可溶甲烷单氧酶中不同组分对甲烷羟基化的协调作用

doi:10.1016/S1872-2067(24)60192-0

催化学报 ›› 2025, Vol. 68: 204-212.DOI: 10.1016/S1872-2067(24)60192-0

可溶甲烷单氧酶中不同组分对甲烷羟基化的协调作用

Yunha Hwang^a, Dong-Heon Lee^a, Seung Jae Lee^a^,^b^,^*()

^a全北国立大学化学系, 韩国
^b全北国立大学分子生物学与遗传学研究所, 韩国

收稿日期:2024-08-29 接受日期:2024-11-02 出版日期:2025-01-18 发布日期:2025-01-02
通讯作者: * 电子信箱: slee026@jbnu.ac.kr (S. J. Lee).

Orchestration of diverse components in soluble methane monooxygenase for methane hydroxylation

Yunha Hwang^a, Dong-Heon Lee^a, Seung Jae Lee^a^,^b^,^*()

^aDepartment of Chemistry, Jeonbuk National University, Jeonju 54896, Korea
^bResearch Institute for the Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Korea

Received:2024-08-29 Accepted:2024-11-02 Online:2025-01-18 Published:2025-01-02
Contact: * E-mail: slee026@jbnu.ac.kr (S. J. Lee).
About author:Seung Jae Lee (Professor, Department of Chemistry and Institute of Molecular Biology and Genetics, Jeonbuk National University) received his B.A. degree from Jeonbuk National University (Korea) in 2000, and Ph.D. degree from University of Maryland, Baltimore (USA) in 2010 under the guidance of Prof. Sarah Michel. He carried out postdoctoral research at Massachusetts Institute of Technology (USA) from 2010 to 2013 in the laboratory of Prof. Stephen J. Lippard. Professor Lee began his independent research at Jeonbuk National University from 2013. His research focuses on the mechanisms of biomolecules, particularly metalloproteins such as soluble methane monooxygenase, zinc finger proteins, and concanavalin A. These enzymes contain metal ions as essential cofactors, and their structural and functional mechanisms are investigated using classical methods of biochemistry.

摘要/Abstract

摘要：

CH₄的热容(104.9 kcal/mol)高于CO₂, 因此降低CH₄排放以减缓全球变暖成为研究热点. 在环境条件下, 甲烷氧化菌能够羟基化甲烷, 这为研究甲烷中强C‒H键的活化提供关键信息. 可溶性甲烷单加氧酶(sMMO)属于细菌多组分单加氧氧酶超家族, 包括羟化酶(MMOH)、调节酶(MMOB)和还原酶(MMOR)三个组分. 近期的结构和生物物理研究表明, 这些组分通过蛋白质相互作用可以加速或延缓MMOH中的甲烷羟基化过程. sMMO具有MMOH-MMOB和MMOH-MMOD等复杂结构, 通过研究其中的调节和抑制成分, 可以理解它们如何协调位于MMOH四螺旋束内的二铁活性位点, 尤其有助于理解这些活性位点如何影响对接表面上的峡谷区域. 此外, 最近的生物物理研究已经证明了MmoR (一种σ⁵⁴依赖性转录调节因子)在调节sMMO表达模式中的重要作用.
本综述文章概述了近期关于sMMO研究的最新成果, 这些成果对于深入理解sMMO的表达模式和功能活动至关重要. 文章详细揭示了sMMO组分如何与MMOH相互作用, 从而调控甲烷的羟基化过程, 并阐明了调控sMMO表达的内在机制以及激活酶与启动子之间的相互作用关系.

关键词: 可溶性甲烷单加氧酶, 非血红素二铁活性位点, 甲烷氧化, C?H活化, O₂活化

Abstract:

Methane (CH₄) has a higher heat capacity (104.9 kcal/mol) than carbon dioxide (CO₂), and this has inspired research aimed at reducing methane levels to retard global warming. Hydroxylation under ambient conditions through methanotrophs can provide crucial information for understanding the harsh C-H activation of methane. Soluble methane monooxygenase (sMMO) belongs to the bacterial multi-component monooxygenase superfamily and requires hydroxylase (MMOH), regulatory (MMOB), and reductase (MMOR) components. Recent structural and biophysical studies have demonstrated that these components accelerate and retard methane hydroxylation in MMOH through protein-protein interactions. Complex structures of sMMO, including MMOH-MMOB and MMOH-MMOD, illustrate how these regulatory and inhibitory components orchestrate the di-iron active sites located within the four-helix bundles of MMOH, specifically at the docking surface known as the canyon region. In addition, recent biophysical studies have demonstrated the role of MmoR, a σ⁵⁴-dependent transcriptional regulator, in regulating sMMO expression. This perspective article introduces remarkable discoveries in recent reports on sMMO components that are crucial for understanding sMMO expression and activities. Our findings provide insight into how sMMO components interact with MMOH to control methane hydroxylation, shedding light on the mechanisms governing sMMO expression and the interactions between activating enzymes and promoters.

Key words: Soluble methane monooxygenase, Non-heme di-iron active site, Methane oxidation, C-H activation, O₂ activation

Yunha Hwang, Dong-Heon Lee, Seung Jae Lee. 可溶甲烷单氧酶中不同组分对甲烷羟基化的协调作用[J]. 催化学报, 2025, 68: 204-212.

Yunha Hwang, Dong-Heon Lee, Seung Jae Lee. Orchestration of diverse components in soluble methane monooxygenase for methane hydroxylation[J]. Chinese Journal of Catalysis, 2025, 68: 204-212.

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链接本文: https://www.cjcatal.com/CN/10.1016/S1872-2067(24)60192-0

https://www.cjcatal.com/CN/Y2025/V68/I1/204

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Fig. 1. Gene clusters and structures of sMMO. (a) Gene clusters of sMMO operon from type II and Type X methanotrophs. X-ray crystallography structure of MMOH (PDB: 1MTY) (b), MMOH-MMOB (PDB: 4GAM) (c), and MMOH-MMOD (PDB: 6D7K) (d). MMOH has a homodimer structure (α2β2γ2) with two canyon regions, which allow the binding of other components, MMOB or MMOD. MMOH: methane monooxygenase hydroxylase; MMOB: methane monooxygenase regulatory protein; MMOD: methane monooxygenase inhibitory protein; sMMO: soluble methane monooxygenase.

Fig. 2. Positional shifts in the four-helix bundle through the complex generation of MMOH and other components. (a) Schematic model depicting the allosteric effect on MMOH induced by MMOB and MMOD. Root-mean square-deviations (RMSD) between MMOH (PDB: 1MTY) and complexes, including MMOH-MMOB (PDB: 4GAM) (b) and MMOH-MMOD (PDB: 6D7K) (c). MMOH: methane monooxygenase hydroxylase; MMOB: methane monooxygenase regulatory protein; MMOD: methane monooxygenase inhibitory protein; sMMO: soluble methane monooxygenase.

Fig. 3. Di-iron active sites in sMMO structure. (a) X-ray, oxidized MMOH (PDB: 1MTY). (b) X-ray, reduced MMOH (PDB: 1FYZ). (c) X-ray, MMOH-MMOB (PDB: 4GAM). (d) XFEL, oxidized MMOH-MMOB (PDB: 6YD0). (e) reduced MMOH-MMOB (PDB: 6YDI). (f) MMOH-MMOD (PDB: 6D7K). Rotameric shifts by the sidechains of T213 (g) and Glu243 (h) induced by MMOB. Rotameric shifts by the sidechains of T213 (i) and Glu243 (j) induced by MMOD. MMOH: methane monooxygenase hydroxylase; MMOB: methane monooxygenase regulatory protein; MMOD: methane monooxygenase inhibitory protein; sMMO: soluble methane monooxygenase; XFEL: X-ray free electron laser.

Fig. 4. Substrate ingress and egress pathways based on the complex formation. Cavities 1, 2, and 3 are shown as surfaces within the interior of MMOH (PDB: 1MTY) (a) and MMOH-MMOB (PDB: 4GAM) (b). (c) The binding of MMOB initiates a cascade reaction that leads to conformational changes in residues associated with cavities. The cavities visualized using PyMOL 2.5.2 are represented as surface models. MMOH: methane monooxygenase hydroxylase; MMOB: methane monooxygenase regulatory protein; sMMO: soluble methane monooxygenase.

Fig. 5. Transcriptional regulator MmoR for sMMO expression. (a) Schematic of the transcriptional mechanism of sMMO mediated by MmoR and Sigma-54. (b) Domain organization of M. sporium 5 MmoR. (c) Upstream activator sequence (UAS) and promoter regions located between mmoG and mmoX in M. sporium 5. (d) Conserved enhancer and promoter sequences from the upstream of mmoX in Methylosinus trichosporium OB3b, Methylosinus sporium 5, and Methylococcus capsulatus Bath. MmoR: methane monooxygenase transcriptional regulator; RNAP: RNA polymerase; IHF: integration host factor; sMMO: soluble methane monooxygenase.

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可溶甲烷单氧酶中不同组分对甲烷羟基化的协调作用

Orchestration of diverse components in soluble methane monooxygenase for methane hydroxylation

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