Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139.
Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814.
Proc Natl Acad Sci U S A. 2024 Oct 8;121(41):e2410995121. doi: 10.1073/pnas.2410995121. Epub 2024 Oct 3.
Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from (CODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our CODH/ACS structure with our CODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization.
大约 2/3 的每年由产甲烷菌产生的估计 10 亿吨甲烷中，有来自于乙酸盐的裂解。乙酸盐在乙酰辅酶 A 合酶（ACS）中的含 Ni-Fe-S 的 A 簇的作用下降解为一氧化碳（CO）和一个甲基（CH）。最终，这个甲基形成温室气体甲烷，而 CO 则在含 Ni-Fe-S 的 C 簇的酶一氧化碳脱氢酶（CODH）的作用下转化为温室气体二氧化碳（CO）。尽管已经解决了从使用这些酶将 CO 转化为乙酸盐的产乙酸菌中的 CODH/ACS 的结构，但尚未报道来自产甲烷菌的 CODH/ACS 的结构。在这项工作中，我们使用冷冻电子显微镜揭示了 （CODH/ACS）的产甲烷菌 CODH 和 CODH/ACS 的结构。我们发现，所有产甲烷菌中缺失的产乙酸菌 ACS 的 N 端结构域被 CODH 的结构域取代。这个 CODH 结构域为 CO 在两个催化 Ni-Fe-S 簇之间的迁移提供了一个通道。它为 ACS 提供了结合表面，并利用来自 CODH 的残基而不是 ACS 在上 A 簇上方创建了一个非常相似的 CO 凹腔。我们的 CODH/ACS 结构与我们的 CODH 结构的比较揭示了一种分子机制，当 ACS 离开时，该机制可以限制来自 CO 通道的气流，防止 CO 逃入细胞。总的来说，这些期待已久的产甲烷菌 CODH/ACS 的结构揭示了与产乙酸菌对应物惊人的功能相似性，尽管在结构域组织上存在很大差异。
