Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF

Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh...

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Published inNature communications Vol. 11; no. 1; p. 4245
Main Authors Gong, Hongri, Gao, Yan, Zhou, Xiaoting, Xiao, Yu, Wang, Weiwei, Tang, Yanting, Zhou, Shan, Zhang, Yuying, Ji, Wenxin, Yu, Lu, Tian, Changlin, Lam, Sin Man, Shui, Guanghou, Guddat, Luke W., Wong, Luet-Lok, Wang, Quan, Rao, Zihe
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 25.08.2020
Nature Publishing Group
Nature Portfolio
Subjects
101/28
631/154
631/326
631/45/535/1258/1259
631/57
Bacteria
Bacterial Proteins - chemistry
Bacterial Proteins - metabolism
Binding Sites
Catalysis
Cryoelectron Microscopy
Drug development
Electron microscopy
Electron Transport
Gram-positive bacteria
Humanities and Social Sciences
Membranes
Menaquinones
Models, Molecular
multidisciplinary
Multienzyme Complexes - chemistry
Multienzyme Complexes - genetics
Multienzyme Complexes - metabolism
Mycobacterium smegmatis
Mycobacterium smegmatis - chemistry
Mycobacterium smegmatis - enzymology
Oxidation
Oxidation-Reduction
Protein Subunits - chemistry
Protein Subunits - metabolism
Protons
Quinones
Science
Science (multidisciplinary)
Structure-Activity Relationship
Succinate dehydrogenase
Succinate Dehydrogenase - chemistry
Succinate Dehydrogenase - metabolism
Succinic Acid - metabolism
Trimers
Vitamin K 2 - metabolism
Online AccessGet full text

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Abstract Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs. Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Sdh2, which reveals membrane-anchored SdhF as a component of the complex and they discuss the electron/proton transfer pathway in the Sdh2 trimer.
AbstractList Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Sdh2, which reveals membrane-anchored SdhF as a component of the complex and they discuss the electron/proton transfer pathway in the Sdh2 trimer.
Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs. Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Sdh2, which reveals membrane-anchored SdhF as a component of the complex and they discuss the electron/proton transfer pathway in the Sdh2 trimer.
Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.
Abstract Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.
Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Sdh2, which reveals membrane-anchored SdhF as a component of the complex and they discuss the electron/proton transfer pathway in the Sdh2 trimer.
ArticleNumber 4245
Author Shui, Guanghou
Gong, Hongri
Wong, Luet-Lok
Xiao, Yu
Lam, Sin Man
Tang, Yanting
Gao, Yan
Guddat, Luke W.
Wang, Quan
Zhou, Xiaoting
Ji, Wenxin
Zhou, Shan
Tian, Changlin
Rao, Zihe
Wang, Weiwei
Zhang, Yuying
Yu, Lu
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  organization: State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Laboratory of Structural Biology, Tsinghua University, Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS
BackLink https://www.ncbi.nlm.nih.gov/pubmed/32843629$$D View this record in MEDLINE/PubMed
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SSID ssj0000391844
Score 2.488522
Snippet Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they...
Abstract Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic...
Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure...
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pubmedcentral
proquest
crossref
pubmed
springer
SourceType Open Website
Open Access Repository
Aggregation Database
Index Database
Publisher
StartPage 4245
SubjectTerms 101/28
631/154
631/326
631/45/535/1258/1259
631/57
Bacteria
Bacterial Proteins - chemistry
Bacterial Proteins - metabolism
Binding Sites
Catalysis
Cryoelectron Microscopy
Drug development
Electron microscopy
Electron Transport
Gram-positive bacteria
Humanities and Social Sciences
Membranes
Menaquinones
Models, Molecular
multidisciplinary
Multienzyme Complexes - chemistry
Multienzyme Complexes - genetics
Multienzyme Complexes - metabolism
Mycobacterium smegmatis
Mycobacterium smegmatis - chemistry
Mycobacterium smegmatis - enzymology
Oxidation
Oxidation-Reduction
Protein Subunits - chemistry
Protein Subunits - metabolism
Protons
Quinones
Science
Science (multidisciplinary)
Structure-Activity Relationship
Succinate dehydrogenase
Succinate Dehydrogenase - chemistry
Succinate Dehydrogenase - metabolism
Succinic Acid - metabolism
Trimers
Vitamin K 2 - metabolism
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Title Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF
URI https://link.springer.com/article/10.1038/s41467-020-18011-9
https://www.ncbi.nlm.nih.gov/pubmed/32843629
https://www.proquest.com/docview/2436974200
https://www.proquest.com/docview/2492786824
https://search.proquest.com/docview/2437400406
https://pubmed.ncbi.nlm.nih.gov/PMC7447783
https://doaj.org/article/d5932fe93121451abccc5a6e036fb4f3
Volume 11
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