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Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach

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Abstract

Chlorophyllide a oxygenase (CAO) is responsible for converting chlorophyll a to chlorophyll b in a two-step oxygenation reaction. CAO belongs to the family of Rieske-mononuclear iron oxygenases. Although the structure and reaction mechanism of other Rieske monooxygenases have been described, a member of plant Rieske non-heme iron-dependent monooxygenase has not been structurally characterized. The enzymes in this family usually form a trimeric structure and electrons are transferred between the non-heme iron site and the Rieske center of the adjoining subunits. CAO is supposed to form a similar structural arrangement. However, in Mamiellales such as Micromonas and Ostreococcus, CAO is encoded by two genes where non-heme iron site and Rieske cluster localize on the distinct polypeptides. It is not clear if they can form a similar structural organization to achieve the enzymatic activity. In this study, the tertiary structures of CAO from the model plant Arabidopsis thaliana and the Prasinophyte Micromonas pusilla were predicted by deep learning-based methods, followed by energy minimization and subsequent stereochemical quality assessment of the predicted models. Furthermore, the chlorophyll a binding cavity and the interaction of ferredoxin, which is the electron donor, on the surface of Micromonas CAO were predicted. The electron transfer pathway was predicted in Micromonas CAO and the overall structure of the CAO active site was conserved even though it forms a heterodimeric complex. The structures presented in this study will serve as a basis for understanding the reaction mechanism and regulation of the plant monooxygenase family to which CAO belongs.

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Acknowledgements

We thank Prof. Ayumi Tanaka and Dr. Atsushi Takabayashi of Hokkaido University for the helpful discussions. This study was supported by funding from the Japan Society for the Promotion of Science through the KAKENHI Grant Numbers 20H03017 to RT.

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  1. Graduate School of Life Science, Hokkaido University, N10 W8, Sapporo, 060-0810, Japan

    Debayan Dey

  2. Institute of Low Temperature Science, Hokkaido University, N19 W8, Sapporo, 060-0819, Japan

    Debayan Dey, Ryouichi Tanaka & Hisashi Ito

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Correspondence to Hisashi Ito.

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Dey, D., Tanaka, R. & Ito, H. Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach. J Mol Evol 91, 225–235 (2023). https://doi.org/10.1007/s00239-023-10100-9

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