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Liang H, Jia Y, Khanal SK, Huang D, Sun L, Lu H. Electrochemical-coupled sulfur-driven autotrophic denitrification for nitrogen removal from raw landfill leachate: Evaluation of performance and mechanisms. WATER RESEARCH 2024; 256:121592. [PMID: 38626614 DOI: 10.1016/j.watres.2024.121592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
The cost-effective and environment-friendly sulfur-driven autotrophic denitrification (SdAD) process has drawn significant attention for advanced nitrogen removal from low carbon-to-nitrogen (C/N) ratio wastewater in recent years. However, achieving efficient nitrogen removal and maintaining system stability of SdAD process in treating low C/N landfill leachate treatment have been a major challenge. In this study, a novel electrochemical-coupled sulfur-driven autotrophic denitrification (ESdAD) system was developed and compared with SdAD system through a long-term continuous study. Superior nitrogen removal performance (removal efficiency of 89.1 ± 2.5 %) was achieved in ESdAD system compared to SdAD process when treating raw landfill leachate (influent total nitrogen (TN) concentration of 241.7 ± 36.3 mg-N/L), and the effluent TN concentration of ESdAD bioreactor was as low as 24.8 ± 5.1 mg-N/L, which meets the discharge standard of China (< 40 mg N/L). Moreover, less sulfate production rate (1.3 ± 0.2 mg SO42--S/mgNOx--N vs 1.7 ± 0.2 mg SO42--S/mgNOx--N) and excellent pH modulation (pH of 6.9 ± 0.2 vs 5.8 ± 0.4) were also achieved in the ESdAD system compared to SdAD system. The improvement of ESdAD system performance was contributed to coexistence and interaction of heterotrophic bacteria (e.g., Rhodanobacter, Thermomonas, etc.), sulfur autotrophic bacteria (e.g., Thiobacillus, Sulfurimonas, Ignavibacterium etc.) and hydrogen autotrophic bacteria (e.g., Thauera, Comamonas, etc.) under current stimulation. In addition, microbial nitrogen metabolic activity, including functional enzyme (e.g., Nar and Nir) activities and electron transfer capacity of extracellular polymeric substances (EPS) and cytochrome c (Cyt-C), were also enhanced during current stimulation, which facilitated the nitrogen removal and maintained system stability. These findings suggested that ESdAD is an effective and eco-friendly process for advanced nitrogen removal for low C/N wastewater.
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Affiliation(s)
- Huiyu Liang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-Sen University), Guangzhou, PR China
| | - Yanyan Jia
- School of Ecology, Sun Yat-Sen University, Shenzhen, PR China
| | - Samir Kumar Khanal
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, USA
| | - Dongqi Huang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-Sen University), Guangzhou, PR China
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-Sen University), Guangzhou, PR China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-Sen University), Guangzhou, PR China.
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2
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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3
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Duré AB, Cristaldi JC, Guevara Cuasapud LA, Dalosto SD, Rivas MG, Ferroni FM, González PJ, Montich GG, Brondino CD. Molecular and kinetic properties of copper nitrite reductase from Sinorhizobium meliloti 2011 upon substituting the interfacial histidine ligand coordinated to the type 2 copper active site for glycine. J Inorg Biochem 2023; 241:112155. [PMID: 36739731 DOI: 10.1016/j.jinorgbio.2023.112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
A copper-containing nitrite reductase catalyzes the reduction of nitrite to nitric oxide in the denitrifier Sinorhizobium meliloti 2011 (SmNirK), a microorganism used as bioinoculant in alfalfa seeds. Wild type SmNirK is a homotrimer that contains two copper centers per monomer, one of type 1 (T1) and other of type 2 (T2). T2 is at the interface of two monomers in a distorted square pyramidal coordination bonded to a water molecule and three histidine side chains, H171 and H136 from one monomer and H342 from the other. We report the molecular, catalytic, and spectroscopic properties of the SmNirK variant H342G, in which the interfacial H342 T2 ligand is substituted for glycine. The molecular properties of H342G are similar to those of wild type SmNirK. Fluorescence-based thermal shift assays and FTIR studies showed that the structural effect of the mutation is only marginal. However, the kinetic reaction with the physiological electron donor was significantly affected, which showed a ∼ 100-fold lower turnover number compared to the wild type enzyme. UV-Vis, EPR and FTIR studies complemented with computational calculations indicated that the drop in enzyme activity are mainly due to the void generated in the protein substrate channel by the point mutation. The main structural changes involve the filling of the void with water molecules, the direct coordination to T2 copper ion of the second sphere aspartic acid ligand, a key residue in catalysis and nitrite sensing in NirK, and to the loss of the 3 N-O coordination of T2.
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Affiliation(s)
- Andrea B Duré
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Julio C Cristaldi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende 5000, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lorieth A Guevara Cuasapud
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Sergio D Dalosto
- Instituto de Física del Litoral, CONICET-UNL, Güemes 3450, S3000GLN, Santa Fe, Argentina
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Felix M Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Pablo J González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Guillermo G Montich
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende 5000, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Carlos D Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina.
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4
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Li X, Zou H. A molecular dynamics and quantum mechanical investigation of intermolecular interaction and electron-transfer mechanism between copper-containing nitrite reductase and redox partner pseudoazurin. Phys Chem Chem Phys 2023; 25:7783-7793. [PMID: 36857651 DOI: 10.1039/d2cp05534a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Much of biological electron transfer occurs between proteins. These molecular processes usually involve molecular recognition and intermolecular electron transfer (inter-ET). The inter-ET reaction between copper-containing nitrite reductase (CuNiR) and partner protein pseudoazurin (PAz) is the first step in denitrification, which is affected by intermolecular association. However, the transient interaction between CuNiR and PAz and the indistinct inter-ET pathway pose challenges for people to understand the biological functions of the CuNiR-PAz complex. Thus, molecular dynamics simulation and quantum mechanical calculation were used to investigate the question in this study. The interaction of the interface residues was determined through hydrogen bonds, root-mean-square deviation, root-mean-square fluctuation, the dynamics cross-correlation matrix, and molecular mechanics Poisson-Boltzmann surface area of molecular dynamics simulations. The interactions among the residues Glu89, Gly200, Asp205, Asn91, Glu204, Thr92, and Met141 on CuNiR and the residues Lys109, Ala15, Lys10, Asn9, Ile110, Met84, and Met16 on PAz are responsible for the stabilization of the complex. The binding free energy is up to -25.33 kcal mol-1. We compared the wild-type and mutant (M84A) interfacial optimized complex models at the CAM-B3LYP level with Grimme dispersion corrections (GD3) to confirm Met84 as a relay station for promoting the inter-ET. Additionally, to test whether Met84 may combine with the adjacent Met141 to form a special two-center, three-electron (S∴S)+ structure to promote the inter-ET, QM/MM was further performed to discuss the possibility of generating an electron stepping stone. Our study will promote a deep understanding of the stable protein-protein interaction, and the identified inter-residue interaction will be theoretical guidance for enhancing the catalytic activity of CuNiR in denitrification.
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Affiliation(s)
- Xin Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China.
| | - Hang Zou
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China.
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5
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Li J, Zheng W, Gu M, Han L, Luo Y, Yu K, Sun M, Zong Y, Ma X, Liu B, Lowder EP, Mendez DL, Kranz RG, Zhang K, Zhu J. Structures of the CcmABCD heme release complex at multiple states. Nat Commun 2022; 13:6422. [PMID: 36307425 PMCID: PMC9616876 DOI: 10.1038/s41467-022-34136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
Cytochromes c use heme as a cofactor to carry electrons in respiration and photosynthesis. The cytochrome c maturation system I, consisting of eight membrane proteins (CcmABCDEFGH), results in the attachment of heme to cysteine residues of cytochrome c proteins. Since all c-type cytochromes are periplasmic, heme is first transported to a periplasmic heme chaperone, CcmE. A large membrane complex, CcmABCD has been proposed to carry out this transport and linkage to CcmE, yet the structural basis and mechanisms underlying the process are unknown. We describe high resolution cryo-EM structures of CcmABCD in an unbound form, in complex with inhibitor AMP-PNP, and in complex with ATP and heme. We locate the ATP-binding site in CcmA and the heme-binding site in CcmC. Based on our structures combined with functional studies, we propose a hypothetic model of heme trafficking, heme transfer to CcmE, and ATP-dependent release of holoCcmE from CcmABCD. CcmABCD represents an ABC transporter complex using the energy of ATP hydrolysis for the transfer of heme from one binding partner (CcmC) to another (CcmE).
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Affiliation(s)
- Jiao Li
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China ,grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511 USA
| | - Wan Zheng
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Ming Gu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Long Han
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511 USA
| | - Yanmei Luo
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Koukou Yu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Mengxin Sun
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Yuliang Zong
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Xiuxiu Ma
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Bing Liu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
| | - Ethan P. Lowder
- grid.4367.60000 0001 2355 7002Department of Biology, Washington University in St. Louis, CB 1137, One Brookings Drive, St. Louis, MO 63130-4899 USA
| | - Deanna L. Mendez
- grid.4367.60000 0001 2355 7002Department of Biology, Washington University in St. Louis, CB 1137, One Brookings Drive, St. Louis, MO 63130-4899 USA
| | - Robert G. Kranz
- grid.4367.60000 0001 2355 7002Department of Biology, Washington University in St. Louis, CB 1137, One Brookings Drive, St. Louis, MO 63130-4899 USA
| | - Kai Zhang
- grid.47100.320000000419368710Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511 USA
| | - Jiapeng Zhu
- grid.410745.30000 0004 1765 1045School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 China
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6
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Hedison T, Iorgu AI, Calabrese D, Heyes DJ, Shanmugam M, Scrutton NS. Solution-State Inter-Copper Distribution of Redox Partner-Linked Copper Nitrite Reductases: A Pulsed Electron-Electron Double Resonance Spectroscopy Study. J Phys Chem Lett 2022; 13:6927-6934. [PMID: 35867774 PMCID: PMC9358711 DOI: 10.1021/acs.jpclett.2c01584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Copper nitrite reductases (CuNiRs) catalyze the reduction of nitrite to form nitric oxide. In recent years, new classes of redox partner linked CuNiRs have been isolated and characterized by crystallographic techniques. Solution-state biophysical studies have shed light on the complex catalytic mechanisms of these enzymes and implied that protein dynamics may play a role in CuNiR catalysis. To investigate the structural, dynamical, and functional relationship of these CuNiRs, we have used protein reverse engineering and pulsed electron-electron double resonance (PELDOR) spectroscopy to determine their solution-state inter-copper distributions. Data show the multidimensional conformational landscape of this family of enzymes and the role of tethering in catalysis. The importance of combining high-resolution crystallographic techniques and low-resolution solution-state approaches in determining the structures and mechanisms of metalloenzymes is emphasized by our approach.
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Affiliation(s)
- Tobias
M. Hedison
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Andreea I. Iorgu
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Donato Calabrese
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Muralidharan Shanmugam
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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7
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8
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Chen L, Li X, Xie Y, Liu N, Qin X, Chen X, Bu Y. Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer. Phys Chem Chem Phys 2022; 24:14592-14602. [PMID: 35667661 DOI: 10.1039/d2cp00666a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.
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Affiliation(s)
- Long Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Li
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxin Xie
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Nian Liu
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Qin
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xiaohua Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, P. R. China.
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9
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Eady RR, Samar Hasnain S. New horizons in structure-function studies of copper nitrite reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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10
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González PJ, Rivas MG, Ferroni FM, Rizzi AC, Brondino CD. Electron transfer pathways and spin–spin interactions in Mo- and Cu-containing oxidoreductases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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12
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Bernabeu E, Miralles-Robledillo JM, Giani M, Valdés E, Martínez-Espinosa RM, Pire C. In Silico Analysis of the Enzymes Involved in Haloarchaeal Denitrification. Biomolecules 2021; 11:biom11071043. [PMID: 34356667 PMCID: PMC8301774 DOI: 10.3390/biom11071043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022] Open
Abstract
During the last century, anthropogenic activities such as fertilization have led to an increase in pollution in many ecosystems by nitrogen compounds. Consequently, researchers aim to reduce nitrogen pollutants following different strategies. Some haloarchaea, owing to their denitrifier metabolism, have been proposed as good model organisms for the removal of not only nitrate, nitrite, and ammonium, but also (per)chlorates and bromate in brines and saline wastewater. Bacterial denitrification has been extensively described at the physiological, biochemical, and genetic levels. However, their haloarchaea counterparts remain poorly described. In previous work the model structure of nitric oxide reductase was analysed. In this study, a bioinformatic analysis of the sequences and the structural models of the nitrate, nitrite and nitrous oxide reductases has been described for the first time in the haloarchaeon model Haloferax mediterranei. The main residues involved in the catalytic mechanism and in the coordination of the metal centres have been explored to shed light on their structural characterization and classification. These results set the basis for understanding the molecular mechanism for haloarchaeal denitrification, necessary for the use and optimization of these microorganisms in bioremediation of saline environments among other potential applications including bioremediation of industrial waters.
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Affiliation(s)
- Eric Bernabeu
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Elena Valdés
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (E.B.); (J.M.M.-R.); (M.G.); (E.V.); (R.M.M.-E.)
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain
- Correspondence: ; Tel.: +34-965903400 (ext. 2064)
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13
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Qin X, Chen X. Remote Water-Mediated Proton Transfer Triggers Inter-Cu Electron Transfer: Nitrite Reduction Activation in Copper-Containing Nitrite Reductase. Chembiochem 2021; 22:1405-1414. [PMID: 33295048 DOI: 10.1002/cbic.202000644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/07/2020] [Indexed: 11/05/2022]
Abstract
The copper-containing nitrite reductase (CuNiR) catalyzes the biological conversion of nitrite to nitric oxide; key long-range electron/proton transfers are involved in the catalysis. However, the details of the electron-/proton-transfer mechanism are still unknown. In particular, the driving force of the electron transfer from the type-1 copper (T1Cu) site to the type-2 copper (T2Cu) site is ambiguous. Here, we explored the two possible proton-transfer channels, the high-pH proton channel and the primary proton channel, by using two-layered ONIOM calculations. Our calculation results reveal that the driving force for electron transfer from T1Cu to T2Cu comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the T2Cu site. These findings explain the detailed proton-/electron-transfer mechanisms of copper-containing nitrite reductase and could extend our understanding of the diverse proton-coupled electron-transfer mechanisms in complicated proteins.
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Affiliation(s)
- Xin Qin
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, 55 University City South Road, Shapingba District, Chongqing, 401331, P. R. China.,National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University, Chongqing, 401331, P. R. China
| | - Xiaohua Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, 55 University City South Road, Shapingba District, Chongqing, 401331, P. R. China.,National-Municipal Joint Engineering Laboratory for Chemical Process Intensification and Reaction, Chongqing University, Chongqing, 401331, P. R. China
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14
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Nunthaboot N, Taniguchi S, Chosrowjan H, Tanaka F. Equivalence between inverted regions of the energy gap law and inverted regions of donor–acceptor distances in photoinduced electron transfer processes in flavoproteins. RSC Adv 2021; 11:8821-8832. [PMID: 35423406 PMCID: PMC8695315 DOI: 10.1039/d0ra09716k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/04/2021] [Indexed: 11/26/2022] Open
Abstract
In the present work, we discuss about the relationship between the energy gap law and extended Dutton law in flavoproteins. The extend Dutton law is defined herein as the dependence of logarithmic rates (ln Rate) of photoinduced electron transfer (ET) from aromatic amino acids to excited isoalloxazine (Iso*) on donor–acceptor distances (Rcs). Both functions of ln Rate vs. negative values of the standard free energy gap and ln Rate vs. Rc display a parabolic behavior, when the ET rates are ultrafast. The negative values of the standard free energy gap at peaks of ln Rate [Xm(ES)] were obtained for FMN-binding protein, wild-type pyranose 2-oxidase, T169S (Thr169 is replaced by Ser) pyranose 2-oxidase, and medium-chain acyl-CoA dehydrogenase. The values of Rc at peaks of ln Rate [Xm(Rc)] were also obtained for these flavoproteins. The negative values of the standard free energy gap decreased with approximate linear functions of Rc. The negative values of standard free energy gap [Xm(ESRc)] at Rc = Xm(Rc) were evaluated using the linear functions of the negative standard free energy gap with Rc. The values of Xm(ESRc) were mostly in very good agreement with the values of Xm(ES). This implies that the energy gap law and the extend Dutton law are equivalent. Xm(ES) values in ET donors displaying the linear extend Dutton law with Rc were obtained by energy gap law, and then Xm(Rc) values were evaluated with the negative standard free energy gap. Thus, the obtained Xm(Rc) values were much smaller than the Rc range obtained by the method of molecular dynamics simulation. This suggests that ET processes with linear profiles of the extend Dutton law could be parabolic when Rc becomes much shorter than the Rc range obtained by the method of molecular dynamics simulation. Relationship between EXDL and SEGL.![]()
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Affiliation(s)
- Nadtanet Nunthaboot
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Mahasarakham University
- Thailand
| | - Seiji Taniguchi
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
| | - Haik Chosrowjan
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
| | - Fumio Tanaka
- Division of Laser Biochemistry
- Institute for Laser Technology
- Osaka 550-0004
- Japan
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15
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Fraggedakis D, McEldrew M, Smith RB, Krishnan Y, Zhang Y, Bai P, Chueh WC, Shao-Horn Y, Bazant MZ. Theory of coupled ion-electron transfer kinetics. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137432] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Cristaldi JC, Ferroni FM, Duré AB, Ramírez CS, Dalosto SD, Rizzi AC, González PJ, Rivas MG, Brondino CD. Heterologous production and functional characterization of Bradyrhizobium japonicum copper-containing nitrite reductase and its physiological redox partner cytochrome c550. Metallomics 2020; 12:2084-2097. [PMID: 33226040 DOI: 10.1039/d0mt00177e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two domain copper-nitrite reductases (NirK) contain two types of copper centers, one electron transfer (ET) center of type 1 (T1) and a catalytic site of type 2 (T2). NirK activity is pH-dependent, which has been suggested to be produced by structural modifications at high pH of some catalytically relevant residues. To characterize the pH-dependent kinetics of NirK and the relevance of T1 covalency in intraprotein ET, we studied the biochemical, electrochemical, and spectroscopic properties complemented with QM/MM calculations of Bradyrhizobium japonicum NirK (BjNirK) and of its electron donor cytochrome c550 (BjCycA). BjNirK presents absorption spectra determined mainly by a S(Cys)3pπ → Cu2+ ligand-to-metal charge-transfer (LMCT) transition. The enzyme shows low activity likely due to the higher flexibility of a protein loop associated with BjNirK/BjCycA interaction. Nitrite is reduced at high pH in a T1-decoupled way without T1 → T2 ET in which proton delivery for nitrite reduction at T2 is maintained. Our results are analyzed in comparison with previous results found by us in Sinorhizobium meliloti NirK, whose main UV-vis absorption features are determined by S(Cys)3pσ/π → Cu2+ LMCT transitions.
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Affiliation(s)
- Julio C Cristaldi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina.
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17
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Hedison TM, Shanmugam M, Heyes DJ, Edge R, Scrutton NS. Active Intermediates in Copper Nitrite Reductase Reactions Probed by a Cryotrapping-Electron Paramagnetic Resonance Approach. Angew Chem Int Ed Engl 2020; 59:13936-13940. [PMID: 32352195 PMCID: PMC7497095 DOI: 10.1002/anie.202005052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Indexed: 11/25/2022]
Abstract
Redox active metalloenzymes catalyse a range of biochemical processes essential for life. However, due to their complex reaction mechanisms, and often, their poor optical signals, detailed mechanistic understandings of them are limited. Here, we develop a cryoreduction approach coupled to electron paramagnetic resonance measurements to study electron transfer between the copper centers in the copper nitrite reductase (CuNiR) family of enzymes. Unlike alternative methods used to study electron transfer reactions, the cryoreduction approach presented here allows observation of the redox state of both metal centers, a direct read-out of electron transfer, determines the presence of the substrate/product in the active site and shows the importance of protein motion in inter-copper electron transfer catalyzed by CuNiRs. Cryoreduction-EPR is broadly applicable for the study of electron transfer in other redox enzymes and paves the way to explore transient states in multiple redox-center containing proteins (homo and hetero metal ions).
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Affiliation(s)
- Tobias M. Hedison
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
- BBSRC and EPSRC funded Future Biomanfacturing Research HubManchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Ruth Edge
- Dalton Cumbrian FacilityThe University of ManchesterCumbriaUK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
- BBSRC and EPSRC funded Future Biomanfacturing Research HubManchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
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18
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Hedison TM, Shanmugam M, Heyes DJ, Edge R, Scrutton NS. Active Intermediates in Copper Nitrite Reductase Reactions Probed by a Cryotrapping‐Electron Paramagnetic Resonance Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tobias M. Hedison
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
- BBSRC and EPSRC funded Future Biomanfacturing Research Hub Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| | - Ruth Edge
- Dalton Cumbrian Facility The University of Manchester Cumbria UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
- BBSRC and EPSRC funded Future Biomanfacturing Research Hub Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
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19
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Xiang L, Zhang P, Liu C, He X, Li HB, Li Y, Wang Z, Hihath J, Kim SH, Beratan DN, Tao N. Conductance and configuration of molecular gold-water-gold junctions under electric fields. MATTER 2020; 3:166-179. [PMID: 33103114 PMCID: PMC7584381 DOI: 10.1016/j.matt.2020.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.
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Affiliation(s)
- Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Lead contact
| | - Peng Zhang
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Chaoren Liu
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Xin He
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Haipeng B. Li
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Zixiao Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Joshua Hihath
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David N. Beratan
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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20
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Hira D, Matsumura M, Kitamura R, Furukawa K, Fujii T. Unique hexameric structure of copper-containing nitrite reductase of an anammox bacterium KSU-1. Biochem Biophys Res Commun 2020; 526:654-660. [DOI: 10.1016/j.bbrc.2020.03.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 10/24/2022]
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21
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Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS. Structures of substrate- and product-bound forms of a multi-domain copper nitrite reductase shed light on the role of domain tethering in protein complexes. IUCRJ 2020; 7:557-565. [PMID: 32431838 PMCID: PMC7201279 DOI: 10.1107/s2052252520005230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) are found in all three kingdoms of life and play a major role in the denitrification branch of the global nitro-gen cycle where nitrate is used in place of di-oxy-gen as an electron acceptor in respiratory energy metabolism. Several C- and N-terminal redox domain tethered CuNiRs have been identified and structurally characterized during the last decade. Our understanding of the role of tethered domains in these new classes of three-domain CuNiRs, where an extra cytochrome or cupredoxin domain is tethered to the catalytic two-domain CuNiRs, has remained limited. This is further compounded by a complete lack of substrate-bound structures for these tethered CuNiRs. There is still no substrate-bound structure for any of the as-isolated wild-type tethered enzymes. Here, structures of nitrite and product-bound states from a nitrite-soaked crystal of the N-terminal cupredoxin-tethered enzyme from the Hyphomicrobium denitrificans strain 1NES1 (Hd 1NES1NiR) are provided. These, together with the as-isolated structure of the same species, provide clear evidence for the role of the N-terminal peptide bearing the conserved His27 in water-mediated anchoring of the substrate at the catalytic T2Cu site. Our data indicate a more complex role of tethering than the intuitive advantage for a partner-protein electron-transfer complex by narrowing the conformational search in such a combined system.
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Affiliation(s)
- Daisuke Sasaki
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Tatiana F. Watanabe
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
- The São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Richard C. Garratt
- The São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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22
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Sasaki D, Watanabe TF, Eady RR, Garratt RC, Antonyuk SV, Hasnain SS. Reverse protein engineering of a novel 4-domain copper nitrite reductase reveals functional regulation by protein-protein interaction. FEBS J 2020; 288:262-280. [PMID: 32255260 DOI: 10.1111/febs.15324] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/16/2020] [Accepted: 04/01/2020] [Indexed: 01/03/2023]
Abstract
Cu-containing nitrite reductases that convert NO2 - to NO are critical enzymes in nitrogen-based energy metabolism. Among organisms in the order Rhizobiales, we have identified two copies of nirK, one encoding a new class of 4-domain CuNiR that has both cytochrome and cupredoxin domains fused at the N terminus and the other, a classical 2-domain CuNiR (Br2D NiR). We report the first enzymatic studies of a novel 4-domain CuNiR from Bradyrhizobium sp. ORS 375 (BrNiR), its genetically engineered 3- and 2-domain variants, and Br2D NiR revealing up to ~ 500-fold difference in catalytic efficiency in comparison with classical 2-domain CuNiRs. Contrary to the expectation that tethering would enhance electron delivery by restricting the conformational search by having a self-contained donor-acceptor system, we demonstrate that 4-domain BrNiR utilizes N-terminal tethering for downregulating enzymatic activity instead. Both Br2D NiR and an engineered 2-domain variant of BrNiR (Δ(Cytc-Cup) BrNiR) have 3 to 5% NiR activity compared to the well-characterized 2-domain CuNiRs from Alcaligenes xylosoxidans (AxNiR) and Achromobacter cycloclastes (AcNiR). Structural comparison of Δ(Cytc-Cup) BrNiR and Br2D NiR with classical 2-domain AxNiR and AcNiR reveals structural differences of the proton transfer pathway that could be responsible for the lowering of activity. Our study provides insights into unique structural and functional characteristics of naturally occurring 4-domain CuNiR and its engineered 3- and 2-domain variants. The reverse protein engineering approach utilized here has shed light onto the broader question of the evolution of transient encounter complexes and tethered electron transfer complexes. ENZYME: Copper-containing nitrite reductase (CuNiR) (EC 1.7.2.1). DATABASE: The atomic coordinate and structure factor of Δ(Cytc-Cup) BrNiR and Br2D NiR have been deposited in the Protein Data Bank (http://www.rcsb.org/) under the accession code 6THE and 6THF, respectively.
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Affiliation(s)
- Daisuke Sasaki
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Tatiana F Watanabe
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK.,The São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Robert R Eady
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Richard C Garratt
- The São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
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23
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Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. Proc Natl Acad Sci U S A 2020; 117:5280-5290. [PMID: 32094184 DOI: 10.1073/pnas.1922133117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.
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24
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Hedison T, Shenoy RT, Iorgu AI, Heyes DJ, Fisher K, Wright GSA, Hay S, Eady RR, Antonyuk SV, Hasnain SS, Scrutton NS. Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis. ACS Catal 2019; 9:6087-6099. [PMID: 32051772 PMCID: PMC7007197 DOI: 10.1021/acscatal.9b01266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/19/2019] [Indexed: 01/26/2023]
Abstract
It is generally assumed that tethering enhances rates of electron harvesting and delivery to active sites in multidomain enzymes by proximity and sampling mechanisms. Here, we explore this idea in a tethered 3-domain, trimeric copper-containing nitrite reductase. By reverse engineering, we find that tethering does not enhance the rate of electron delivery from its pendant cytochrome c to the catalytic copper-containing core. Using a linker that harbors a gatekeeper tyrosine in a nitrite access channel, the tethered haem domain enables catalysis by other mechanisms. Tethering communicates the redox state of the haem to the distant T2Cu center that helps initiate substrate binding for catalysis. It also tunes copper reduction potentials, suppresses reductive enzyme inactivation, enhances enzyme affinity for substrate, and promotes intercopper electron transfer. Tethering has multiple unanticipated beneficial roles, the combination of which fine-tunes function beyond simplistic mechanisms expected from proximity and restrictive sampling models.
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Affiliation(s)
- Tobias
M. Hedison
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rajesh T. Shenoy
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Andreea I. Iorgu
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Karl Fisher
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Gareth S. A. Wright
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Robert R. Eady
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Svetlana V. Antonyuk
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - S. Samar Hasnain
- Molecular
Biophysics Group, Institute of Integrative Biology, Faculty of Health
and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and School of Chemistry, Faculty of Science
and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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25
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Opperman DJ, Murgida DH, Dalosto SD, Brondino CD, Ferroni FM. A three-domain copper-nitrite reductase with a unique sensing loop. IUCRJ 2019; 6:248-258. [PMID: 30867922 PMCID: PMC6400189 DOI: 10.1107/s2052252519000241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
Dissimilatory nitrite reductases are key enzymes in the denitrification pathway, reducing nitrite and leading to the production of gaseous products (NO, N2O and N2). The reaction is catalysed either by a Cu-containing nitrite reductase (NirK) or by a cytochrome cd 1 nitrite reductase (NirS), as the simultaneous presence of the two enzymes has never been detected in the same microorganism. The thermophilic bacterium Thermus scotoductus SA-01 is an exception to this rule, harbouring both genes within a denitrification cluster, which encodes for an atypical NirK. The crystal structure of TsNirK has been determined at 1.63 Å resolution. TsNirK is a homotrimer with subunits of 451 residues that contain three copper atoms each. The N-terminal region possesses a type 2 Cu (T2Cu) and a type 1 Cu (T1CuN) while the C-terminus contains an extra type 1 Cu (T1CuC) bound within a cupredoxin motif. T1CuN shows an unusual Cu atom coordination (His2-Cys-Gln) compared with T1Cu observed in NirKs reported so far (His2-Cys-Met). T1CuC is buried at ∼5 Å from the molecular surface and located ∼14.1 Å away from T1CuN; T1CuN and T2Cu are ∼12.6 Å apart. All these distances are compatible with an electron-transfer process T1CuC → T1CuN → T2Cu. T1CuN and T2Cu are connected by a typical Cys-His bridge and an unexpected sensing loop which harbours a SerCAT residue close to T2Cu, suggesting an alternative nitrite-reduction mechanism in these enzymes. Biophysicochemical and functional features of TsNirK are discussed on the basis of X-ray crystallography, electron paramagnetic resonance, resonance Raman and kinetic experiments.
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Affiliation(s)
- Diederik Johannes Opperman
- Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein, Free State 9300, South Africa
| | - Daniel Horacio Murgida
- Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2 piso 1, Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Sergio Daniel Dalosto
- Instituto de Física del Litoral, CONICET-UNL, Güemes 3450, Santa Fe, Santa Fe S3000ZAA, Argentina
| | - Carlos Dante Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe S3000ZAA, Argentina
| | - Felix Martín Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe S3000ZAA, Argentina
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26
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Long distance electron transfer through the aqueous solution between redox partner proteins. Nat Commun 2018; 9:5157. [PMID: 30514833 PMCID: PMC6279779 DOI: 10.1038/s41467-018-07499-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/06/2018] [Indexed: 11/25/2022] Open
Abstract
Despite the importance of electron transfer between redox proteins in photosynthesis and respiration, the inter-protein electron transfer rate between redox partner proteins has never been measured as a function of their separation in aqueous solution. Here, we use electrochemical tunneling spectroscopy to show that the current between two protein partners decays along more than 10 nm in the solution. Molecular dynamics simulations reveal a reduced ionic density and extended electric field in the volume confined between the proteins. The distance-decay factor and the calculated local barrier for electron transfer are regulated by the electrochemical potential applied to the proteins. Redox partners could use electrochemically gated, long distance electron transfer through the solution in order to conciliate high specificity with weak binding, thus keeping high turnover rates in the crowded environment of cells. Electron transport chains rely on interactions between redox proteins, but the distance-dependence of the electron transfer rate through the solution is unknown. Here, the authors show that the current between two redox protein partners occurs at long distances and is electrochemically gated.
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27
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Le Poul N, Colasson B, Thiabaud G, Dit Fouque DJ, Iacobucci C, Memboeuf A, Douziech B, Řezáč J, Prangé T, de la Lande A, Reinaud O, Le Mest Y. Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic. Chem Sci 2018; 9:8282-8290. [PMID: 30542577 PMCID: PMC6240898 DOI: 10.1039/c8sc03124j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 08/29/2018] [Indexed: 11/21/2022] Open
Abstract
Functionality of enzymes is strongly related to water dynamic processes.
Functionality of enzymes is strongly related to water dynamic processes. The control of the redox potential for metallo-enzymes is intimately linked to the mediation of water molecules in the first and second coordination spheres. Here, we report a unique example of supramolecular control of the redox properties of a biomimetic monocopper complex by water molecules. It is shown that the copper complex based on a calix[6]arene covalently capped with a tetradentate [tris(2-methylpyridyl)amine] (tmpa) core, embedding the metal ion in a hydrophobic cavity, can exist in three different states. The first system displays a totally irreversible redox behaviour. It corresponds to the reduction of the 5-coordinate mono-aqua-CuII complex, which is the thermodynamic species in the +II state. The second system is detected at a high redox potential. It is ascribed to an “empty cavity” or “water-free” state, where the CuI ion sits in a 4-coordinate trigonal environment provided by the tmpa cap. This complex is the thermodynamic species in the +I state under “dry conditions”. Surprisingly, a third redox system appears as the water concentration is increased. Under water-saturation conditions, it displays a pseudo-reversible behaviour at a low scan rate at the mid-point from the water-free and aqua species. This third system is not observed with the Cu-tmpa complex deprived of a cavity. In the calix[6]cavity environment, it is ascribed to a species where a pair of water molecules is hosted by the calixarene cavity. A molecular mechanism for the CuII/CuI redox process with an interplay of (H2O)x (x = 0, 1, 2) hosting is proposed on the basis of computational studies. Such an unusual behaviour is ascribed to the unexpected stabilization of the CuI state by inclusion of the pair of water molecules. This phenomenon strongly evidences the drastic influence of the interaction between water molecules and a hydrophobic cavity on controlling the thermodynamics and kinetics of the CuII/CuI electron transfer process.
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Affiliation(s)
- Nicolas Le Poul
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Benoit Colasson
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Grégory Thiabaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Dany Jeanne Dit Fouque
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Claudio Iacobucci
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Antony Memboeuf
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Bénédicte Douziech
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Flemingovonám. 2 , 166 10 Prague 6 , Czech Republic .
| | - Thierry Prangé
- Laboratoire de Cristallographie et de Résonance Magnétique Nucléaire , Biologiques (CNRS UMR 8015) , Université Paris Descartes , 4, Avenue de l'Observatoire , 75006 Paris , France .
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , UMR CNRS 8000 , Université Paris Sud , 91405 Orsay , France .
| | - Olivia Reinaud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques , UMR CNRS 8601 , Université Paris Descartes , 75006 Paris , France . ;
| | - Yves Le Mest
- Laboratoire de Chimie , Electrochimie Moléculaires et Chimie Analytique , UMR CNRS 6521 , Université de Brest , 29238 Brest , France . ; ; ; ; ;
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28
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Sen K, Hough MA, Strange RW, Yong CW, Keal TW. A QM/MM Study of Nitrite Binding Modes in a Three-Domain Heme-Cu Nitrite Reductase. Molecules 2018; 23:molecules23112997. [PMID: 30453538 PMCID: PMC6278305 DOI: 10.3390/molecules23112997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 11/16/2022] Open
Abstract
Copper-containing nitrite reductases (CuNiRs) play a key role in the global nitrogen cycle by reducing nitrite (NO2−) to nitric oxide, a reaction that involves one electron and two protons. In typical two-domain CuNiRs, the electron is acquired from an external electron-donating partner. The recently characterised Rastonia picketti (RpNiR) system is a three-domain CuNiR, where the cupredoxin domain is tethered to a heme c domain that can function as the electron donor. The nitrite reduction starts with the binding of NO2− to the T2Cu centre, but very little is known about how NO2− binds to native RpNiR. A recent crystallographic study of an RpNiR mutant suggests that NO2− may bind via nitrogen rather than through the bidentate oxygen mode typically observed in two-domain CuNiRs. In this work we have used combined quantum mechanical/molecular mechanical (QM/MM) methods to model the binding mode of NO2− with native RpNiR in order to determine whether the N-bound or O-bound orientation is preferred. Our results indicate that binding via nitrogen or oxygen is possible for the oxidised Cu(II) state of the T2Cu centre, but in the reduced Cu(I) state the N-binding mode is energetically preferred.
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Affiliation(s)
- Kakali Sen
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK.
| | - Michael A Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Richard W Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Chin W Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK.
| | - Thomas W Keal
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK.
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29
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Dong J, Sasaki D, Eady RR, Antonyuk SV, Hasnain SS. Identification of a tyrosine switch in copper-haem nitrite reductases. IUCRJ 2018; 5:510-518. [PMID: 30002851 PMCID: PMC6038957 DOI: 10.1107/s2052252518008242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
There are few cases where tyrosine has been shown to be involved in catalysis or the control of catalysis despite its ability to carry out chemistry at much higher potentials (1 V versus NHE). Here, it is shown that a tyrosine that blocks the hydrophobic substrate-entry channel in copper-haem nitrite reductases can be activated like a switch by the treatment of crystals of Ralstonia pickettii nitrite reductase (RpNiR) with nitric oxide (NO) (-0.8 ± 0.2 V). Treatment with NO results in an opening of the channel originating from the rotation of Tyr323 away from AspCAT97. Remarkably, the structure of a catalytic copper-deficient enzyme also shows Tyr323 in the closed position despite the absence of type 2 copper (T2Cu), clearly demonstrating that the status of Tyr323 is not controlled by T2Cu or its redox chemistry. It is also shown that the activation by NO is not through binding to haem. It is proposed that activation of the Tyr323 switch is controlled by NO through proton abstraction from tyrosine and the formation of HNO. The insight gained here for the use of tyrosine as a switch in catalysis has wider implications for catalysis in biology.
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Affiliation(s)
- Jianshu Dong
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - Daisuke Sasaki
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, England
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30
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Okuda-Shimazaki J, Loew N, Hirose N, Kojima K, Mori K, Tsugawa W, Sode K. Construction and characterization of flavin adenine dinucleotide glucose dehydrogenase complex harboring a truncated electron transfer subunit. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.04.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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31
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Eichorst SA, Trojan D, Roux S, Herbold C, Rattei T, Woebken D. Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environ Microbiol 2018; 20:1041-1063. [PMID: 29327410 PMCID: PMC5900883 DOI: 10.1111/1462-2920.14043] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
Abstract
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large-scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected - both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2 , now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large-scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment.
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Affiliation(s)
- Stephanie A. Eichorst
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Daniela Trojan
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Simon Roux
- Department of EnergyJoint Genome InstituteWalnut CreekCAUSA
| | - Craig Herbold
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem ScienceResearch Network “Chemistry Meets Biology”, University of ViennaViennaAustria
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32
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Lintuluoto M, Lintuluoto JM. Intra-electron transfer induced by protonation in copper-containing nitrite reductase. Metallomics 2018. [DOI: 10.1039/c7mt00323d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Electron transfer between two Cu sites in the enzyme induced by protonation of remote catalytic residues.
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Affiliation(s)
- Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
- Kyoto 606-8522
- Japan
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33
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Halsted TP, Yamashita K, Hirata K, Ago H, Ueno G, Tosha T, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. An unprecedented dioxygen species revealed by serial femtosecond rotation crystallography in copper nitrite reductase. IUCRJ 2018; 5:22-31. [PMID: 29354268 PMCID: PMC5755574 DOI: 10.1107/s2052252517016128] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 11/07/2017] [Indexed: 05/24/2023]
Abstract
Synchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis. Using the newly developed approach of serial femtosecond rotation crystallography (SF-ROX), an X-ray damage-free structure of the as-isolated copper nitrite reductase (CuNiR) was visualized. The sub-10 fs X-ray pulse length from the SACLA X-ray free-electron laser allowed diffraction data to be collected to 1.6 Å resolution in a 'time-frozen' state. The extremely short duration of the X-ray pulses ensures the capture of data prior to the onset of radiation-induced changes, including radiolysis. Unexpectedly, an O2 ligand was identified bound to the T2Cu in a brand-new binding mode for a diatomic ligand in CuNiRs. The observation of O2 in a time-frozen structure of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from Alcaligenes xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have ∼56% of the dismutase activity of the bovine SOD enzyme some two decades ago.
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Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Takehiko Tosha
- Biometal Science Laboratory, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
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34
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Qin X, Deng L, Hu C, Li L, Chen X. Copper-Containing Nitrite Reductase Employing Proton-Coupled Spin-Exchanged Electron-Transfer and Multiproton Synchronized Transfer to Reduce Nitrite. Chemistry 2017; 23:14900-14910. [DOI: 10.1002/chem.201703221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Xin Qin
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Li Deng
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Caihong Hu
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Li Li
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
| | - Xiaohua Chen
- National-Municipal Joint Engineering Laboratory for Chemical; Process Intensification and Reaction; School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 401331 P.R. China
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35
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Dynamics of nitric oxide controlled by protein complex in bacterial system. Proc Natl Acad Sci U S A 2017; 114:9888-9893. [PMID: 28847930 DOI: 10.1073/pnas.1621301114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitric oxide (NO) plays diverse and significant roles in biological processes despite its cytotoxicity, raising the question of how biological systems control the action of NO to minimize its cytotoxicity in cells. As a great example of such a system, we found a possibility that NO-generating nitrite reductase (NiR) forms a complex with NO-decomposing membrane-integrated NO reductase (NOR) to efficiently capture NO immediately after its production by NiR in anaerobic nitrate respiration called denitrification. The 3.2-Å resolution structure of the complex of one NiR functional homodimer and two NOR molecules provides an idea of how these enzymes interact in cells, while the structure may not reflect the one in cells due to the membrane topology. Subsequent all-atom molecular dynamics (MD) simulations of the enzyme complex model in a membrane and structure-guided mutagenesis suggested that a few interenzyme salt bridges and coulombic interactions of NiR with the membrane could stabilize the complex of one NiR homodimer and one NOR molecule and contribute to rapid NO decomposition in cells. The MD trajectories of the NO diffusion in the NiR:NOR complex with the membrane showed that, as a plausible NO transfer mechanism, NO released from NiR rapidly migrates into the membrane, then binds to NOR. These results help us understand the mechanism of the cellular control of the action of cytotoxic NO.
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36
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Matsuoka M, Kumar A, Muddassar M, Matsuyama A, Yoshida M, Zhang KYJ. Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium oxysporum. J Chem Inf Model 2017; 57:203-213. [DOI: 10.1021/acs.jcim.6b00649] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masaki Matsuoka
- Chemical
Genomics Research Group, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ashutosh Kumar
- Structural
Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Muhammad Muddassar
- Structural
Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akihisa Matsuyama
- Chemical
Genomics Research Group, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical
Genomics Research Group, Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- CREST Research
Project, Japan Science and Technology Corporation, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kam Y. J. Zhang
- Structural
Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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37
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Horrell S, Kekilli D, Strange RW, Hough MA. Recent structural insights into the function of copper nitrite reductases. Metallomics 2017; 9:1470-1482. [DOI: 10.1039/c7mt00146k] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper nitrite reductases (CuNiRs) catalyse the reduction of nitrite to nitric oxide as part of the denitrification pathway. In this review, we describe insights into CuNiR function from structural studies.
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Affiliation(s)
- Sam Horrell
- School of Biological Sciences
- University of Essex
- Colchester
- UK
| | - Demet Kekilli
- School of Biological Sciences
- University of Essex
- Colchester
- UK
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38
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Sheu SY, Schlag EW, Yang DY. A model for ultra-fast charge transport in membrane proteins. Phys Chem Chem Phys 2016; 17:23088-94. [PMID: 26274051 DOI: 10.1039/c5cp01442e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isolated proteins have recently been observed to transport charge and reactivity over very long distances with extraordinary rates and near perfect efficiencies in spite of their site. This is not the case if the peptide is in water, where the efficiency of charge hopping to the next site is reduced to approximately 2%. Here, water is not an ideal solvent for charge transport. The issue at hand is how to explain such enormous charge transfer quenching in water compared to another typical medium, namely lipid. We performed molecular dynamics simulations to computationally substantiate the novel long-distance charge transfer yield of the polypeptides in lipids. This is characterized by the charge transfer persistent-distance decay constant and not by the rate, which is seldom, if ever, measured and hence not directly addressed here. This model can encompass an extremely wide range of yields over very long distances in peptides in various media. The calculations here demonstrate the good charge transport efficiency in lipids in contrast to the poor efficiency in water. The protein charge transport also exhibits a very strong anisotropic effect in lipids. The peptide secondary structure effect of charge transfer in membranes is analyzed in contrast to that in water. These results suggest that this model can be useful for the prediction of charge transfer efficiency in various environments of interest and indicate that the charge transfer is highly efficient in membrane proteins.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences, and Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan.
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39
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Eady RR, Antonyuk SV, Hasnain SS. Fresh insight to functioning of selected enzymes of the nitrogen cycle. Curr Opin Chem Biol 2016; 31:103-12. [DOI: 10.1016/j.cbpa.2016.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/18/2016] [Indexed: 11/26/2022]
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40
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McGrath AP, Laming EL, Casas Garcia GP, Kvansakul M, Guss JM, Trewhella J, Calmes B, Bernhardt PV, Hanson GR, Kappler U, Maher MJ. Structural basis of interprotein electron transfer in bacterial sulfite oxidation. eLife 2015; 4:e09066. [PMID: 26687009 PMCID: PMC4760952 DOI: 10.7554/elife.09066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/12/2015] [Indexed: 11/13/2022] Open
Abstract
Interprotein electron transfer underpins the essential processes of life and relies on the formation of specific, yet transient protein-protein interactions. In biological systems, the detoxification of sulfite is catalyzed by the sulfite-oxidizing enzymes (SOEs), which interact with an electron acceptor for catalytic turnover. Here, we report the structural and functional analyses of the SOE SorT from Sinorhizobium meliloti and its cognate electron acceptor SorU. Kinetic and thermodynamic analyses of the SorT/SorU interaction show the complex is dynamic in solution, and that the proteins interact with Kd = 13.5 ± 0.8 μM. The crystal structures of the oxidized SorT and SorU, both in isolation and in complex, reveal the interface to be remarkably electrostatic, with an unusually large number of direct hydrogen bonding interactions. The assembly of the complex is accompanied by an adjustment in the structure of SorU, and conformational sampling provides a mechanism for dissociation of the SorT/SorU assembly.
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Affiliation(s)
- Aaron P McGrath
- Structural Biology Program, Centenary Institute, Sydney, Australia
| | - Elise L Laming
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - G Patricia Casas Garcia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - J Mitchell Guss
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Benoit Calmes
- Centre for Metals in Biology, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Paul V Bernhardt
- Centre for Metals in Biology, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Graeme R Hanson
- Centre for Metals in Biology, The University of Queensland, Brisbane, Australia
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Ulrike Kappler
- Centre for Metals in Biology, The University of Queensland, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Megan J Maher
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Appl Environ Microbiol 2015; 82:51-61. [PMID: 26452555 DOI: 10.1128/aem.02602-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 10/07/2015] [Indexed: 01/06/2023] Open
Abstract
Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.
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Blakeley MP, Hasnain SS, Antonyuk SV. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential. IUCRJ 2015; 2:464-74. [PMID: 26175905 PMCID: PMC4491318 DOI: 10.1107/s2052252515011239] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/09/2015] [Indexed: 05/20/2023]
Abstract
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.
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Affiliation(s)
- Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38000, France
| | - Samar S. Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZX, UK
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43
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Jeszenői N, Horváth I, Bálint M, van der Spoel D, Hetényi C. Mobility-based prediction of hydration structures of protein surfaces. Bioinformatics 2015; 31:1959-65. [DOI: 10.1093/bioinformatics/btv093] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/10/2015] [Indexed: 12/31/2022] Open
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Aas FE, Li X, Edwards J, Hongrø Solbakken M, Deeudom M, Vik Å, Moir J, Koomey M, Aspholm M. Cytochrome c-based domain modularity governs genus-level diversification of electron transfer to dissimilatory nitrite reduction. Environ Microbiol 2014; 17:2114-32. [PMID: 25330335 DOI: 10.1111/1462-2920.12661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/04/2014] [Indexed: 12/19/2022]
Abstract
The genus Neisseria contains two pathogenic species (N. meningitidis and N. gonorrhoeae) in addition to a number of commensal species that primarily colonize mucosal surfaces in man. Within the genus, there is considerable diversity and apparent redundancy in the components involved in respiration. Here, we identify a unique c-type cytochrome (cN ) that is broadly distributed among commensal Neisseria, but absent in the pathogenic species. Specifically, cN supports nitrite reduction in N. gonorrhoeae strains lacking the cytochromes c5 and CcoP established to be critical to NirK nitrite reductase activity. The c-type cytochrome domain of cN shares high sequence identity with those localized c-terminally in c5 and CcoP and all three domains were shown to donate electrons directly to NirK. Thus, we identify three distinct but paralogous proteins that donate electrons to NirK. We also demonstrate functionality for a N. weaverii NirK variant with a C-terminal c-type heme extension. Taken together, modular domain distribution and gene rearrangement events related to these respiratory electron carriers within Neisseria are concordant with major transitions in the macroevolutionary history of the genus. This work emphasizes the importance of denitrification as a selectable trait that may influence speciation and adaptive diversification within this largely host-restricted bacterial genus.
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Affiliation(s)
- Finn Erik Aas
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - Xi Li
- Department of Biology, University of York, York, YO10 5DD, UK
| | - James Edwards
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Monica Hongrø Solbakken
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, N-0316, Norway
| | - Manu Deeudom
- Department of Biology, University of York, York, YO10 5DD, UK.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Åshild Vik
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
| | - James Moir
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Michael Koomey
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway.,Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, N-0316, Norway
| | - Marina Aspholm
- Department of Biosciences, University of Oslo, Oslo, N-0316, Norway
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45
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Zampino AP, Masters FM, Bladholm EL, Panzner MJ, Berry SM, Leeper TC, Ziegler CJ. Mercury metallation of the copper protein azurin and structural insight into possible heavy metal reactivity. J Inorg Biochem 2014; 141:152-160. [DOI: 10.1016/j.jinorgbio.2014.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 01/17/2023]
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46
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Candas D, Lu CL, Fan M, Chuang FYS, Sweeney C, Borowsky AD, Li JJ. Mitochondrial MKP1 is a target for therapy-resistant HER2-positive breast cancer cells. Cancer Res 2014; 74:7498-509. [PMID: 25377473 DOI: 10.1158/0008-5472.can-14-0844] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The MAPK phosphatase MKP1 (DUSP1) is overexpressed in many human cancers, including chemoresistant and radioresistant breast cancer cells, but its functional contributions in these settings are unclear. Here, we report that after cell irradiation, MKP1 translocates into mitochondria, where it prevents apoptotic induction by limiting accumulation of phosphorylated active forms of the stress kinase JNK. Increased levels of mitochondrial MKP1 after irradiation occurred in the mitochondrial inner membrane space. Notably, cell survival regulated by mitochondrial MKP1 was responsible for conferring radioresistance in HER2-overexpressing breast cancer cells, due to the fact that MKP1 serves as a major downstream effector in the HER2-activated RAF-MEK-ERK pathway. Clinically, we documented MKP1 expression exclusively in HER2-positive breast tumors, relative to normal adjacent tissue from the same patients. MKP1 overexpression was also detected in irradiated HER2-positive breast cancer stem-like cells (HER2(+)/CD44(+)/CD24(-/low)) isolated from a radioresistant breast cancer cell population after long-term radiation treatment. MKP1 silencing reduced clonogenic survival and enhanced radiosensitivity in these stem-like cells. Combined inhibition of MKP1 and HER2 enhanced cell killing in breast cancer. Together, our findings identify a new mechanism of resistance in breast tumors and reveal MKP1 as a novel therapeutic target for radiosensitization.
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Affiliation(s)
- Demet Candas
- Department of Radiation Oncology, University of California Davis School of Medicine, Sacramento, California
| | - Chung-Ling Lu
- Department of Radiation Oncology, University of California Davis School of Medicine, Sacramento, California
| | - Ming Fan
- Department of Radiation Oncology, University of California Davis School of Medicine, Sacramento, California
| | - Frank Y S Chuang
- Center for Biophotonics, Science and Technology, University of California Davis School of Medicine, Sacramento, California. Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Colleen Sweeney
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Alexander D Borowsky
- Center for Comparative Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Jian Jian Li
- Department of Radiation Oncology, University of California Davis School of Medicine, Sacramento, California. NCI-designated Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, California.
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47
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Leferink NGH, Antonyuk SV, Houwman JA, Scrutton NS, Eady RR, Hasnain SS. Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase. Nat Commun 2014; 5:4395. [PMID: 25022223 PMCID: PMC4104443 DOI: 10.1038/ncomms5395] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/13/2014] [Indexed: 11/29/2022] Open
Abstract
Enzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of catalysis. Evidence for long-range effects on enzyme mechanism resulting from mutations remains sparse, limiting the design/redesign of synthetic catalysts in a predictable way. Here we show that improving the accessibility of the active site pocket of copper nitrite reductase by mutation of a surface-exposed phenylalanine residue (Phe306), located 12 Å away from the catalytic site type-2 Cu (T2Cu), profoundly affects intra-molecular electron transfer, substrate-binding and catalytic activity. Structures and kinetic studies provide an explanation for the lower affinity for the substrate and the alteration of the rate-limiting step in the reaction. Our results demonstrate that distant residues remote from the active site can have marked effects on enzyme catalysis, by driving mechanistic change through relatively minor structural perturbations. Residues within the catalytic site of enzymes are important for activity, but whether more distant residues are also sensitive to mutation is unclear. Here, Leferink et al. show that mutation of residues in copper nitrate reductase that are 12Å away from the active site perturb enzyme function.
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Affiliation(s)
- Nicole G H Leferink
- 1] Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK [2]
| | - Svetlana V Antonyuk
- 1] Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK [2]
| | - Joseline A Houwman
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Robert R Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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48
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Wang Z, Fan M, Candas D, Zhang TQ, Qin L, Eldridge A, Wachsmann-Hogiu S, Ahmed KM, Chromy BA, Nantajit D, Duru N, He F, Chen M, Finkel T, Weinstein LS, Li JJ. Cyclin B1/Cdk1 coordinates mitochondrial respiration for cell-cycle G2/M progression. Dev Cell 2014; 29:217-32. [PMID: 24746669 DOI: 10.1016/j.devcel.2014.03.012] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 10/30/2013] [Accepted: 03/18/2014] [Indexed: 10/25/2022]
Abstract
A substantial amount of mitochondrial energy is required for cell-cycle progression. The mechanisms underlying the coordination of the mitochondrial respiration with cell-cycle progression, especially the G2/M transition, remain to be elucidated. Here, we show that a fraction of cyclin B1/Cdk1 proteins localizes to the matrix of mitochondria and phosphorylates a cluster of mitochondrial proteins, including the complex I (CI) subunits in the respiratory chain. Cyclin B1/Cdk1-mediated CI phosphorylation enhances CI activity, whereas deficiency of such phosphorylation in each of the relevant CI subunits results in impairment of CI function. Mitochondria-targeted cyclin B1/Cdk1 increases mitochondrial respiration with enhanced oxygen consumption and ATP generation, which provides cells with efficient bioenergy for G2/M transition and shortens overall cell-cycle time. Thus, cyclin B1/Cdk1-mediated phosphorylation of mitochondrial substrates allows cells to sense and respond to increased energy demand for G2/M transition and, subsequently, to upregulate mitochondrial respiration for successful cell-cycle progression.
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Affiliation(s)
- Zhaoqing Wang
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA
| | - Ming Fan
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA
| | - Demet Candas
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA
| | - Tie-Qiao Zhang
- Center for Biophotonics Science and Technology, University of California, Davis, Sacramento, CA 95817, USA
| | - Lili Qin
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA
| | - Angela Eldridge
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Sebastian Wachsmann-Hogiu
- Center for Biophotonics Science and Technology, University of California, Davis, Sacramento, CA 95817, USA
| | - Kazi M Ahmed
- Life Sciences Division, Department of Cancer and DNA Damage Response, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brett A Chromy
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Danupon Nantajit
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA
| | - Nadire Duru
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteomics Research Center, Beijing 102206, China
| | - Min Chen
- Signal Transduction Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Toren Finkel
- Center for Molecular Medicine, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lee S Weinstein
- Signal Transduction Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jian Jian Li
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA 95817, USA; NCI-Designated Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA 95817, USA.
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49
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Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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50
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Fukuda Y, Koteishi H, Yoneda R, Tamada T, Takami H, Inoue T, Nojiri M. Structural and functional characterization of the Geobacillus copper nitrite reductase: involvement of the unique N-terminal region in the interprotein electron transfer with its redox partner. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:396-405. [PMID: 24440558 DOI: 10.1016/j.bbabio.2014.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/19/2013] [Accepted: 01/07/2014] [Indexed: 11/28/2022]
Abstract
The crystal structures of copper-containing nitrite reductase (CuNiR) from the thermophilic Gram-positive bacterium Geobacillus kaustophilus HTA426 and the amino (N)-terminal 68 residue-deleted mutant were determined at resolutions of 1.3Å and 1.8Å, respectively. Both structures show a striking resemblance with the overall structure of the well-known CuNiRs composed of two Greek key β-barrel domains; however, a remarkable structural difference was found in the N-terminal region. The unique region has one β-strand and one α-helix extended to the northern surface of the type-1 copper site. The superposition of the Geobacillus CuNiR model on the electron-transfer complex structure of CuNiR with the redox partner cytochrome c551 in other denitrifier system led us to infer that this region contributes to the transient binding with the partner protein during the interprotein electron transfer reaction in the Geobacillus system. Furthermore, electron-transfer kinetics experiments using N-terminal residue-deleted mutant and the redox partner, Geobacillus cytochrome c551, were carried out. These structural and kinetics studies demonstrate that the region is directly involved in the specific partner recognition.
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Affiliation(s)
- Yohta Fukuda
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan; Molecular Biology Research Center, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Hiroyasu Koteishi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryohei Yoneda
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Taro Tamada
- Molecular Biology Research Center, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan
| | - Tsuyoshi Inoue
- Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Nojiri
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
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