Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI
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 am...
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Nature Portfolio
2025-04-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08008-9 |
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| author | Xiao Wang Yue Yin Wen-Long Cheng Ya-Fei Duan Yu-Shuai Li Jia Wang Mingzhu Wang Huai-En Dai Lin Liu |
| author_facet | Xiao Wang Yue Yin Wen-Long Cheng Ya-Fei Duan Yu-Shuai Li Jia Wang Mingzhu Wang Huai-En Dai Lin Liu |
| author_sort | Xiao Wang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-014fe37cb2a04be39e00063e5de5e5df |
| institution | DOAJ |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-014fe37cb2a04be39e00063e5de5e5df2025-08-20T03:10:10ZengNature PortfolioCommunications Biology2399-36422025-04-018111010.1038/s42003-025-08008-9Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyIXiao Wang0Yue Yin1Wen-Long Cheng2Ya-Fei Duan3Yu-Shuai Li4Jia Wang5Mingzhu Wang6Huai-En Dai7Lin Liu8School of Life Sciences, Anhui UniversitySchool of Life Sciences, Anhui UniversitySchool of Life Sciences, Anhui UniversitySchool of Life Sciences, Anhui UniversitySchool of Life Sciences, Anhui UniversitySchool of Life Sciences, Anhui UniversityInstitutes of Physical Science and Information Technology, Anhui UniversitySchool of Life Sciences, Anhui UniversitySchool of Life Sciences, Anhui UniversityAbstract 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.https://doi.org/10.1038/s42003-025-08008-9 |
| spellingShingle | Xiao Wang Yue Yin Wen-Long Cheng Ya-Fei Duan Yu-Shuai Li Jia Wang Mingzhu Wang Huai-En Dai Lin Liu Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI Communications Biology |
| title | Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI |
| title_full | Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI |
| title_fullStr | Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI |
| title_full_unstemmed | Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI |
| title_short | Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI |
| title_sort | structural insights into the catalytic mechanism of the microcystin tailoring enzyme mcyi |
| url | https://doi.org/10.1038/s42003-025-08008-9 |
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