7CXS

Crystal structure of CmnK, a L-Dap formation enzyme in capreomycin biosynthesis

Summary for 7CXS

• Entry DOI: 10.2210/pdb7cxs/pdb
• Descriptor: CmnK (2 entities in total)
• Functional Keywords: cmnb, lyase, capreomycin, biosynthetic protein
• Biological source: Saccharothrix mutabilis subsp. capreolus
• Total number of polymer chains: 2
• Total formula weight: 74418.05

Authors

Chang, C.Y.,Hsu, S.H. (deposition date: 2020-09-02, release date: 2021-07-14, Last modification date: 2023-11-29)

Primary citation

Hsu, S.H.,Zhang, S.,Huang, S.C.,Wu, T.K.,Xu, Z.,Chang, C.Y.
Characterization of Enzymes Catalyzing the Formation of the Nonproteinogenic Amino Acid l-Dap in Capreomycin Biosynthesis.
Biochemistry, 60:77-84, 2021

PubMed Abstract: Capreomycin (CMN) and viomycin (VIO) are nonribosomal peptide antituberculosis antibiotics, the structures of which contain four nonproteinogenic amino acids, including l-2,3-diaminopropionic acid (l-Dap), β-ureidodehydroalanine, l-capreomycidine, and β-lysine. Previous bioinformatics analysis suggested that CmnB/VioB and CmnK/VioK participate in the formation of l-Dap; however, the real substrates of these enzymes are yet to be confirmed. We herein show that starting from -phospho-l-Ser (OPS) and l-Glu precursors, CmnB catalyzes the condensation reaction to generate a metabolite intermediate -(1-amino-1-carboxyl-2-ethyl)glutamic acid (ACEGA), which undergoes NAD-dependent oxidative hydrolysis by CmnK to generate l-Dap. Furthermore, the binding site of ACEGA and the catalytic mechanism of CmnK were elucidated with the assistance of three crystal structures, including those of apo-CmnK, the NAD-CmnK complex, and CmnK in an alternative conformation. The CmnK-ACEGA docking model revealed that the glutamate α-hydrogen points toward the nicotinamide moiety. It provides evidence that the reaction is dependent on hydride transfer to form an imine intermediate, which is subsequently hydrolyzed by a water molecule to produce l-Dap. These findings modify the original proposed pathway and provide insights into l-Dap formation in the biosynthesis of other related natural products.

PubMed: 33356147
DOI: 10.1021/acs.biochem.0c00808

Experimental method

X-RAY DIFFRACTION (1.83 Å)