Insights into the structure and function of the rate-limiting enzyme of chlorophyll degradation through analysis of a bacterial Mg-dechelatase homolog

• Published in: Computational and structural biotechnology journal Vol. 19; pp. 5333 - 5347
• Main Authors: Dey, Debayan, Dhar, Dipanjana, Fortunato, Helena, Obata, Daichi, Tanaka, Ayumi, Tanaka, Ryouichi, Basu, Soumalee, Ito, Hisashi
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.01.2021; Research Network of Computational and Structural Biotechnology; Elsevier
• Subjects: Anaerolineae; Chlorophyll degradation; Mg-dechelatase; Molecular dynamics simulation; Protein structure prediction; Stay-Green; Stay-Green; Protein structure prediction; Molecular dynamics simulation; Mg-dechelatase; Anaerolineae; Chlorophyll degradation
• ISSN: 2001-0370; 2001-0370
• DOI: 10.1016/j.csbj.2021.09.023

[Display omitted] The Mg-dechelatase enzyme encoded by the Stay-Green (SGR) gene catalyzes Mg2+ dechelation from chlorophyll a. This reaction is the first committed step of chlorophyll degradation pathway in plants and is thus indispensable for the process of leaf senescence. There is no structural information available for this or its related enzymes. This study aims to provide insights into the structure and reaction mechanism of the enzyme through biochemical and computational analysis of an SGR homolog from the Chloroflexi Anaerolineae (AbSGR-h). Recombinant AbSGR-h with its intact sequence and those with mutations were overexpressed in Escherichia coli and their Mg-dechelatase activity were compared. Two aspartates – D34 and D62 were found to be essential for catalysis, while R26, Y28, T29 and D114 were responsible for structural maintenance. Gel filtration analysis of the recombinant AbSGR-h indicates that it forms a homo-oligomer. The three-dimensional structure of AbSGR-h was predicted by a deep learning-based method, which was evaluated by protein structure quality evaluation programs while structural stability of wild-type and mutant forms were investigated through molecular dynamics simulations. Furthermore, in concordance with the results of enzyme assay, molecular docking concluded the significance of D34 in ligand interaction. By combining biochemical analysis and computational prediction, this study unveils the detailed structural characteristics of the enzyme, including the probable pocket of interaction and the residues of structural and functional importance. It also serves as a basis for further studies on Mg-dechelatase such as elucidation of its reaction mechanism or inhibitor screening.