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Siletsky SA, Borisov VB. Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives. Int J Mol Sci 2021; 22:10852. [PMID: 34639193 PMCID: PMC8509429 DOI: 10.3390/ijms221910852] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.
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Affiliation(s)
- Sergey A. Siletsky
- Department of Bioenergetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - Vitaliy B. Borisov
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia;
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2
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Tosha T, Yamagiwa R, Sawai H, Shiro Y. NO Dynamics in Microbial Denitrification System. CHEM LETT 2021. [DOI: 10.1246/cl.200629] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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3
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Takeda H, Kimura T, Nomura T, Horitani M, Yokota A, Matsubayashi A, Ishii S, Shiro Y, Kubo M, Tosha T. Timing of NO Binding and Protonation in the Catalytic Reaction of Bacterial Nitric Oxide Reductase as Established by Time-Resolved Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hanae Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Tetsunari Kimura
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Masaki Horitani
- Department of Applied Biochemistry & Food Science, Saga University, Saga 840-8502, Japan
| | - Azusa Yokota
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Akiko Matsubayashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Shoko Ishii
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
| | - Takehiko Tosha
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
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Borisov VB, Siletsky SA. Features of Organization and Mechanism of Catalysis of Two Families of Terminal Oxidases: Heme-Copper and bd-Type. BIOCHEMISTRY (MOSCOW) 2019; 84:1390-1402. [DOI: 10.1134/s0006297919110130] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kahle M, Ter Beek J, Hosler JP, Ädelroth P. The insertion of the non-heme Fe B cofactor into nitric oxide reductase from P. denitrificans depends on NorQ and NorD accessory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1051-1058. [PMID: 29874552 DOI: 10.1016/j.bbabio.2018.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/27/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
Bacterial NO reductases (NOR) catalyze the reduction of NO into N2O, either as a step in denitrification or as a detoxification mechanism. cNOR from Paracoccus (P.) denitrificans is expressed from the norCBQDEF operon, but only the NorB and NorC proteins are found in the purified NOR complex. Here, we established a new purification method for the P. denitrificans cNOR via a His-tag using heterologous expression in E. coli. The His-tagged enzyme is both structurally and functionally very similar to non-tagged cNOR. We were also able to express and purify cNOR from the structural genes norCB only, in absence of the accessory genes norQDEF. The produced protein is a stable NorCB complex containing all hemes and it can bind gaseous ligands (CO) to heme b3, but it is catalytically inactive. We show that this deficient cNOR lacks the non-heme iron cofactor FeB. Mutational analysis of the nor gene cluster revealed that it is the norQ and norD genes that are essential to form functional cNOR. NorQ belongs to the family of MoxR P-loop AAA+ ATPases, which are in general considered to facilitate enzyme activation processes often involving metal insertion. Our data indicates that NorQ and NorD work together in order to facilitate non-heme Fe insertion. This is noteworthy since in many cases Fe cofactor binding occurs spontaneously. We further suggest a model for NorQ/D-facilitated metal insertion into cNOR.
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Affiliation(s)
- Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Josy Ter Beek
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jonathan P Hosler
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.
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Yamagiwa R, Kurahashi T, Takeda M, Adachi M, Nakamura H, Arai H, Shiro Y, Sawai H, Tosha T. Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:333-341. [PMID: 29499184 DOI: 10.1016/j.bbabio.2018.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/18/2018] [Accepted: 02/24/2018] [Indexed: 11/30/2022]
Abstract
Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N2O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO2-) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies.
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Affiliation(s)
- Raika Yamagiwa
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Takuya Kurahashi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mariko Takeda
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Mayuho Adachi
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Hiro Nakamura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroyuki Arai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
| | - Yoshitsugu Shiro
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hitomi Sawai
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
| | - Takehiko Tosha
- RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan.
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Characterization of the quinol-dependent nitric oxide reductase from the pathogen Neisseria meningitidis, an electrogenic enzyme. Sci Rep 2018; 8:3637. [PMID: 29483528 PMCID: PMC5826923 DOI: 10.1038/s41598-018-21804-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/09/2018] [Indexed: 12/01/2022] Open
Abstract
Bacterial nitric oxide reductases (NORs) catalyse the reduction of NO to N2O and H2O. NORs are found either in denitrification chains, or in pathogens where their primary role is detoxification of NO produced by the immune defense of the host. Although NORs belong to the heme-copper oxidase superfamily, comprising proton-pumping O2-reducing enzymes, the best studied NORs, cNORs (cytochrome c-dependent), are non-electrogenic. Here, we focus on another type of NOR, qNOR (quinol-dependent). Recombinant qNOR from Neisseria meningitidis, a human pathogen, purified from Escherichia coli, showed high catalytic activity and spectroscopic properties largely similar to cNORs. However, in contrast to cNOR, liposome-reconstituted qNOR showed respiratory control ratios above two, indicating that NO reduction by qNOR was electrogenic. Further, we determined a 4.5 Å crystal structure of the N. meningitidis qNOR, allowing exploration of a potential proton transfer pathway from the cytoplasm by mutagenesis. Most mutations had little effect on the activity, however the E-498 variants were largely inactive, while the corresponding substitution in cNOR was previously shown not to induce significant effects. We thus suggest that, contrary to cNOR, the N. meningitidis qNOR uses cytoplasmic protons for NO reduction. Our results allow possible routes for protons to be discussed.
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Wikström M, Krab K, Sharma V. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Chem Rev 2018; 118:2469-2490. [PMID: 29350917 PMCID: PMC6203177 DOI: 10.1021/acs.chemrev.7b00664] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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This review focuses on the type
A cytochrome c oxidases (CcO), which
are found in all mitochondria
and also in several aerobic bacteria. CcO catalyzes
the respiratory reduction of dioxygen (O2) to water by
an intriguing mechanism, the details of which are fairly well understood
today as a result of research for over four decades. Perhaps even
more intriguingly, the membrane-bound CcO couples
the O2 reduction chemistry to translocation of protons
across the membrane, thus contributing to generation of the electrochemical
proton gradient that is used to drive the synthesis of ATP as catalyzed
by the rotary ATP synthase in the same membrane. After reviewing the
structure of the core subunits of CcO, the active
site, and the transfer paths of electrons, protons, oxygen, and water,
we describe the states of the catalytic cycle and point out the few
remaining uncertainties. Finally, we discuss the mechanism of proton
translocation and the controversies in that area that still prevail.
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Affiliation(s)
- Mårten Wikström
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland
| | - Klaas Krab
- Department of Molecular Cell Physiology , Vrije Universiteit , P.O. Box 7161 , Amsterdam 1007 MC , The Netherlands
| | - Vivek Sharma
- Institute of Biotechnology , University of Helsinki , P.O. Box 56 , Helsinki FI-00014 , Finland.,Department of Physics , University of Helsinki , P.O. Box 64 , Helsinki FI-00014 , Finland
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Ter Beek J, Kahle M, Ädelroth P. Modulation of protein function in membrane mimetics: Characterization of P. denitrificans cNOR in nanodiscs or liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1951-1961. [PMID: 28668220 DOI: 10.1016/j.bbamem.2017.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/03/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
Abstract
For detailed functional characterization, membrane proteins are usually studied in detergent. However, it is becoming clear that detergent micelles are often poor mimics of the lipid environment in which these proteins function. In this work we compared the catalytic properties of the membrane-embedded cytochrome c-dependent nitric oxide reductase (cNOR) from Paracoccus (P.) denitrificans in detergent, lipid/protein nanodiscs, and proteoliposomes. We used two different lipid mixtures, an extract of soybean lipids and a defined mix of synthetic lipids mimicking the original P. denitrificans membrane. We show that the catalytic activity of detergent-solubilized cNOR increased threefold upon reconstitution from detergent into proteoliposomes with the P. denitrificans lipid mixture, and above two-fold when soybean lipids were used. In contrast, there was only a small activity increase in nanodiscs. We further show that binding of the gaseous ligands CO and O2 are affected differently by reconstitution. In proteoliposomes the turnover rates are affected much more than in nanodiscs, but CO-binding is more significantly accelerated in liposomes with soybean lipids, while O2-binding is faster with the P. denitrificans lipid mix. We also investigated proton-coupled electron transfer during the reaction between fully reduced cNOR and O2, and found that the pKa of the internal proton donor was increased in proteoliposomes but not in nanodiscs. Taking our results together, the liposome-reconstituted enzyme shows significant differences to detergent-solubilized protein. Nanodiscs show much more subtle effects, presumably because of their much lower lipid to protein ratio. Which of these two membrane-mimetic systems best mimics the native membrane is discussed.
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Affiliation(s)
- Josy Ter Beek
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
| | - Maximilian Kahle
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
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Correction: Investigating the Proton Donor in the NO Reductase from Paracoccus denitrificans. PLoS One 2016; 11:e0155365. [PMID: 27203242 PMCID: PMC4874662 DOI: 10.1371/journal.pone.0155365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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