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C-methylation programming of non-reducing polyketide synthases: based on AlphaFold 2 and molecular docking
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Shiyu LIAO1, 2, Qingpei LIU3, Fusheng CHEN1, 2, *
Acta Microbiologica Sinica | 2024, 64(1) : 143 - 160
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Acta Microbiologica Sinica | 2024, 64(1): 143-160
• Research Articles •
C-methylation programming of non-reducing polyketide synthases: based on AlphaFold 2 and molecular docking
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Shiyu LIAO1, 2, Qingpei LIU3, Fusheng CHEN1, 2, *
Affiliations
  • 1 National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • 2 College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
  • 3 School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430070, Hubei, China
Published: 2024-01-04 doi: 10.13343/j.cnki.wsxb.20230338
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[Objective] To explore the reasons for differences in the C-methylation programming of non-reducing polyketide synthases (NR-Pkss).[Methods] We used bioinformatics tools and AlphaFold 2 to compare the domain sequences and structures of the NR-Pkss involved in the synthesis ofMonascus pigment and citrinin inMonascus ruber M7, i.e., Mr-PksPT and Mr-PksCT. Furthermore, we employed molecular docking to compare the binding of C-methyltransferase domains (CMeTs) with other domains and the intermediates of the two NR-Pkss.[Results] The large differences of the overall structure and the high similarity of domain sequence and structure between the two NR-Pkss suggested that the differences of C-methylation programming between NR-Pkss may be resulted from domain interactions. The CMeT of Mr-PksCT was more likely to bind to the acyl carrier protein (ACP) carrying the substrate than that of Mr-PksPT, making the intermediate more easily catalyzed by CMeT. Moreover, CMeT had lower binding free energy to methyl receptor substrate than theβ-ketosynthase domain (KS).[Conclusion] The CMeTs of NR-Pkss can affect the C-methylation of the products by competing with KS. The findings provide a new idea for the study of C-methylation programming of Pkss.

non-reducing polyketide synthase  /  Monascus spp.  /  C-methyltransferase  /  AlphaFold 2  /  molecular docking
Shiyu LIAO, Qingpei LIU, Fusheng CHEN. C-methylation programming of non-reducing polyketide synthases: based on AlphaFold 2 and molecular docking[J]. Acta Microbiologica Sinica, 2024 , 64 (1) : 143 -160 . DOI: 10.13343/j.cnki.wsxb.20230338
Funding
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  • National Natural Science Foundation of China(31730068)
  • National Natural Science Foundation of China(31330059)
Appendix
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Year 2024 volume 64 Issue 1
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Article Info
doi: 10.13343/j.cnki.wsxb.20230338
  • Receive Date：2023-05-13
  • Online Date：2026-03-18
  • Published：2024-01-04
Article Data
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History
  • Received：2023-05-13
  • Accepted：2023-08-28
Funding
National Natural Science Foundation of China(31730068)
National Natural Science Foundation of China(31330059)
Affiliations
    1 National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
    2 College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
    3 School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430070, Hubei, China

Corresponding:

*CHEN Fusheng, E-mail:
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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