYCEROL (3 entities in total)
• 機能のキーワード: lincomycin, plp, biosynthesis, lyase
• 由来する生物種: Streptomyces lincolnensis
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 96930.82

構造登録者

Mori, T.,Lyu, S.,Kadlcik, S.,Abe, I. (登録日: 2023-08-09, 公開日: 2024-08-14, 最終更新日: 2025-02-26)

主引用文献

Mori, T.,Moriwaki, Y.,Sakurada, K.,Lyu, S.,Kadlcik, S.,Janata, J.,Mazumdar, A.,Koberska, M.,Terada, T.,Kamenik, Z.,Abe, I.
Molecular basis for the diversification of lincosamide biosynthesis by pyridoxal phosphate-dependent enzymes.
Nat.Chem., 17:256-264, 2025

PubMed Abstract: The biosynthesis of the lincosamide antibiotics lincomycin A and celesticetin involves the pyridoxal-5'-phosphate (PLP)-dependent enzymes LmbF and CcbF, which are responsible for bifurcation of the biosynthetic pathways. Despite recognizing the same S-glycosyl-L-cysteine structure of the substrates, LmbF catalyses thiol formation through β-elimination, whereas CcbF produces S-acetaldehyde through decarboxylation-coupled oxidative deamination. The structural basis for the diversification mechanism remains largely unexplored. Here we conduct structure-function analyses of LmbF and CcbF. X-ray crystal structures, docking and molecular dynamics simulations reveal that active-site aromatic residues play important roles in controlling the substrate binding mode and the reaction outcome. Furthermore, the reaction selectivity and oxygen-utilization of LmbF and CcbF were rationally engineered through structure- and calculation-based mutagenesis. Thus, the catalytic function of CcbF was switched to that of LmbF, and, remarkably, both LmbF and CcbF variants gained the oxidative-amidation activity to produce an unnatural S-acetamide derivative of lincosamide.

PubMed: 39643667
DOI: 10.1038/s41557-024-01687-7

実験手法

X-RAY DIFFRACTION (1.7 Å)