8WPS

Anabaena McyI R166M with prebound NAD and malate

Summary for 8WPS

• Entry DOI: 10.2210/pdb8wps/pdb
• Descriptor: McyI, (2S)-2-hydroxybutanedioic acid, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: hepatotoxin, microcystin, cofactor, anabaena, oxidoreductase
• Biological source: Anabaena sp. 90
• Total number of polymer chains: 1
• Total formula weight: 39733.46

Authors

Wang, X.,Yin, Y.,Duan, Y.,Liu, L. (deposition date: 2023-10-10, release date: 2024-10-16, Last modification date: 2025-04-30)

Primary citation

Wang, X.,Yin, Y.,Cheng, W.L.,Duan, Y.F.,Li, Y.S.,Wang, J.,Wang, M.,Dai, H.E.,Liu, L.
Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI.
Commun Biol, 8:578-578, 2025

PubMed Abstract: The most common cyanotoxin microcystin is a cyclic heptapeptide produced by non-ribosomal peptide-polyketide synthetases and tailoring enzymes. The tailoring enzyme McyI, a 2-hydroxyacid dehydrogenase, converts (3-methyl)malate into (3-methyl)oxaloacetate to produce the non-proteinogenic amino acid (3-methyl)aspartate. The reaction is NAD(P)-dependent but the catalytic mechanism remains unclear. Here we describe the crystal structures of McyI at three states: bound with copurified NAD, cocrystallized with NAD/NADP, and cocrystallized with malate or the substrate analogue citrate. An McyI protomer has unusual three nicotinamide cofactor-binding sites, named the NAD-prebound, NADP specific, and non-specific sites. Biochemical studies confirmed the NADP preference during oxidoreductase reaction. Molecular basis for McyI catalysis was revealed by the structures of McyI-NAD binary complex, McyI-NAD-NADP and McyI-NAD-malate ternary complexes, which demonstrate different opening angles between the substrate-binding domain and the nucleotide-binding domain. These findings indicate that McyI is a unique member of the 2-hydroxyacid dehydrogenase superfamily and provide detailed structural insights into its catalytic mechanism. In addition, the structural ensemble representing various binding states offers clues for designing enzyme for bioengineering applications.

PubMed: 40195441
DOI: 10.1038/s42003-025-08008-9

Experimental method

X-RAY DIFFRACTION (1.9 Å)