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Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae
| Title: | Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae |
| Authors: | Dey, Debayan Browse this author | | Nishijima, Masayoshi Browse this author | | Tanaka, Ryouichi Browse this author →KAKEN DB | | Kurisu, Genji Browse this author | | Tanaka, Hideaki Browse this author | | Ito, Hisashi Browse this author |
| Keywords: | catalytic triad | | chlorophyll degradation | | crystal structure | | Mg-dechelatase | | Stay-Green |
| Issue Date: | Oct-2022 |
| Publisher: | John Wiley & Sons |
| Journal Title: | Protein Science |
| Volume: | 31 |
| Issue: | 10 |
| Start Page: | e4430 |
| Publisher DOI: | 10.1002/pro.4430 |
| Abstract: | Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 angstrom resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases. |
| Rights: | This is the peer reviewed version of the following article: Dey, D, Nishijima, M, Tanaka, R, Kurisu, G, Tanaka, H, Ito, H. Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae. Protein Science. 2022; 31( 10):e4430. https://doi.org/10.1002/pro.4430, which has been published in final form at https://doi.org/10.1002/pro.4430. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. This article may not be enhanced, enriched or otherwise transformed into a derivative work, without express permission from Wiley or by statutory rights under applicable legislation. Copyright notices must not be removed, obscured or modified. The article must be linked to Wiley’s version of record on Wiley Online Library and any embedding, framing or otherwise making available the article or pages thereof by third parties from platforms, services and websites other than Wiley Online Library must be prohibited. |
| Type: | article (author version) |
| URI: | http://hdl.handle.net/2115/90450 |
| Appears in Collections: | 低温科学研究所 (Institute of Low Temperature Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)
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Submitter: 伊藤 寿
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