1
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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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2
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Ferric heme as a CO/NO sensor in the nuclear receptor Rev-Erbß by coupling gas binding to electron transfer. Proc Natl Acad Sci U S A 2021; 118:2016717118. [PMID: 33436410 DOI: 10.1073/pnas.2016717118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Rev-Erbβ is a nuclear receptor that couples circadian rhythm, metabolism, and inflammation. Heme binding to the protein modulates its function as a repressor, its stability, its ability to bind other proteins, and its activity in gas sensing. Rev-Erbβ binds Fe3+-heme more tightly than Fe2+-heme, suggesting its activities may be regulated by the heme redox state. Yet, this critical role of heme redox chemistry in defining the protein's resting state and function is unknown. We demonstrate by electrochemical and whole-cell electron paramagnetic resonance experiments that Rev-Erbβ exists in the Fe3+ form within the cell allowing the protein to be heme replete even at low concentrations of labile heme in the nucleus. However, being in the Fe3+ redox state contradicts Rev-Erb's known function as a gas sensor, which dogma asserts must be Fe2+ This paper explains why the resting Fe3+ state is congruent both with heme binding and cellular gas sensing. We show that the binding of CO/NO elicits a striking increase in the redox potential of the Fe3+/Fe2+ couple, characteristic of an EC mechanism in which the unfavorable Electrochemical reduction of heme is coupled to the highly favorable Chemical reaction of gas binding, making the reduction spontaneous. Thus, Fe3+-Rev-Erbβ remains heme-loaded, crucial for its repressor activity, and undergoes reduction when diatomic gases are present. This work has broad implications for proteins in which ligand-triggered redox changes cause conformational changes influencing its function or interprotein interactions (e.g., between NCoR1 and Rev-Erbβ). This study opens up the possibility of CO/NO-mediated regulation of the circadian rhythm through redox changes in Rev-Erbβ.
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3
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Sellner M, Fischer A, Don CG, Smieško M. Conformational Landscape of Cytochrome P450 Reductase Interactions. Int J Mol Sci 2021; 22:1023. [PMID: 33498551 PMCID: PMC7864194 DOI: 10.3390/ijms22031023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023] Open
Abstract
Oxidative reactions catalyzed by Cytochrome P450 enzymes (CYPs), which constitute the most relevant group of drug-metabolizing enzymes, are enabled by their redox partner Cytochrome P450 reductase (CPR). Both proteins are anchored to the membrane of the endoplasmic reticulum and the CPR undergoes a conformational change in order to interact with the respective CYP and transfer electrons. Here, we conducted over 22 microseconds of molecular dynamics (MD) simulations in combination with protein-protein docking to investigate the conformational changes necessary for the formation of the CPR-CYP complex. While some structural features of the CPR and the CPR-CYP2D6 complex that we highlighted confirmed previous observations, our simulations revealed additional mechanisms for the conformational transition of the CPR. Unbiased simulations exposed a movement of the whole protein relative to the membrane, potentially to facilitate interactions with its diverse set of redox partners. Further, we present a structural mechanism for the susceptibility of the CPR to different redox states based on the flip of a glycine residue disrupting the local interaction network that maintains inter-domain proximity. Simulations of the CPR-CYP2D6 complex pointed toward an additional interaction surface of the FAD domain and the proximal side of CYP2D6. Altogether, this study provides novel structural insight into the mechanism of CPR-CYP interactions and underlying conformational changes, improving our understanding of this complex machinery Cytochrome P450 reductase; CPR; conformational; dynamicsrelevant for drug metabolism.
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Affiliation(s)
| | | | | | - Martin Smieško
- Computational Pharmacy, Departement of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland; (M.S.); (A.F.); (C.G.D.)
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4
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Khan T, Khan A, Ali SS, Ali S, Wei DQ. A computational perspective on the dynamic behaviour of recurrent drug resistance mutations in the pncA gene from Mycobacterium tuberculosis. RSC Adv 2021; 11:2476-2486. [PMID: 35424144 PMCID: PMC8693711 DOI: 10.1039/d0ra09326b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis is still one of the top 10 causes of death worldwide, particularly with the emergence of multidrug-resistant tuberculosis. As the most effective first-line anti-tuberculosis drug, pyrazinamide also develops resistance due to the mutation in the pncA gene. Among these mutations, seven mutations at positions F94L, F94S, K96N, K96R, G97C, G97D, and G97S are classified as high-level resistance mutations. However, the resistance mechanism of Mtb to PZA (pyrazinamide) caused by these mutations is still unclear. In this work, we combined molecular dynamics simulation, molecular mechanics/generalized-Born surface area calculation, principal component analysis, and free energy landscape analysis to explore the resistance mechanism of Mtb to PZA due to F94L, F94S, K96N, K96R, G97C, G97D, and G97S mutations, as well as compare interaction changes in wild-type and mutant PZA-bound complexes. The results of molecular mechanics/generalized-Born surface area calculations indicated that the binding free energy of PZA with seven mutants decreased. In mutant systems, the most significant interactions with His137 and Cys138 were lost. Besides, PCA and FEL confirmed significant variations in the protein dynamics during the simulation specifically by altering the Fe2+ binding and its destabilization. Furthermore, mutants also flipped the β-sheet 2, which also affects the binding of Fe2+ and PZA. In the G97D mutant, reported as most lethal, mutation causes the binding pocket to change considerably, so that the position of PZA has a large movement in the binding pocket. In this study, the resistance mechanism of PZA at the atomic level is proposed. The proposed drug-resistance mechanism will provide valuable guidance for the design of anti-tuberculosis drugs.
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Affiliation(s)
- Taimoor Khan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Abbas Khan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat Swat KP Pakistan
| | - Shahid Ali
- Center for Biotechnology and Microbiology, University of Swat Swat KP Pakistan
| | - Dong-Qing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200240 P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai 200030 P.R. China
- Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nashan District Shenzhen Guangdong 518055 P.R. China
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5
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Zhang L, Bill E, Kroneck PMH, Einsle O. Histidine-Gated Proton-Coupled Electron Transfer to the CuA Site of Nitrous Oxide Reductase. J Am Chem Soc 2020; 143:830-838. [DOI: 10.1021/jacs.0c10057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
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6
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Junaid M, Li CD, Li J, Khan A, Ali SS, Jamal SB, Saud S, Ali A, Wei DQ. Structural insights of catalytic mechanism in mutant pyrazinamidase of Mycobacterium tuberculosis. J Biomol Struct Dyn 2020; 39:3172-3185. [PMID: 32340563 DOI: 10.1080/07391102.2020.1761879] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pyrazinamidase (PZase) is a member of Fe-dependent amidohydrolases that activates pyrazinamide (PZA) into active pyrazinoic acid (POA). PZA, a nicotinamide analogue, is an essential first-line drug used in Mycobacterium tuberculosis (Mtb) treatment. The active form of PZA, POA, is toxic and potently inhibits the growth of latent Mtb, which makes it possible to shorten the conventional 9-month tuberculosis treatment to 6 months. In this study, an extensive molecular dynamics simulation was carried out to the study the resistance mechanism offered by the three mutations Q10P and D12A and G97D. Our results showed that two regions Gln10-His43, Phe50-Gly75 are profoundly affected by these mutations. Among the three mutations, Q10P and D12A mutations strongly disturb the communication among the catalytic triad (Asp8, Lys98 and Cys138). The oxyanion hole is formed between the backbone nitrogen atoms of A134 and C138 which stabilizes the hydroxyl anion of nicotinamide. The D12A mutation greatly disturbs the oxyanion hole formation followed by the Q10P and G97D. Our results also showed that these mutations destabilize the interaction between Fe2+ ion and Asp49, His51, His57 and His71. The binding pocket analysis showed that these mutations increase the cavity volume, which results in loose binding of PZA. MMGBSA analyzes have shown that these mutations reduce the binding affinity to the PZA drug. Our results may provide useful information for the design of new and effective PZase inhibitors based on structural information of WT and mutant PZases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Junaid
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China.,Ministry of Education, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, P.R China
| | - Cheng-Dong Li
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China.,Ministry of Education, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, P.R China
| | - Jiayi Li
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Abbas Khan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China.,Ministry of Education, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, P.R China
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Syed Baber Jamal
- Department of biological sciences, National University of Medical Sciences, Punjab, Rawalpendi, Pakistan
| | - Shah Saud
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China
| | - Arif Ali
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China.,Ministry of Education, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, P.R China
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, China.,Peng Cheng Laboratory, Shenzhen, Guangdong, P.R China.,Ministry of Education, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, P.R China
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7
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Breslmayr E, Laurent CVFP, Scheiblbrandner S, Jerkovic A, Heyes DJ, Oostenbrink C, Ludwig R, Hedison TM, Scrutton NS, Kracher D. Protein Conformational Change Is Essential for Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase. ACS Catal 2020; 10:4842-4853. [PMID: 32382450 PMCID: PMC7199207 DOI: 10.1021/acscatal.0c00754] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/30/2020] [Indexed: 12/30/2022]
Abstract
Large-scale protein domain dynamics and electron transfer are often associated. However, as protein motions span a broad range of time and length scales, it is often challenging to identify and thus link functionally relevant dynamic changes to electron transfer in proteins. It is hypothesized that large-scale domain motions direct electrons through a FAD and a heme b cofactor of the fungal cellobiose dehydrogenase (CDH) enzymes to the type-II copper center (T2Cu) of the polysaccharide-degrading lytic polysaccharide monooxygenases (LPMOs). However, as of yet, domain motions in CDH have not been linked formally to enzyme-catalyzed electron transfer reactions. The detailed structural features of CDH, which govern the functional conformational landscapes of the enzyme, have only been partially resolved. Here, we use a combination of pressure, viscosity, ionic strength, and temperature perturbation stopped-flow studies to probe the conformational landscape associated with the electron transfer reactions of CDH. Through the use of molecular dynamics simulations, potentiometry, and stopped-flow spectroscopy, we investigated how a conserved Tyr99 residue plays a key role in shaping the conformational landscapes for both the interdomain electron transfer reactions of CDH (from FAD to heme) and the delivery of electrons from the reduced heme cofactor to the LPMO T2Cu. Our studies show how motions gate the electron transfer within CDH and from CDH to LPMO and illustrate the conformational landscape for interdomain and interprotein electron transfer in this extracellular fungal electron transfer chain.
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Affiliation(s)
- Erik Breslmayr
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Christophe V. F. P. Laurent
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Stefan Scheiblbrandner
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Anita Jerkovic
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Derren J. Heyes
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Roland Ludwig
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Tobias M. Hedison
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- EPSRC/BBSRC funded Future Biomanufacturing Research Hub, The Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- EPSRC/BBSRC funded Future Biomanufacturing Research Hub, The Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
| | - Daniel Kracher
- Manchester Institute of Biotechnology, The University of Manchester, M1 7DN Manchester, United Kingdom
- Biocatalysis and Biosensing Laboratory, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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8
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Khan MT, Junaid M, Mao X, Wang Y, Hussain A, Malik SI, Wei DQ. Pyrazinamide resistance and mutations L19R, R140H, and E144K in Pyrazinamidase of Mycobacterium tuberculosis. J Cell Biochem 2019; 120:7154-7166. [PMID: 30485476 DOI: 10.1002/jcb.27989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023]
Abstract
Pyrazinamide (PZA) is an important component of first-line antituberculosis drugs activated by Mycobacterium tuberculosis pyrazinamidase (PZase) into its active form pyrazinoic acid. Mutations in the pncA gene have been recognized as the major cause of PZA resistance. We detected some novel mutations, Leucine19Arginine (L19R), Arginine140Histidine (R140H), and Glutamic acid144 Lysine (E144K), in the pncA gene of PZA-resistant isolates in our wet lab PZA drug susceptibility testing and sequencing. As the molecular mechanism of resistance of these variants has not been reported earlier, we have performed multiple analyses to unveil different mechanisms of resistance because of PZase mutations L19R, R140H, and E144K. The mutants and native PZase structures were subjected to comprehensive computational molecular dynamics (MD) simulations at 100 nanoseconds in apo and drug-bound form. Mutants and native PZase binding pocket were compared to observe the consequence of mutations on the binding pocket size. Hydrogen bonding, Gibbs free energy, and natural ligand Fe +2 effect were also analyzed between native and mutants. A significant variation between native and mutant PZase structure activity was observed. The native PZase protein docking score was found to be the maximum, showing strong binding affinity in comparison with mutants. MD simulations explored the effect of the variants on the biological function of PZase. Hydrogen bonding, metal ion Fe +2 deviation, and fluctuation also seemed to be affected because of the mutations L19R, R140H, and E144K. The variants L19R, R140H, and E144K play a significant role in PZA resistance, altering the overall activity of native PZase, including metal ion Fe +2 displacement and free energy. This study offers valuable evidence for better management of drug-resistant tuberculosis.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan.,Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Junaid
- Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xueying Mao
- Department of Bioinformatics and Biostatistics, Qianweichang College, Shanghai University, Shanghai, China
| | - Yanjie Wang
- Department of Computer Science, College of Computer Science and Information Tech, Henan Normal University, Xixiang, China
| | - Abid Hussain
- Department of Pharmaceutics, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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9
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Junaid M, Khan MT, Malik SI, Wei DQ. Insights into the Mechanisms of the Pyrazinamide Resistance of Three Pyrazinamidase Mutants N11K, P69T, and D126N. J Chem Inf Model 2018; 59:498-508. [PMID: 30481017 DOI: 10.1021/acs.jcim.8b00525] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In an effort to discover the mechanism of resistance offered by Mycobacterium tuberculosis (Mtb) toward the pyrazinamide (PZA) drug, an extensive molecular dynamics strategy was employed. PZA is a first-line prodrug that effectively cuts therapy time by 33% (from 9 to 6 months). Pyrazinamidase enzyme (PZase), encoded by the pncA gene, is responsible for the activation of prodrug PZA into pyrazinoic acid (POA). POA is toxic and potently inhibits the growth of latent Mtb even at low pH values. PZA resistance is caused by three genes pncA, rpsA, and panD. Among them, the pncA gene contributes 72-99% to the resistance. Hence, the present study focused on the novel mutations N11K, P69T, and D126N in the pncA gene. In the present study, the possible mechanism of these three mutations was studied through molecular dynamics simulation and docking techniques. Our in-depth analysis and results are in strong agreement with our experimental observation. The binding pocket analysis showed that mutations decrease the volume of the active site and hinder the correct orientation of PZA drug in the active site. Moreover, the Patchdock score was found to be low as compared to WT showing the disturbance of shape complementarity between PZase and PZA drug. These mutations were found to disturb the position of the Fe2+ ion. Among the mutations, D126N allosterically disturbed the position of the Fe2+ ion. MMGBSA analyses showed that these mutations decrease the binding affinity toward the PZA drug. In conclusion, mutations N11K, P69T, and D126N result in weak binding affinity with PZA and also cause significant structural deformations that lead to PZA resistance. This study provides useful information that mutations in other than active parts may also cause protein folding and ligand displacement effects, altering the biological functions.
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Affiliation(s)
- Muhammad Junaid
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai , Minhang District, China 200240
| | - Muhammad Tahir Khan
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai , Minhang District, China 200240.,Department of Bioinformatics and Biosciences , Capital University of Science and Technology , Islamabad , Pakistan 44000
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences , Capital University of Science and Technology , Islamabad , Pakistan 44000
| | - Dong-Qing Wei
- College of Life Sciences and Biotechnology, The State Key Laboratory of Microbial Metabolism , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai , Minhang District, China 200240
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10
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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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11
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Cloning, purification and characterization of novel Cu-containing nitrite reductase from the Bacillus firmus GY-49. World J Microbiol Biotechnol 2017; 34:10. [DOI: 10.1007/s11274-017-2383-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/22/2017] [Indexed: 11/27/2022]
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12
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Dai Y, Haque MM, Stuehr DJ. Restricting the conformational freedom of the neuronal nitric-oxide synthase flavoprotein domain reveals impact on electron transfer and catalysis. J Biol Chem 2017; 292:6753-6764. [PMID: 28232486 DOI: 10.1074/jbc.m117.777219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/16/2017] [Indexed: 01/02/2023] Open
Abstract
The signaling molecule nitric oxide (NO) is synthesized in animals by structurally related NO synthases (NOSs), which contain NADPH/FAD- and FMN-binding domains. During catalysis, NADPH-derived electrons transfer into FAD and then distribute into the FMN domain for further transfer to internal or external heme groups. Conformational freedom of the FMN domain is thought to be essential for the electron transfer (ET) reactions in NOSs. To directly examine this concept, we utilized a "Cys-lite" neuronal NOS flavoprotein domain and substituted Cys for two residues (Glu-816 and Arg-1229) forming a salt bridge between the NADPH/FAD and FMN domains in the conformationally closed structure to allow cross-domain disulfide bond formation or cross-linking by bismaleimides of various lengths. The disulfide bond cross-link caused a ≥95% loss of cytochrome c reductase activity that was reversible with DTT treatment, whereas graded cross-link lengthening gradually increased activity, thus defining the conformational constraints in the catalytic process. We used spectroscopic and stopped-flow techniques to further investigate how the changes in FMN domain conformational freedom impact the following: (i) the NADPH interaction; (ii) kinetics of electron loading (flavin reduction); (iii) stabilization of open versus closed conformational forms in two different flavin redox states; (iv) reactivity of the reduced FMN domain toward cytochrome c; (v) response to calmodulin binding; and (vi) the rates of interflavin ET and the FMN domain conformational dynamics. Together, our findings help explain how the spatial and temporal behaviors of the FMN domain impact catalysis by the NOS flavoprotein domain and how these behaviors are governed to enable electron flow through the enzyme.
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Affiliation(s)
- Yue Dai
- From the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and.,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Mohammad Mahfuzul Haque
- From the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
| | - Dennis J Stuehr
- From the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195 and
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13
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Trana EN, Nocek JM, Woude JV, Span I, Smith SM, Rosenzweig AC, Hoffman BM. Charge-Disproportionation Symmetry Breaking Creates a Heterodimeric Myoglobin Complex with Enhanced Affinity and Rapid Intracomplex Electron Transfer. J Am Chem Soc 2016; 138:12615-28. [PMID: 27646786 DOI: 10.1021/jacs.6b07672] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report rapid photoinitiated intracomplex electron transfer (ET) within a "charge-disproportionated" myoglobin (Mb) dimer with greatly enhanced affinity. Two mutually supportive Brownian Dynamics (BD) interface redesign strategies, one a new "heme-filtering" approach, were employed to "break the symmetry" of a Mb homodimer by pairing Mb constructs with complementary highly positive and highly negative net surface charges, introduced through D/E → K and K → E mutations, respectively. BD simulations using a previously developed positive mutant, Mb(+6) = Mb(D44K/D60K/E85K), led to construction of the complementary negative mutant Mb(-6) = Mb(K45E, K63E, K95E). Simulations predict the pair will form a well-defined complex comprising a tight ensemble of conformations with nearly parallel hemes, at a metal-metal distance ∼18-19 Å. Upon expression and X-ray characterization of the partners, BD predictions were verified through ET photocycle measurements enabled by Zn-deuteroporphyrin substitution, forming the [ZnMb(-6), Fe(3+)Mb(+6)] complex. Triplet ET quenching shows charge disproportionation increases the binding constant by no less than ∼5 orders of magnitude relative to wild-type Mb values. All progress curves for charge separation (CS) and charge recombination (CR) are reproduced by a generalized kinetic model for the interprotein ET photocycle. The intracomplex ET rate constants for both CS and CR are increased by over 5 orders of magnitude, and their viscosity independence is indicative of true interprotein ET, rather than dynamic gating as seen in previous studies. The complex displays an unprecedented timecourse for CR of the CS intermediate I. After a laser flash, I forms through photoinduced CS, accumulates to a maximum concentration, then dies away through CR. However, before completely disappearing, I reappears without another flash and reaches a second maximum before disappearing completely.
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Affiliation(s)
- Ethan N Trana
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Judith M Nocek
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Jon Vander Woude
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Ingrid Span
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Stephen M Smith
- Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
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14
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Lintuluoto M, Lintuluoto JM. DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase. Biochemistry 2016; 55:4697-707. [DOI: 10.1021/acs.biochem.6b00423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho,
Sakyo, Kyoto 606-8522, Japan
| | - Juha M. Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
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15
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Hedison TM, Leferink NGH, Hay S, Scrutton NS. Correlating Calmodulin Landscapes with Chemical Catalysis in Neuronal Nitric Oxide Synthase using Time-Resolved FRET and a 5-Deazaflavin Thermodynamic Trap. ACS Catal 2016; 6:5170-5180. [PMID: 27563493 PMCID: PMC4993522 DOI: 10.1021/acscatal.6b01280] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 06/23/2016] [Indexed: 11/28/2022]
Abstract
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A major challenge in enzymology is
the need to correlate the dynamic
properties of enzymes with, and understand the impact on, their catalytic
cycles. This is especially the case with large, multicenter enzymes
such as the nitric oxide synthases (NOSs), where the importance of
dynamics has been inferred from a variety of structural, single-molecule,
and ensemble spectroscopic approaches but where motions have not been
correlated experimentally with mechanistic steps in the reaction cycle.
Here we take such an approach. Using time-resolved spectroscopy employing
absorbance and Förster resonance energy transfer (FRET) and
exploiting the properties of a flavin analogue (5-deazaflavin mononucleotide
(5-dFMN)) and isotopically labeled nicotinamide coenzymes, we correlate
the timing of CaM structural changes when bound to neuronal nitric
oxide synthase (nNOS) with the nNOS catalytic cycle. We show that
remodeling of CaM occurs early in the electron transfer sequence (FAD
reduction), not at later points in the reaction cycle (e.g., FMN reduction).
Conformational changes are tightly correlated with FAD reduction kinetics
and reflect a transient “opening” and then “closure”
of the bound CaM molecule. We infer that displacement of the C-terminal
tail on binding NADPH and subsequent FAD reduction are the likely
triggers of conformational change. By combining the use of cofactor/coenzyme
analogues and time-resolved FRET/absorbance spectrophotometry, we
show how the reaction cycles of complex enzymes can be simplified,
enabling a detailed study of the relationship between protein dynamics
and reaction cycle chemistry—an approach that can also be used
with other complex multicenter enzymes.
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Affiliation(s)
- Tobias M. Hedison
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Sam Hay
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Synthetic Biology
Research Centre for Fine and Speciality Chemicals (SYNBIOCHEM), Manchester
Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
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16
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Berstis L, Beckham GT, Crowley MF. Electronic coupling through natural amino acids. J Chem Phys 2015; 143:225102. [PMID: 26671404 DOI: 10.1063/1.4936588] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Laura Berstis
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
| | - Gregg T. Beckham
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
| | - Michael F. Crowley
- National Renewable Energy Laboratory, National Bioenergy Center, 15013 Denver West Pkwy, Golden, Colorado 80401, USA
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17
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Characterization of the free energy dependence of an interprotein electron transfer reaction by variation of pH and site-directed mutagenesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1181-6. [PMID: 26087387 DOI: 10.1016/j.bbabio.2015.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 11/22/2022]
Abstract
The interprotein electron transfer (ET) reactions of the cupredoxin amicyanin, which mediates ET from the tryptophan tryptophylquinone (TTQ) cofactor of methylamine dehydrogenase to cytochrome c-551i have been extensively studied. However, it was not possible to perform certain key experiments in that native system. This study examines the ET reaction from reduced amicyanin to an alternative electron acceptor, the diheme protein MauG. It was possible to vary the ΔG° for this ET reaction by simply changing pH to determine the dependence of kET on ΔG°. A P94A mutation of amicyanin significantly altered its oxidation-reduction midpoint potential value. It was not possible to study the ET from reduced P94A amicyanin to cytochrome c-551i in the native system because that reaction was kinetically coupled. However, the reaction from reduced P94A amicyanin to MauG was a true ET reaction and it was possible to determine values of reorganization energy (λ) and electronic coupling for the reactions of this variant as well as native amicyanin. Comparison of the λ values associated with the ET reactions between amicyanin and the TTQ of methylamine dehydrogenase, the diheme center of MauG and the single heme of cytochrome c-551i, provides insight into the factors that dictate the λ values for the respective reactions. These results demonstrate how study of ET reactions with alternative redox partner proteins can complement and enhance our understanding of the reactions with the natural redox partners, and further our understanding of mechanisms of protein ET reactions.
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18
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Haque MM, Bayachou M, Tejero J, Kenney CT, Pearl NM, Im SC, Waskell L, Stuehr DJ. Distinct conformational behaviors of four mammalian dual-flavin reductases (cytochrome P450 reductase, methionine synthase reductase, neuronal nitric oxide synthase, endothelial nitric oxide synthase) determine their unique catalytic profiles. FEBS J 2014; 281:5325-40. [PMID: 25265015 DOI: 10.1111/febs.13073] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/27/2014] [Accepted: 09/25/2014] [Indexed: 12/14/2022]
Abstract
Multidomain enzymes often rely on large conformational motions to function. However, the conformational setpoints, rates of domain motions and relationships between these parameters and catalytic activity are not well understood. To address this, we determined and compared the conformational setpoints and the rates of conformational switching between closed unreactive and open reactive states in four mammalian diflavin NADPH oxidoreductases that catalyze important biological electron transfer reactions: cytochrome P450 reductase, methionine synthase reductase and endothelial and neuronal nitric oxide synthase. We used stopped-flow spectroscopy, single turnover methods and a kinetic model that relates electron flux through each enzyme to its conformational setpoint and its rates of conformational switching. The results show that the four flavoproteins, when fully-reduced, have a broad range of conformational setpoints (from 12% to 72% open state) and also vary 100-fold with respect to their rates of conformational switching between unreactive closed and reactive open states (cytochrome P450 reductase > neuronal nitric oxide synthase > methionine synthase reductase > endothelial nitric oxide synthase). Furthermore, simulations of the kinetic model could explain how each flavoprotein can support its given rate of electron flux (cytochrome c reductase activity) based on its unique conformational setpoint and switching rates. The present study is the first to quantify these conformational parameters among the diflavin enzymes and suggests how the parameters might be manipulated to speed or slow biological electron flux.
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Affiliation(s)
- Mohammad M Haque
- Department of Pathobiology, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, USA
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19
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Salazar-Salinas K, Baldera-Aguayo PA, Encomendero-Risco JJ, Orihuela M, Sheen P, Seminario JM, Zimic M. Metal-ion effects on the polarization of metal-bound water and infrared vibrational modes of the coordinated metal center of Mycobacterium tuberculosis pyrazinamidase via quantum mechanical calculations. J Phys Chem B 2014; 118:10065-75. [PMID: 25055049 PMCID: PMC4514207 DOI: 10.1021/jp504096d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
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Mycobacterium tuberculosis pyrazinamidase
(PZAse) is a key enzyme to activate the pro-drug pyrazinamide (PZA).
PZAse is a metalloenzyme that coordinates in vitro different divalent metal cofactors in the metal coordination site
(MCS). Several metals including Co2+, Mn2+,
and Zn2+ are able to reactivate the metal-depleted PZAse in vitro. We use quantum mechanical calculations to investigate
the Zn2+, Fe2+, and Mn2+ metal cofactor
effects on the local MCS structure, metal–ligand or metal–residue
binding energy, and charge distribution. Results suggest that the
major metal-dependent changes occur in the metal–ligand binding
energy and charge distribution. Zn2+ shows the highest
binding energy to the ligands (residues). In addition, Zn2+ and Mn2+ within the PZAse MCS highly polarize the O–H
bond of coordinated water molecules in comparison with Fe2+. This suggests that the coordination of Zn2+ or Mn2+ to the PZAse protein facilitates the deprotonation of coordinated
water to generate a nucleophile for catalysis as in carboxypeptidase
A. Because metal ion binding is relevant to enzymatic reaction, identification
of the metal binding event is important. The infrared vibrational
mode shift of the C=Nε (His) bond from the M. tuberculosis MCS is the best IR probe to metal
complexation.
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Affiliation(s)
- Karim Salazar-Salinas
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia , San Martin de Porres, Lima 31 Lima, Perú
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20
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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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21
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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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22
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Lu Z, Ma G, Veinot JGC, Wong CS. Disruption of biomolecule function by nanoparticles: how do gold nanoparticles affect Phase I biotransformation of persistent organic pollutants? CHEMOSPHERE 2013; 93:123-32. [PMID: 23763865 DOI: 10.1016/j.chemosphere.2013.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 04/23/2013] [Accepted: 05/02/2013] [Indexed: 05/22/2023]
Abstract
The potential influence of nanoparticles on cytochrome P-450 (CYP) isozyme mediated Phase I biotransformation of persistent organic pollutants (POPs) in vitro was investigated using citrate-capped gold nanoparticles (AuNPs) and 2,2',3,5',6-pentachlorobiphenyl (PCB 95) as the probe nanoparticle and compound, respectively. AuNPs affected the biotransformation activity of rat CYP2B1 and changed the atropisomeric composition of PCB 95, depending on the incubation time and the AuNP concentration. Electrostatic repulsion between citrate-coated AuNPs and rat CYP2B1 may influence the active conformation of the isozyme and consequently affect its activity and stereoselectivity. In addition, the effects of AuNPs on rat CYP2B1 activity also appeared to be through interference with the CYP catalytic cycle's electron transfer chain. Incubations with AuNPs had a decline in buffer conductance and an absorbance band red shift of AuNPs, from electrostatic interactions of K(+) with negatively-charged AuNP aggregates. These ionic strength changes affected the formation rate of nicotinamide adenine dinucleotide phosphate, which provides electrons for the oxidative reaction cycle, and the biotransformation activity and stereoselectivity of CYP. This study suggests that charged nanoparticles may be able to alter the functions of biomolecules directly, by electrostatic interaction, or indirectly, by changes to the surrounding ionic strength. These factors should be taken into account for further understanding and prediction of the environmental behavior and fate of POPs and nanoparticles.
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Affiliation(s)
- Zhe Lu
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
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23
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Abstract
The conditions for nitrite reductase (NiRs) produced by Lactobacillus plantarum from salted fish were optimized. Enzyme activity of nitrite reductase was used as evaluation index. The results showed that the pH value had greatest influence on enzyme activity. The optimum conditions of producing nitrite reductase were inoculate quantity 4 %, pH 6.3, culture temperature 35 °C, incubation time 48 h. The enzyme activity of nitrite reductase reached to 89.672 U/mL, which increased by 71 % after optimization. This work provided the foundation for the research of enzymatic properties of nitrite reductase. This may be useful to the production of salted fish products.
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24
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Tralau T, Luch A. The evolution of our understanding of endo-xenobiotic crosstalk and cytochrome P450 regulation and the therapeutic implications. Expert Opin Drug Metab Toxicol 2013; 9:1541-54. [DOI: 10.1517/17425255.2013.828692] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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25
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Iyanagi T, Xia C, Kim JJP. NADPH-cytochrome P450 oxidoreductase: prototypic member of the diflavin reductase family. Arch Biochem Biophys 2012; 528:72-89. [PMID: 22982532 PMCID: PMC3606592 DOI: 10.1016/j.abb.2012.09.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 09/01/2012] [Accepted: 09/03/2012] [Indexed: 12/31/2022]
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR) and nitric oxide synthase (NOS), two members of the diflavin oxidoreductase family, are multi-domain enzymes containing distinct FAD and FMN domains connected by a flexible hinge. FAD accepts a hydride ion from NADPH, and reduced FAD donates electrons to FMN, which in turn transfers electrons to the heme center of cytochrome P450 or NOS oxygenase domain. Structural analysis of CYPOR, the prototype of this enzyme family, has revealed the exact nature of the domain arrangement and the role of residues involved in cofactor binding. Recent structural and biophysical studies of CYPOR have shown that the two flavin domains undergo large domain movements during catalysis. NOS isoforms contain additional regulatory elements within the reductase domain that control electron transfer through Ca(2+)-dependent calmodulin (CaM) binding. The recent crystal structure of an iNOS Ca(2+)/CaM-FMN construct, containing the FMN domain in complex with Ca(2+)/CaM, provided structural information on the linkage between the reductase and oxgenase domains of NOS, making it possible to model the holo iNOS structure. This review summarizes recent advances in our understanding of the dynamics of domain movements during CYPOR catalysis and the role of the NOS diflavin reductase domain in the regulation of NOS isozyme activities.
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Affiliation(s)
- Takashi Iyanagi
- Department of Biochemistry, Medical College of Wisconsin, USA
- Department of Life Science, The Himeji Institute of Technology, University of Hyogo, Japan
| | - Chuanwu Xia
- Department of Biochemistry, Medical College of Wisconsin, USA
| | - Jung-Ja P. Kim
- Department of Biochemistry, Medical College of Wisconsin, USA
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Leferink NGH, Eady RR, Hasnain SS, Scrutton NS. Laser-flash photolysis indicates that internal electron transfer is triggered by proton uptake by Alcaligenes xylosoxidans copper-dependent nitrite reductase. FEBS J 2012; 279:2174-81. [DOI: 10.1111/j.1742-4658.2012.08601.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Hira D, Toh H, Migita CT, Okubo H, Nishiyama T, Hattori M, Furukawa K, Fujii T. Anammox organism KSU-1 expresses a NirK-type copper-containing nitrite reductase instead of a NirS-type with cytochromecd1. FEBS Lett 2012; 586:1658-63. [DOI: 10.1016/j.febslet.2012.04.041] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 10/28/2022]
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