8KDK

Crystal structure of CcbF in complex with PLP

Summary for 8KDK

• Entry DOI: 10.2210/pdb8kdk/pdb
• Descriptor: CcbF (2 entities in total)
• Functional Keywords: lincomycin, plp, biosynthesis, lyase
• Biological source: Streptomyces caelestis
• Total number of polymer chains: 4
• Total formula weight: 193180.09

Authors

Mori, T.,Lyu, S.,Kadlcik, S.,Abe, I. (deposition date: 2023-08-09, release date: 2024-08-14, Last modification date: 2025-02-26)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.8 Å)