1
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Cryo-EM structures of Na +-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae. Nat Commun 2022; 13:4082. [PMID: 35882843 PMCID: PMC9325719 DOI: 10.1038/s41467-022-31718-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
The Na+-pumping NADH-ubiquinone oxidoreductase (Na+-NQR) couples electron transfer from NADH to ubiquinone with Na+-pumping, generating an electrochemical Na+ gradient that is essential for energy-consuming reactions in bacteria. Since Na+-NQR is exclusively found in prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular mechanism of inhibition is not well-understood for lack of the atomic structural information about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na+-NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-Å resolution. The structures reveal the arrangement of all six redox cofactors including a herein identified 2Fe-2S cluster located between the NqrD and NqrE subunits. A large part of the hydrophilic NqrF is barely visible in the density map, suggesting a high degree of flexibility. This flexibility may be responsible to reducing the long distance between the 2Fe-2S centers in NqrF and NqrD/E. Two different types of specific inhibitors bind to the N-terminal region of NqrB, which is disordered in the absence of inhibitors. The present study provides a foundation for understanding the function of Na+-NQR and the binding manner of specific inhibitors.
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2
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Ishikawa M, Masuya T, Kuroda S, Uno S, Butler NL, Foreman S, Murai M, Barquera B, Miyoshi H. The side chain of ubiquinone plays a critical role in Na + translocation by the NADH-ubiquinone oxidoreductase (Na +-NQR) from Vibrio cholerae. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148547. [PMID: 35337841 DOI: 10.1016/j.bbabio.2022.148547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/18/2022] [Accepted: 03/17/2022] [Indexed: 11/19/2022]
Abstract
The Na+-pumping NADH-ubiquinone (UQ) oxidoreductase (Na+-NQR) is an essential bacterial respiratory enzyme that generates a Na+ gradient across the cell membrane. However, the mechanism that couples the redox reactions to Na+ translocation remains unknown. To address this, we examined the relation between reduction of UQ and Na+ translocation using a series of synthetic UQs with Vibrio cholerae Na+-NQR reconstituted into liposomes. UQ0 that has no side chain and UQCH3 and UQC2H5, which have methyl and ethyl side chains, respectively, were catalytically reduced by Na+-NQR, but their reduction generated no membrane potential, indicating that the overall electron transfer and Na+ translocation are not coupled. While these UQs were partly reduced by electron leak from the cofactor(s) located upstream of riboflavin, this complete loss of Na+ translocation cannot be explained by the electron leak. Lengthening the UQ side chain to n-propyl (C3H7) or longer significantly restored Na+ translocation. It has been considered that Na+ translocation is completed when riboflavin, a terminal redox cofactor residing within the membrane, is reduced. In this view, the role of UQ is simply to accept electrons from the reduced riboflavin to regenerate the stable neutral riboflavin radical and reset the catalytic cycle. However, the present study revealed that the final UQ reduction via reduced riboflavin makes an important contribution to Na+ translocation through a critical role of its side chain. Based on the results, we discuss the critical role of the UQ side chain in Na+ translocation.
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Affiliation(s)
- Moe Ishikawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Seina Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shinpei Uno
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Nicole L Butler
- Department of Biological Science, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Sara Foreman
- Department of Biological Science, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Blanca Barquera
- Department of Biological Science, Rensselaer Polytechnic Institute, Troy, NY 12180, United States; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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3
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Willow SY, Yuan M, Juárez O, Minh DDL. Electrostatics and water occlusion regulate covalently-bound flavin mononucleotide cofactors of Vibrio cholerae respiratory complex NQR. Proteins 2021; 89:1376-1385. [PMID: 34091964 DOI: 10.1002/prot.26158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/20/2021] [Accepted: 06/01/2021] [Indexed: 12/20/2022]
Abstract
Proteins like NADH:ubiquinone oxidoreductase (NQR), an essential enzyme and ion pump in the physiology of several pathogenic bacteria, tightly regulate the redox properties of their cofactors. Although flavin mononucleotide (FMN) is fully reduced in aqueous solution, FMN in subunits B and C of NQR exclusively undergo one-electron transitions during its catalytic cycle. Here, we perform ab initio calculations and molecular dynamics simulations to elucidate the mechanisms that regulate the redox state of FMN in NQR. QM/MM calculations show that binding site electrostatics disfavor anionic forms of FMNH2 , but permit a neutral form of the fully reduced flavin. The potential energy surface is unaffected by covalent bonding between FMN and threonine. Molecular dynamics simulations show that the FMN binding sites are inaccessible by water, suggesting that further reductions of the cofactors are limited or prohibited by the availability of water and other proton donors. These findings provide a deeper understanding of the mechanisms used by NQR to regulate electron transfer through the cofactors and perform its physiologic role. They also provide the first, to our knowledge, evidence of the simple concept that proteins regulate flavin redox states via water occlusion.
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Affiliation(s)
- Soohaeng Yoo Willow
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Ming Yuan
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - David D L Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois, USA
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4
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Melin F, Hellwig P. Redox Properties of the Membrane Proteins from the Respiratory Chain. Chem Rev 2020; 120:10244-10297. [DOI: 10.1021/acs.chemrev.0c00249] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Frederic Melin
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
| | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140, Laboratoire de Bioelectrochimie et Spectroscopie, CNRS-Université de Strasbourg, 1 rue Blaise Pascal, 67070 Strasbourg, France
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5
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Masuya T, Sano Y, Tanaka H, Butler NL, Ito T, Tosaki T, Morgan JE, Murai M, Barquera B, Miyoshi H. Inhibitors of a Na +-pumping NADH-ubiquinone oxidoreductase play multiple roles to block enzyme function. J Biol Chem 2020; 295:12739-12754. [PMID: 32690607 DOI: 10.1074/jbc.ra120.014229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/18/2020] [Indexed: 11/06/2022] Open
Abstract
The Na+-pumping NADH-ubiquinone (UQ) oxidoreductase (Na+-NQR) is present in the respiratory chain of many pathogenic bacteria and is thought to be a promising antibiotic target. Whereas many details of Na+-NQR structure and function are known, the mechanisms of action of potent inhibitors is not well-understood; elucidating the mechanisms would not only advance drug design strategies but might also provide insights on a terminal electron transfer from riboflavin to UQ. To this end, we performed photoaffinity labeling experiments using photoreactive derivatives of two known inhibitors, aurachin and korormicin, on isolated Vibrio cholerae Na+-NQR. The inhibitors labeled the cytoplasmic surface domain of the NqrB subunit including a protruding N-terminal stretch, which may be critical to regulate the UQ reaction in the adjacent NqrA subunit. The labeling was blocked by short-chain UQs such as ubiquinone-2. The photolabile group (2-aryl-5-carboxytetrazole (ACT)) of these inhibitors reacts with nucleophilic amino acids, so we tested mutations of nucleophilic residues in the labeled region of NqrB, such as Asp49 and Asp52 (to Ala), and observed moderate decreases in labeling yields, suggesting that these residues are involved in the interaction with ACT. We conclude that the inhibitors interfere with the UQ reaction in two ways: the first is blocking structural rearrangements at the cytoplasmic interface between NqrA and NqrB, and the second is the direct obstruction of UQ binding at this interfacial area. Unusual competitive behavior between the photoreactive inhibitors and various competitors corroborates our previous proposition that there may be two inhibitor binding sites in Na+-NQR.
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Affiliation(s)
- Takahiro Masuya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yuki Sano
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hinako Tanaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | | | - Tatsuhiko Tosaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Joel E Morgan
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Masatoshi Murai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Blanca Barquera
- Department of Biological Science and.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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6
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The aerobic respiratory chain of Pseudomonas aeruginosa cultured in artificial urine media: Role of NQR and terminal oxidases. PLoS One 2020; 15:e0231965. [PMID: 32324772 PMCID: PMC7179901 DOI: 10.1371/journal.pone.0231965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/04/2020] [Indexed: 12/26/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative γ-proteobacterium that forms part of the normal human microbiota and it is also an opportunistic pathogen, responsible for 30% of all nosocomial urinary tract infections. P. aeruginosa carries a highly branched respiratory chain that allows the colonization of many environments, such as the urinary tract, catheters and other medical devices. P. aeruginosa respiratory chain contains three different NADH dehydrogenases (complex I, NQR and NDH-2), whose physiologic roles have not been elucidated, and up to five terminal oxidases: three cytochrome c oxidases (COx), a cytochrome bo3 oxidase (CYO) and a cyanide-insensitive cytochrome bd-like oxidase (CIO). In this work, we studied the composition of the respiratory chain of P. aeruginosa cells cultured in Luria Broth (LB) and modified artificial urine media (mAUM), to understand the metabolic adaptations of this microorganism to the growth in urine. Our results show that the COx oxidases play major roles in mAUM, while P. aeruginosa relies on CYO when growing in LB medium. Moreover, our data demonstrate that the proton-pumping NQR complex is the main NADH dehydrogenase in both LB and mAUM. This enzyme is resistant to HQNO, an inhibitory molecule produced by P. aeruginosa, and may provide an advantage against the natural antibacterial agents produced by this organism. This work offers a clear picture of the composition of this pathogen’s aerobic respiratory chain and the main roles that NQR and terminal oxidases play in urine, which is essential to understand its physiology and could be used to develop new antibiotics against this notorious multidrug-resistant microorganism.
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Mezic KG, Juárez O, Neehaul Y, Cho J, Cook D, Hellwig P, Barquera B. Glutamate 95 in NqrE Is an Essential Residue for the Translocation of Cations in Na +-NQR. Biochemistry 2019; 58:2167-2175. [PMID: 30907577 DOI: 10.1021/acs.biochem.8b01294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sodium-pumping NADH:quinone oxidoreductase (Na+-NQR) is a bacterial enzyme that oxidizes NADH, reduces ubiquinone, and translocates Na+ across the membrane. We previously identified three acidic residues in the membrane-spanning helices, near the cytosol, NqrB-D397, NqrD-D133, and NqrE-E95, as candidates likely to be involved in Na+ uptake, and replacement of any one of them by a non-acidic residue affects the Na+-dependent kinetics of the enzyme. Here, we have inquired further into the role of the NqrE-E95 residue by constructing a series of mutants in which this residue is replaced by amino acids with charges and/or sizes different from those of the glutamate of the wild-type enzyme. All of the mutants showed altered steady-state kinetics with the acceleration of turnover by Na+ greatly diminished. Selected mutants were studied by other physical methods. Membrane potential measurements showed that NqrE-E95D and A are significantly less efficient in ion transport. NqrE-E95A, Q, and D were studied by transient kinetic measurements of the reduction of the enzyme by NADH. In all three cases, the results indicated inhibition of the electron-transfer step in which the FMNC becomes reduced. This is the first Na+-dependent step and is associated with Na+ uptake by the enzyme. Electrochemical measurements on NqrE-E95Q showed that the Na+ dependence of the redox potential of the FMN cofactors has been lost. The fact that the mutations at the NqrE-E95 site have specific effects related to translocation of Na+ and Li+ strongly indicates a definite role for NqrE-E95 in the cation transport process of Na+-NQR.
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Affiliation(s)
- Katherine G Mezic
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Oscar Juárez
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Yashvin Neehaul
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe , Université de Strasbourg-CNRS , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Jonathan Cho
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Darcie Cook
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe , Université de Strasbourg-CNRS , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Blanca Barquera
- Department of Biological Sciences and Center of Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
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8
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Raba DA, Rosas-Lemus M, Menzer WM, Li C, Fang X, Liang P, Tuz K, Minh DDL, Juárez O. Characterization of the Pseudomonas aeruginosa NQR complex, a bacterial proton pump with roles in autopoisoning resistance. J Biol Chem 2018; 293:15664-15677. [PMID: 30135204 DOI: 10.1074/jbc.ra118.003194] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/13/2018] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium responsible for a large number of nosocomial infections. The P. aeruginosa respiratory chain contains the ion-pumping NADH:ubiquinone oxidoreductase (NQR). This enzyme couples the transfer of electrons from NADH to ubiquinone to the pumping of sodium ions across the cell membrane, generating a gradient that drives essential cellular processes in many bacteria. In this study, we characterized P. aeruginosa NQR (Pa-NQR) to elucidate its physiologic function. Our analyses reveal that Pa-NQR, in contrast with NQR homologues from other bacterial species, is not a sodium pump, but rather a completely new form of proton pump. Homology modeling and molecular dynamics simulations suggest that cation selectivity could be determined by the exit ion channels. We also show that Pa-NQR is resistant to the inhibitor 2-n-heptyl-4-hydroxyquinoline N-oxide (HQNO). HQNO is a quinolone secreted by P. aeruginosa during infection that acts as a quorum sensing agent and also has bactericidal properties against other bacteria. Using comparative analysis and computational modeling of the ubiquinone-binding site, we identified the specific residues that confer resistance toward this inhibitor. In summary, our findings indicate that Pa-NQR is a proton pump rather than a sodium pump and is highly resistant against the P. aeruginosa-produced compound HQNO, suggesting an important role in the adaptation against autotoxicity. These results provide a deep understanding of the metabolic role of NQR in P. aeruginosa and provide insight into the structural factors that determine the functional specialization in this family of respiratory complexes.
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Affiliation(s)
| | | | - William M Menzer
- From the Departments of Biological Sciences and.,Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Chen Li
- Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Xuan Fang
- From the Departments of Biological Sciences and
| | | | - Karina Tuz
- From the Departments of Biological Sciences and
| | - David D L Minh
- Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616
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9
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Fang X, Liang P, Raba DA, Rosas-Lemus M, Chakravarthy S, Tuz K, Juárez O. Kinetic characterization of Vibrio cholerae ApbE: Substrate specificity and regulatory mechanisms. PLoS One 2017; 12:e0186805. [PMID: 29065131 PMCID: PMC5655446 DOI: 10.1371/journal.pone.0186805] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/06/2017] [Indexed: 12/20/2022] Open
Abstract
ApbE is a member of a novel family of flavin transferases that incorporates flavin mononucleotide (FMN) to subunits of diverse respiratory complexes, which fulfill important homeostatic functions. In this work a detailed characterization of Vibrio cholerae ApbE physiologic activity, substrate specificity and pH dependency was carried out. The data obtained show novel characteristics of the regulation and function of this family. For instance, our experiments indicate that divalent cations are essential for ApbE function, and that the selectivity depends largely on size and the coordination sphere of the cation. Our data also show that ApbE regulation by pH, ADP and potassium is an important mechanism that enhances the adaptation, survival and colonization of V. cholerae in the small intestine. Moreover, studies of the pH-dependency of the activity show that the reaction is favored under alkaline conditions, with a pKa of 8.4. These studies, together with sequence and structure analysis allowed us to identify His257, which is absolutely conserved in the family, as a candidate for the residue whose deprotonation controls the activity. Remarkably, the mutant H257G abolished the flavin transfer activity, strongly indicating that this residue plays an important role in the catalytic mechanism of ApbE.
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Affiliation(s)
- Xuan Fang
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Pingdong Liang
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Daniel Alexander Raba
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Mónica Rosas-Lemus
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Srinivas Chakravarthy
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
- Biophysics Collaborative Access Team, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Karina Tuz
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Oscar Juárez
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
- * E-mail:
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10
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Sellamuthu S, Singh M, Kumar A, Singh SK. Type-II NADH Dehydrogenase (NDH-2): a promising therapeutic target for antitubercular and antibacterial drug discovery. Expert Opin Ther Targets 2017; 21:559-570. [PMID: 28472892 DOI: 10.1080/14728222.2017.1327577] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is highly dangerous due to the development of resistance to first-line drugs. Moreover, Mycobacterium tuberculosis (Mtb) has also developed resistance to newly approved antitubercular drug bedaquiline. This necessitates the search for drugs acting on newer molecular targets. The energy metabolism of mycobacteria is the prime focus for the discovery of novel antitubercular drugs. Targeting type-2 NADH dehydrogenase (NDH-2) involved in the production of respiratory ATP could, therefore, be effective in treating the disease. Areas covered: This review describes the energetics of mycobacteria and the role of NDH-2 in ATP synthesis. Special attention has been given for genetic and chemical validations of NDH-2 as a molecular target. The reported kinetics and crystal structures of NDH-2 have been given in detail for better understanding of the enzyme. Expert opinion: NDH-2 is an essential enzyme for ATP synthesis and has a potential role in dormancy and persistence of Mtb. The human counterpart lacks this enzyme and hence NDH-2 inhibitors could have more clinical importance. Phenothiazines are potent inhibitor of NDH-2 and are effective against both drug-susceptible and drug-resistant Mtb. Thus, it is highly desirable to optimize phenothiazine class of compounds for the development of next generation anti-TB drugs.
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Affiliation(s)
- Satheeshkumar Sellamuthu
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Meenakshi Singh
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Ashok Kumar
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Sushil Kumar Singh
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
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11
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Toulouse C, Claussen B, Muras V, Fritz G, Steuber J. Strong pH dependence of coupling efficiency of the Na+ – translocating NADH:quinone oxidoreductase (Na+-NQR) of Vibrio cholerae. Biol Chem 2017; 398:251-260. [DOI: 10.1515/hsz-2016-0238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 09/06/2016] [Indexed: 12/23/2022]
Abstract
Abstract
The Na+-translocating NADH:quinone oxidoreductase (NQR) is the entry site for electrons into the respiratory chain of Vibrio cholerae, the causative agent of cholera disease. NQR couples the electron transfer from NADH to ubiquinone to the translocation of sodium ions across the membrane. We investigated the pH dependence of electron transfer and generation of a transmembrane voltage (ΔΨ) by NQR reconstituted in liposomes with Na+ or Li+ as coupling cation. ΔΨ formation was followed with the voltage-sensitive dye oxonol. With Na+, ΔΨ was barely influenced by pH (6.5–8.5), while Q reduction activity exhibited a maximum at pH 7.5–8.0. With Li+, ΔΨ was generally lower, and the pH profile of electron transfer activity did not reveal a pronounced maximum. We conclude that the coupling efficiency of NQR is influenced by the nature of the transported cation, and by the concentration of protons. The 3D structure of NQR reveals a transmembrane channel in subunit NqrB. It is proposed that partial uncoupling of the NQR observed with the smaller Li+, or with Na+ at pH 7.5–8.0, is caused by the backflow of the coupling cation through the channel in NqrB.
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12
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Neehaul Y, Kriegel S, Barquera B, Hellwig P. Functional Studies on Membrane Proteins by Means of H/D Exchange in Infrared: Structural Changes in Na + NQR from V. cholerae in the Presence of Lipids. Methods Mol Biol 2017; 1635:247-257. [PMID: 28755373 DOI: 10.1007/978-1-4939-7151-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
H/D exchange kinetics at the level of the amide proton in the mid infrared (1700-1500 cm-1) make it possible to study the conformational flexibility of membrane proteins, independent of size or the presence of detergent or lipids. Slow, medium, and fast exchanging domains are distinguished, which reveal a different accessibility to the solvent. Whereas amide hydrogens undergo rapid exchange with solvent in an open structure, hydrogens experience much slower exchange when involved in H-bonded structures or when sterically inaccessible to the solvent. Here, we describe the protocol that was used to study the effect of phospholipids on the overall structure of the Na+ NQR from V. cholerae, a sodium pumping membrane protein.
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Affiliation(s)
- Yashvin Neehaul
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France
- Mauritius Oceanography Institute, Avenue des Anchois, Albion, Mauritius
| | - Sebastien Kriegel
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France
| | - Blanca Barquera
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France.
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13
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Kriegel S, Srour B, Steimle S, Friedrich T, Hellwig P. Involvement of Acidic Amino Acid Residues in Zn2+Binding to Respiratory Complex I. Chembiochem 2015; 16:2080-5. [DOI: 10.1002/cbic.201500273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Sébastien Kriegel
- Laboratoire de Bioelectrochimie et Spectroscopie; UMR 7140; Chimie de la Matière Complexe; Université de Strasbourg; CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
- Université Paris Diderot; Sorbonne Paris Cité; Laboratoire d'Electrochimie Moléculaire; Unité Mixte de Recherche Université-; CNRS No. 7591; Bâtiment Lavoisier 15 rue Jean de Baïf 75205 Paris Cedex 13 France
| | - Batoul Srour
- Laboratoire de Bioelectrochimie et Spectroscopie; UMR 7140; Chimie de la Matière Complexe; Université de Strasbourg; CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
| | - Stefan Steimle
- Albert-Ludwigs-Universität Freiburg; Institut für Biochemie; Albertstrasse 21 79104 Freiburg Germany
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg; Institut für Biochemie; Albertstrasse 21 79104 Freiburg Germany
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie; UMR 7140; Chimie de la Matière Complexe; Université de Strasbourg; CNRS; 1 rue Blaise Pascal 67070 Strasbourg France
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14
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Tuz K, Mezic KG, Xu T, Barquera B, Juárez O. The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase. J Biol Chem 2015; 290:20009-21. [PMID: 26004776 DOI: 10.1074/jbc.m115.658773] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 11/06/2022] Open
Abstract
The sodium-dependent NADH dehydrogenase (Na(+)-NQR) is the main ion transporter in Vibrio cholerae. Its activity is linked to the operation of the respiratory chain and is essential for the development of the pathogenic phenotype. Previous studies have described different aspects of the enzyme, including the electron transfer pathways, sodium pumping structures, cofactor and subunit composition, among others. However, the mechanism of the enzyme remains to be completely elucidated. In this work, we have studied the kinetic mechanism of Na(+)-NQR with the use of steady state kinetics and stopped flow analysis. Na(+)-NQR follows a hexa-uni ping-pong mechanism, in which NADH acts as the first substrate, reacts with the enzyme, and the oxidized NAD leaves the catalytic site. In this conformation, the enzyme is able to capture two sodium ions and transport them to the external side of the membrane. In the last step, ubiquinone is bound and reduced, and ubiquinol is released. Our data also demonstrate that the catalytic cycle involves two redox states, the three- and five-electron reduced forms. A model that gathers all available information is proposed to explain the kinetic mechanism of Na(+)-NQR. This model provides a background to understand the current structural and functional information.
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Affiliation(s)
- Karina Tuz
- From the Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616 and
| | - Katherine G Mezic
- the Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Tianhao Xu
- From the Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616 and
| | - Blanca Barquera
- the Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Oscar Juárez
- From the Department of Biological Sciences, Illinois Institute of Technology, Chicago, Illinois 60616 and
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15
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Paulus B, Bajzath C, Melin F, Heidinger L, Kromm V, Herkersdorf C, Benz U, Mann L, Stehle P, Hellwig P, Weber S, Schleicher E. Spectroscopic characterization of radicals and radical pairs in fruit fly cryptochrome - protonated and nonprotonated flavin radical-states. FEBS J 2015; 282:3175-89. [PMID: 25879256 DOI: 10.1111/febs.13299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/21/2015] [Accepted: 04/14/2015] [Indexed: 01/05/2023]
Abstract
Drosophila melanogaster cryptochrome is one of the model proteins for animal blue-light photoreceptors. Using time-resolved and steady-state optical spectroscopy, we studied the mechanism of light-induced radical-pair formation and decay, and the photoreduction of the FAD cofactor. Exact kinetics on a microsecond to minutes timescale could be extracted for the wild-type protein using global analysis. The wild-type exhibits a fast photoreduction reaction from the oxidized FAD to the FAD(•-) state with a very positive midpoint potential of ~ +125 mV, although no further reduction could be observed. We could also demonstrate that the terminal tryptophan of the conserved triad, W342, is directly involved in electron transfer; however, photoreduction could not be completely inhibited in a W342F mutant. The investigation of another mutation close to the FAD cofactor, C416N, rather unexpectedly reveals accumulation of a protonated flavin radical on a timescale of several seconds. The obtained data are critically discussed with the ones obtained from another protein, Escherichia coli photolyase, and we conclude that the amino acid opposite N(5) of the isoalloxazine moiety of FAD is able to (de)stabilize the protonated FAD radical but not to significantly modulate the kinetics of any light-inducted reactions.
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Affiliation(s)
- Bernd Paulus
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Csaba Bajzath
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Viktoria Kromm
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | | | - Ulrike Benz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Lisa Mann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Patricia Stehle
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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16
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Shea ME, Mezic KG, Juárez O, Barquera B. A mutation in Na(+)-NQR uncouples electron flow from Na(+) translocation in the presence of K(+). Biochemistry 2014; 54:490-6. [PMID: 25486106 DOI: 10.1021/bi501266e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The sodium-pumping NADH:ubiquinone oxidoreductase (Na(+)-NQR) is a bacterial respiratory enzyme that obtains energy from the redox reaction between NADH and ubiquinone and uses this energy to create an electrochemical Na(+) gradient across the cell membrane. A number of acidic residues in transmembrane helices have been shown to be important for Na(+) translocation. One of these, Asp-397 in the NqrB subunit, is a key residue for Na(+) uptake and binding. In this study, we show that when this residue is replaced with asparagine, the enzyme acquires a new sensitivity to K(+); in the mutant, K(+) both activates the redox reaction and uncouples it from the ion translocation reaction. In the wild-type enzyme, Na(+) (or Li(+)) accelerates turnover while K(+) alone does not activate. In the NqrB-D397N mutant, K(+) accelerates the same internal electron transfer step (2Fe-2S → FMNC) that is accelerated by Na(+). This is the same step that is inhibited in mutants in which Na(+) uptake is blocked. NqrB-D397N is able to translocate Na(+) and Li(+), but when K(+) is introduced, no ion translocation is observed, regardless of whether Na(+) or Li(+) is present. Thus, this mutant, when it turns over in the presence of K(+), is the first, and currently the only, example of an uncoupled Na(+)-NQR. The fact the redox reaction and ion pumping become decoupled from each other only in the presence of K(+) provides a switch that promises to be a useful experimental tool.
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Affiliation(s)
- Michael E Shea
- Department of Biological Sciences and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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17
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Schulte M, Mattay D, Kriegel S, Hellwig P, Friedrich T. Inhibition of Escherichia coli respiratory complex I by Zn(2+). Biochemistry 2014; 53:6332-9. [PMID: 25238255 DOI: 10.1021/bi5009276] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, couples NADH oxidation and quinone reduction with the translocation of protons across the membrane. Complex I exhibits a unique L shape with a peripheral arm extending in the aqueous phase and a membrane arm embedded in the lipid bilayer. Both arms have a length of ∼180 Å. The electron transfer reaction is catalyzed by a series of cofactors in the peripheral arm, while the membrane arm catalyzes proton translocation. We used the inhibition of complex I by zinc to shed light on the coupling of the two processes, which is not yet understood. Enzyme kinetics revealed the presence of two high-affinity binding sites for Zn(2+) that are attributed to the proton translocation pathways in the membrane arm. Electrochemically induced Fourier transform infrared difference spectroscopy demonstrated that zinc binding involves at least two protonated acidic residues. Electron paramagnetic resonance spectroscopy showed that one of the cofactors is only partially reduced by NADH in the presence of Zn(2+). We conclude that blocking the proton channels in the membrane arm leads to a partial block of the electron transfer in the peripheral arm, indicating the long-range coupling between both processes.
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Affiliation(s)
- Marius Schulte
- Institut für Biochemie, Albert-Ludwigs-Universität , 79104 Freiburg, Germany
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18
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Melin F, Noor MR, Pardieu E, Boulmedais F, Banhart F, Cecchini G, Soulimane T, Hellwig P. Investigating the thermostability of succinate: quinone oxidoreductase enzymes by direct electrochemistry at SWNTs-modified electrodes and FTIR spectroscopy. Chemphyschem 2014; 15:3572-9. [PMID: 25139263 DOI: 10.1002/cphc.201402354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/27/2014] [Indexed: 11/07/2022]
Abstract
Succinate: quinone reductases (SQRs) are the enzymes that couple the oxidation of succinate and the reduction of quinones in the respiratory chain of prokaryotes and eukaryotes. Herein, we compare the temperature-dependent activity and structural stability of two SQRs, the first from the mesophilic bacterium Escherichia coli and the second from the thermophilic bacterium Thermus thermophilus, using a combined electrochemical and infrared spectroscopy approach. Direct electron transfer was achieved with full membrane protein complexes at single-walled carbon nanotube (SWNT)-modified electrodes. The possible structural factors that contribute to the temperature-dependent activity of the enzymes and, in particular, to the thermostability of the Thermus thermophilus SQR are discussed.
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Affiliation(s)
- Frederic Melin
- Laboratoire de Bioélectrochimie et Spectroscopie, Chimie de la Matière Complexe (UMR 7140), Université de Strasbourg, 1 Rue Blaise Pascal, 67000 Strasbourg (France)
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19
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Strickland M, Juárez O, Neehaul Y, Cook DA, Barquera B, Hellwig P. The conformational changes induced by ubiquinone binding in the Na+-pumping NADH:ubiquinone oxidoreductase (Na+-NQR) are kinetically controlled by conserved glycines 140 and 141 of the NqrB subunit. J Biol Chem 2014; 289:23723-33. [PMID: 25006248 DOI: 10.1074/jbc.m114.574640] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Na(+)-pumping NADH:ubiquinone oxidoreductase (Na(+)-NQR) is responsible for maintaining a sodium gradient across the inner bacterial membrane. This respiratory enzyme, which couples sodium pumping to the electron transfer between NADH and ubiquinone, is not present in eukaryotes and as such could be a target for antibiotics. In this paper it is shown that the site of ubiquinone reduction is conformationally coupled to the NqrB subunit, which also hosts the final cofactor in the electron transport chain, riboflavin. Previous work showed that mutations in conserved NqrB glycine residues 140 and 141 affect ubiquinone reduction and the proper functioning of the sodium pump. Surprisingly, these mutants did not affect the dissociation constant of ubiquinone or its analog HQNO (2-n-heptyl-4-hydroxyquinoline N-oxide) from Na(+)-NQR, which indicates that these residues do not participate directly in the ubiquinone binding site but probably control its accessibility. Indeed, redox-induced difference spectroscopy showed that these mutations prevented the conformational change involved in ubiquinone binding but did not modify the signals corresponding to bound ubiquinone. Moreover, data are presented that demonstrate the NqrA subunit is able to bind ubiquinone but with a low non-catalytically relevant affinity. It is also suggested that Na(+)-NQR contains a single catalytic ubiquinone binding site and a second site that can bind ubiquinone but is not active.
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Affiliation(s)
- Madeleine Strickland
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
| | - Oscar Juárez
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Yashvin Neehaul
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
| | - Darcie A Cook
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Blanca Barquera
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Petra Hellwig
- From the Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, CNRS Université de Strasbourg, Strasbourg, France, 67000 and
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20
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Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PLoS One 2014; 9:e96696. [PMID: 24809444 PMCID: PMC4014512 DOI: 10.1371/journal.pone.0096696] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/11/2014] [Indexed: 11/27/2022] Open
Abstract
The sodium -pumping NADH: ubiquinone oxidoreductase (Na+-NQR) is the main ion pump and the primary entry site for electrons into the respiratory chain of many different types of pathogenic bacteria. This enzymatic complex creates a transmembrane gradient of sodium that is used by the cell to sustain ionic homeostasis, nutrient transport, ATP synthesis, flagellum rotation and other essential processes. Comparative genomics data demonstrate that the nqr operon, which encodes all Na+-NQR subunits, is found in a large variety of bacterial lineages with different habitats and metabolic strategies. Here we studied the distribution, origin and evolution of this enzymatic complex. The molecular phylogenetic analyses and the organizations of the nqr operon indicate that Na+-NQR evolved within the Chlorobi/Bacteroidetes group, after the duplication and subsequent neofunctionalization of the operon that encodes the homolog RNF complex. Subsequently, the nqr operon dispersed through multiple horizontal transfer events to other bacterial lineages such as Chlamydiae, Planctomyces and α, β, γ and δ -proteobacteria. Considering the biochemical properties of the Na+-NQR complex and its physiological role in different bacteria, we propose a detailed scenario to explain the molecular mechanisms that gave rise to its novel redox- dependent sodium -pumping activity. Our model postulates that the evolution of the Na+-NQR complex involved a functional divergence from its RNF homolog, following the duplication of the rnf operon, the loss of the rnfB gene and the recruitment of the reductase subunit of an aromatic monooxygenase.
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21
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Shea ME, Juárez O, Cho J, Barquera B. Aspartic acid 397 in subunit B of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholerae forms part of a sodium-binding site, is involved in cation selectivity, and affects cation-binding site cooperativity. J Biol Chem 2013; 288:31241-9. [PMID: 24030824 DOI: 10.1074/jbc.m113.510776] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+)-pumping NADH:quinone complex is found in Vibrio cholerae and other marine and pathogenic bacteria. NADH:ubiquinone oxidoreductase oxidizes NADH and reduces ubiquinone, using the free energy released by this reaction to pump sodium ions across the cell membrane. In a previous report, a conserved aspartic acid residue in the NqrB subunit at position 397, located in the cytosolic face of this protein, was proposed to be involved in the capture of sodium. Here, we studied the role of this residue through the characterization of mutant enzymes in which this aspartic acid was substituted by other residues that change charge and size, such as arginine, serine, lysine, glutamic acid, and cysteine. Our results indicate that NqrB-Asp-397 forms part of one of the at least two sodium-binding sites and that both size and charge at this position are critical for the function of the enzyme. Moreover, we demonstrate that this residue is involved in cation selectivity, has a critical role in the communication between sodium-binding sites, by promoting cooperativity, and controls the electron transfer step involved in sodium uptake (2Fe-2S → FMNC).
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Affiliation(s)
- Michael E Shea
- From the Department of Biology and Center of Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 121801
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