8IF7

Crystal structure of CmnB

Summary for 8IF7

• Entry DOI: 10.2210/pdb8if7/pdb
• Descriptor: CmnB, 2-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]ACRYLIC ACID (3 entities in total)
• Functional Keywords: plp-dependent enzyme, cmnb, capreomycin, l-dap, biosynthetic protein
• Biological source: Saccharothrix mutabilis subsp. capreolus
• Total number of polymer chains: 1
• Total formula weight: 40766.07

Authors

Chang, C.Y.,Toh, S.I.,Lo, C.L. (deposition date: 2023-02-17, release date: 2023-07-26, Last modification date: 2024-10-23)

Primary citation

Toh, S.I.,Lo, C.L.,Chang, C.Y.
Crystal structure of CmnB involved in the biosynthesis of the nonproteinogenic amino acid L-2,3-diaminopropionic acid.
Acta Crystallogr.,Sect.F, 79:193-199, 2023

PubMed Abstract: L-2,3-Diaminopropionic acid (L-Dap) is a nonproteinogenic amino acid that plays as an important role as a building block in the biosynthesis of several natural products, including capreomycin, viomycin, zwittermicin, staphyloferrin and dapdiamide. A previous study reported that CmnB and CmnK are two enzymes that are involved in the formation of L-Dap in the biosynthesis of capreomycin. CmnB catalyzes the condensation reaction of O-phospho-L-serine and L-glutamic acid to generate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid, which subsequently undergoes oxidative hydrolysis via CmnK to generate the product L-Dap. Here, the crystal structure of CmnB in complex with the reaction intermediate PLP-α-aminoacrylate is reported at 2.2 Å resolution. Notably, CmnB is the second known example of a PLP-dependent enzyme that forms a monomeric structure in crystal packing. The crystal structure of CmnB also provides insights into the catalytic mechanism of the enzyme and supports the biosynthetic pathway of L-Dap reported in previous studies.

PubMed: 37405487
DOI: 10.1107/S2053230X23005769

Experimental method

X-RAY DIFFRACTION (2.2 Å)