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来自人类肠道细菌的糖苷代谢氧化还原酶D3dgpA

Glycoside-metabolizing oxidoreductase D3dgpA from human gut bacterium.

作者信息

Kim Heji, Mi Huynh Thi Ngoc, Ahn Joong-Hoon, Lee Jong Suk, Eser Bekir Engin, Choi Jongkeun, Han Jaehong

机构信息

Metalloenzyme Research Group and Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea.

Department of Integrative Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Republic of Korea.

出版信息

Front Bioeng Biotechnol. 2024 Jun 28;12:1413854. doi: 10.3389/fbioe.2024.1413854. eCollection 2024.

DOI:10.3389/fbioe.2024.1413854
PMID:39007053
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11239390/
Abstract

The Gfo/Idh/MocA family enzyme DgpA was known to catalyze the regiospecific oxidation of puerarin to 3"-oxo-puerarin in the presence of 3-oxo-glucose. Here, we discovered that D3dgpA, cloned from the human gut bacterium sp. MRG-IFC3, catalyzed the regiospecific oxidation of various -/-glycosides, including puerarin, in the presence of methyl β-D-3-oxo-glucopyranoside. While -glycosides were converted to 3"- and 2"-oxo-products by D3dgpA, -glycosides resulted in the formation of aglycones and hexose enediolone from the 3"-oxo-products. From DFT calculations, it was found that isomerization of 3"-oxo-puerarin to 2"-oxo-puerarin required a small activation energy of 9.86 kcal/mol, and the -glycosidic bond cleavage of 3"-oxo-products was also thermodynamically favored with a small activation energy of 3.49 kcal/mol. In addition, the reaction mechanism of D3dgpA was discussed in comparison to those of Gfo/Idh/MocA and GMC family enzymes. The robust reactivity of D3dgpA was proposed as a new general route for derivatization of glycosides.

摘要

已知Gfo/Idh/MocA家族酶DgpA在3-氧代葡萄糖存在下催化葛根素区域特异性氧化为3''-氧代葛根素。在此，我们发现从人肠道细菌sp. MRG-IFC3克隆的D3dgpA在甲基β-D-3-氧代吡喃葡萄糖苷存在下催化包括葛根素在内的各种β-糖苷的区域特异性氧化。虽然β-糖苷被D3dgpA转化为3''-和2''-氧代产物，但α-糖苷导致从3''-氧代产物形成苷元和己糖烯二醇。通过密度泛函理论计算发现，3''-氧代葛根素异构化为2''-氧代葛根素需要9.86 kcal/mol的小活化能，并且3''-氧代产物的α-糖苷键断裂在热力学上也有利，活化能为3.49 kcal/mol。此外，还将D3dgpA的反应机制与Gfo/Idh/MocA和GMC家族酶的反应机制进行了比较。D3dgpA强大的反应活性被认为是糖苷衍生化的一种新的通用途径。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/f13fe4b0ccb9/fbioe-12-1413854-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/bb911f6431db/fbioe-12-1413854-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/8d1fdcdf64bc/fbioe-12-1413854-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/e3d083990781/fbioe-12-1413854-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/266b830bb918/fbioe-12-1413854-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/0b7b7cf7d659/fbioe-12-1413854-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/778c547a4691/fbioe-12-1413854-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/f13fe4b0ccb9/fbioe-12-1413854-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/bb911f6431db/fbioe-12-1413854-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/8d1fdcdf64bc/fbioe-12-1413854-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/e3d083990781/fbioe-12-1413854-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/266b830bb918/fbioe-12-1413854-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/0b7b7cf7d659/fbioe-12-1413854-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/778c547a4691/fbioe-12-1413854-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/acfa/11239390/f13fe4b0ccb9/fbioe-12-1413854-g007.jpg

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本文引用的文献

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Mechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms.参与土壤微生物 C-糖苷代谢的糖苷 3-氧化酶的作用机制研究。
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Enzymatic β-elimination in natural product O- and C-glycoside deglycosylation.
天然产物 O-和 C-糖苷去糖基化中的酶促β-消除。
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J Microbiol Biotechnol. 2023 Dec 28;33(12):1606-1614. doi: 10.4014/jmb.2308.08021. Epub 2023 Sep 21.
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