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

Bacterial Proteins / chemistry Binding Sites Catalysis Cryoelectron Microscopy Electron Transport Models, Molecular Multienzyme Complexes / chemistry Mycobacterium smegmatis / chemistry Oxidation-Reduction Protein Subunits / chemistry Structure-Activity Relationship Succinate Dehydrogenase / chemistry Succinic Acid / metabolism Vitamin K 2 / metabolism

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
25 08 2020
Historique:
received: 16 01 2020
accepted: 24 07 2020
entrez: 27 8 2020
pubmed: 28 8 2020
medline: 17 9 2020
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-020-18011-9 PMID: 32843629 PMC: PMC7447783
pubmed: 32843629
doi: 10.1038/s41467-020-18011-9
pii: 10.1038/s41467-020-18011-9
pmc: PMC7447783
doi:

Substances chimiques

Bacterial Proteins 0
Multienzyme Complexes 0
Protein Subunits 0
Vitamin K 2 11032-49-8
Succinic Acid AB6MNQ6J6L
Succinate Dehydrogenase EC 1.3.99.1

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

4245

Commentaires et corrections

Type : ErratumIn

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Auteurs

Hongri Gong (H)

State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China. gonghr@nankai.edu.cn.
ORCID: 0000-0002-2596-7635

Yan Gao (Y)

Laboratory of Structural Biology, Tsinghua University, 100084, Beijing, China.

Xiaoting Zhou (X)

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.

Yu Xiao (Y)

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.

Weiwei Wang (W)

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.

Yanting Tang (Y)

State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China.

Shan Zhou (S)

State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China.

Yuying Zhang (Y)

State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China.

Wenxin Ji (W)

National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS, 100101, Beijing, China.

Lu Yu (L)

High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China.
ORCID: 0000-0002-2581-4612

Changlin Tian (C)

High Magnetic Field Laboratory, Chinese Academy of Sciences, 230031, Hefei, China.
Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China.

Sin Man Lam (SM)

State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, 100101, Beijing, China.

Guanghou Shui (G)

State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, CAS, 100101, Beijing, China.
ORCID: 0000-0002-1621-9643

Luke W Guddat (LW)

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia.
ORCID: 0000-0002-8204-8408

Luet-Lok Wong (LL)

Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK.
ORCID: 0000-0003-4875-1092

Quan Wang (Q)

Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. wangq@ibp.ac.cn.
National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS, 100101, Beijing, China. wangq@ibp.ac.cn.
ORCID: 0000-0001-5148-5210

Zihe Rao (Z)

State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300353, Tianjin, China. raozh@tsinghua.edu.cn.
Laboratory of Structural Biology, Tsinghua University, 100084, Beijing, China. raozh@tsinghua.edu.cn.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. raozh@tsinghua.edu.cn.
National Laboratory of Biomacromolecules,omolecules, Institute of Biophysics, CAS, 100101, Beijing, China. raozh@tsinghua.edu.cn.
ORCID: 0000-0001-9866-2384

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Sites de fixation › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Phénomènes chimiques › Catalyse › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Techniques d'investigation › Microscopie électronique › Cryomicroscopie électronique › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Métabolisme › Voies et réseaux métaboliques › Transport d'électrons › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles moléculaires › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Complexes multienzymatiques › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Bactéries › Bactéries à Gram positif › Bâtonnets à Gram positif › Bâtonnets asporogènes à Gram positif › Bâtonnets asporogènes réguliers à Gram positif › Mycobacteriaceae › Mycobacterium › Mycobactéries non tuberculeuses › Mycobacterium smegmatis › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Métabolisme › Métabolisme énergétique › Oxydoréduction › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Sous-unités de protéines › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Phénomènes physiologiques › Phénomènes pharmacologiques et toxicologiques › Phénomènes pharmacologiques › Relation structure-activité › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Métalloprotéines › Protéines de liaison au fer › Protéines à fer non hème › Ferrosulfoprotéines › Complexe II de la chaîne respiratoire › Succinate Dehydrogenase › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Composés chimiques organiques › Acides carboxyliques › Acides acycliques › Diacides carboxyliques › Succinates › Acide succinique › Cryo-EM structure of trimeric Mycobacterium...
questionsmedicales.fr › Composés polycycliques › Hydrocarbures aromatiques polycycliques › Naphtalènes › Naphtoquinones › Vitamine K › Vitamine K2 › Cryo-EM structure of trimeric Mycobacterium...