Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach
Structural Characterization of the Chlorophyllide a Oxygenase (CAO) Enzyme Through an In Silico Approach
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DOI：
10.1007/s00239-023-10100-9
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发表时间：
2023-03
影响因子：
3.9
通讯作者：
D. Dey;R. Tanaka;Hisashi Ito
中科院分区：
文献类型：
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作者：
D. Dey;R. Tanaka;Hisashi Ito
叶绿素加氧酶（chlorophyllideaoxygenase，CAO）是将叶绿素转化为叶绿素的两步加氧反应。CAO属于Rieske单核铁加氧酶家族。虽然其他Rieske单加氧酶的结构和反应机制已被描述，但植物Rieske非血红素铁依赖性单加氧酶的成员尚未被结构表征。该家族中的酶通常形成三聚体结构，电子在非血红素铁位点和相邻亚基的Rieske中心之间转移。CAO应该形成类似的结构安排。然而，在Mamiellales如Micromonas和Ostreococcus中，CAO由两个基因编码，其中非血红素铁位点和Rieske簇定位于不同的多肽上。目前尚不清楚它们是否可以形成类似的结构组织以实现酶活性。在这项研究中，通过基于深度学习的方法预测了模式植物拟南芥和PrasinophyteMicromonas pusilla的CAO的三级结构，然后对预测模型进行了能量最小化和随后的立体化学质量评估。此外，还预测了微单胞菌CAO表面的叶绿素结合空腔和电子供体铁氧还蛋白的相互作用。预测了微单胞菌CAO的电子传递途径，CAO活性位点的整体结构是保守的，即使它形成异二聚体复合物。本研究中所呈现的结构将作为理解CAO所属的植物单加氧酶家族的反应机制和调控的基础。
Chlorophyllideaoxygenase (CAO) is responsible for converting chlorophyllato chlorophyllbin 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 asMicromonasandOstreococcus, 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 plantArabidopsis thalianaand the PrasinophyteMicromonas pusillawere predicted by deep learning-based methods, followed by energy minimization and subsequent stereochemical quality assessment of the predicted models. Furthermore, the chlorophyllabinding cavity and the interaction of ferredoxin, which is the electron donor, on the surface ofMicromonasCAO were predicted. The electron transfer pathway was predicted inMicromonasCAO 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.