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Varfolomeeva LA, Shipkov NS, Dergousova NI, Boyko KM, Khrenova MG, Tikhonova TV, Popov VO. Molecular mechanism of thiocyanate dehydrogenase at atomic resolution. Int J Biol Macromol 2024; 279:135058. [PMID: 39191340 DOI: 10.1016/j.ijbiomac.2024.135058] [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: 05/26/2024] [Revised: 08/16/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024]
Abstract
Some sulfur-oxidizing bacteria playing an important role in global geochemical cycles utilize thiocyanate as the sole source of energy and nitrogen. In these bacteria the process of thiocyanate into cyanate conversion is mediated by thiocyanate dehydrogenases - a recently discovered family of copper-containing enzymes with the three‑copper active site unique among the other copper proteins. To get a deeper insight into the structure and molecular mechanism of action of thiocyanate dehydrogenases we isolated, purified, and comprehensively characterized an enzyme from the bacterium Pelomicrobium methylotrophicum. High-resolution crystal structures of the thiocyanate dehydrogenase in the free state and in the complexes with the transition state analog, thiourea, and the closest substrate analog, selenocyanate, unveiled the fine details of molecular events occurring at the enzyme active site. During the reaction thiocyanate dehydrogenase undergoes profound conformational change that affects the position of the constituent copper ions and results in the activation of the attacking water molecule. The structure of the enzyme complex with the selenium atom bridged in-between two copper ions was obtained representing an important transient intermediate. Structures of the complexes with inhibitors supplemented with quantum chemical calculations clarify the role of copper ions and refine molecular mechanism of catalysis by thiocyanate dehydrogenase.
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Affiliation(s)
- Larisa A Varfolomeeva
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation
| | - Nikolai S Shipkov
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation
| | - Natalia I Dergousova
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation
| | - Konstantin M Boyko
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation
| | - Maria G Khrenova
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation; Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1, Moscow 119991, Russian Federation
| | - Tamara V Tikhonova
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation
| | - Vladimir O Popov
- Laboratory of Enzyme Engineering, Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow 119071, Russian Federation; Department of Biology, Lomonosov Moscow State University, Leninskiye Gory 1, Moscow 119991, Russian Federation.
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2
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Roger M, Leone P, Blackburn NJ, Horrell S, Chicano TM, Biaso F, Giudici-Orticoni MT, Abriata LA, Hura GL, Hough MA, Sciara G, Ilbert M. Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features. Dalton Trans 2024; 53:1794-1808. [PMID: 38170898 PMCID: PMC10804444 DOI: 10.1039/d3dt03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.
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Affiliation(s)
- Magali Roger
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Philippe Leone
- CNRS, Aix-Marseille University, Laboratoire d'Ingénierie des Systèmes Macromoléculaires, LISM UMR7255, 13009 Marseille, France
| | - Ninian J Blackburn
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Sam Horrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Tadeo Moreno Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
| | - Frédéric Biaso
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Marie-Thérèse Giudici-Orticoni
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
| | - Luciano A Abriata
- Laboratory for Biomolecular Modeling and Protein Purification and Structure Core Facility, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Giuliano Sciara
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
- Aix Marseille Univ, INRAE, BBF UMR1163, Biodiversité et Biotechnologie Fongiques, 13288 Marseille, France
| | - Marianne Ilbert
- CNRS, Aix-Marseille University, Bioenergetic and Protein Engineering Laboratory, BIP UMR 7281, Mediterranean Institute of Microbiology, 13009 Marseille, France.
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Valianti VK, Tselios C, Pinakoulaki E. Reversible thermally induced spin crossover in the myoglobin-nitrito adduct directly monitored by resonance Raman spectroscopy. RSC Adv 2023; 13:9020-9025. [PMID: 36950070 PMCID: PMC10025812 DOI: 10.1039/d3ra00225j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/12/2023] [Indexed: 03/24/2023] Open
Abstract
Myoglobin has been demonstrated to function as a nitrite reductase to produce nitric oxide during hypoxia. One of the most intriguing aspects of the myoglobin/nitrite interactions revealed so far is the unusual O-binding mode of nitrite to the ferric heme iron, although conflicting data have been reported for the electronic structure of this complex also raising the possibility of linkage isomerism. In this work, we applied resonance Raman spectroscopy in a temperature-dependent approach to investigate the binding of nitrite to ferric myoglobin and the properties of the formed adduct from ambient to low temperatures (293 K to 153 K). At ambient temperature the high spin state of the ferric heme Fe-O-N[double bond, length as m-dash]O species is present and upon decreasing the temperature the low spin state is populated, demonstrating that a thermally-induced spin crossover phenomenon takes place analogous to what has been observed in many transition metal complexes. The observed spin crossover is fully reversible and is not due to linkage isomerism, since the O-binding mode is retained upon the spin transition. The role of the heme pocket environment in controlling the nitrite binding mode and spin transition is discussed.
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Affiliation(s)
| | - Charalampos Tselios
- Department of Chemistry, University of Cyprus 2109 Aglantzia Cyprus
- Department of Chemical Engineering, Cyprus University of Technology Lemesos Cyprus
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4
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Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases. Proc Natl Acad Sci U S A 2022; 119:e2205664119. [PMID: 35862453 PMCID: PMC9335323 DOI: 10.1073/pnas.2205664119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
X-rays used to collect crystallographic data can change the redox states of transition metals utilized by many biological systems including metalloproteins. This disadvantage has been harnessed to drive a complex chemical reaction requiring the delivery of an electron to the active site and recording the structural changes accompanying catalysis, providing a real-time structural movie of an enzymatic reaction, which has been a dream of enzymologists for decades. By coupling the multiple-structures from one crystal technique with single-crystal and solution optical spectroscopy, we show that the electron transfer between the electron accepting type-1 Cu and catalytic type-2 Cu redox centers is gated in a recently characterized copper nitrite reductase. This combined structural/spectroscopic approach is applicable to many complex redox biological systems. Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.
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5
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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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6
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Chang YL, Chen HY, Chen SH, Kao CL, Chiang MY, Hsu SCN. An investigation on catalytic nitrite reduction reaction by bioinspired Cu II complexes. Dalton Trans 2022; 51:7715-7722. [PMID: 35522169 DOI: 10.1039/d1dt04102a] [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
Catalytic nitrite reductions by CuII complexes containing anionic Me2Tp, neutral Me2Tpm, or neutral iPrTIC ligands in the presence of L-ascorbic acid, which served as an electron donor and proton source, were investigated. The results showed that auxiliary ligands are important for copper-mediated catalytic nitrite reduction. Furthermore, the electronic effects of the ligand govern the nitrite reduction efficiency, which should be considered at two control points: one is the susceptibility of the LCuI-nitrite species to protonation and the other is the susceptibility of LCuII to reduction giving LCuI. In addition, an external strong acid leads to the production of nitrous acid, which may suggest that the reactivity of nitrous acid toward the LCuI species is a third control point.
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Affiliation(s)
- Yu-Lun Chang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Si-Hong Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Michael Y Chiang
- Department of Chemistry, National Sun Yat-Sen University No. 70, Lienhai Rd., Kaohsiung 804, Taiwan
| | - Sodio C N Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan. .,Department of Chemistry, National Sun Yat-Sen University No. 70, Lienhai Rd., Kaohsiung 804, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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Gupta S, Arora S, Mondal A, Stieber SCE, Gupta P, Kundu S. A Copper(II)‐Nitrite Complex Hydrogen‐Bonded to a Protonated Amine in the Second‐Coordination‐Sphere. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shourya Gupta
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram Chemistry INDIA
| | - Sumangla Arora
- IIT Roorkee: Indian Institute of Technology Roorkee Chemistry INDIA
| | - Aditesh Mondal
- IISER-TVM: Indian Institute of Science Education Research Thiruvananthapuram Chemistry INDIA
| | | | - Puneet Gupta
- IIT Roorkee: Indian Institute of Technology Roorkee Chemistry INDIA
| | - Subrata Kundu
- Indian Institute of Science Education and Research Thiruvananthapuram Chemistry Maruthamala POVithura 695551 Thiruvananthapuram INDIA
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8
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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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Ramírez CS, Tolmie C, Opperman DJ, González PJ, Rivas MG, Brondino CD, Ferroni FM. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator. Protein Sci 2021; 30:2310-2323. [PMID: 34562300 DOI: 10.1002/pro.4195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/08/2022]
Abstract
We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
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Affiliation(s)
- Cintia Soledad Ramírez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Carmien Tolmie
- Department of Microbiology and Biochemistry, University of the Free State (UFS), Bloemfontein, South Africa
| | - Diederik Johannes Opperman
- Department of Microbiology and Biochemistry, University of the Free State (UFS), Bloemfontein, South Africa
| | - Pablo Javier González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Carlos Dante Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Felix Martín Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
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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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2.85 and 2.99 Å resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy. J Struct Biol 2021; 213:107768. [PMID: 34217801 DOI: 10.1016/j.jsb.2021.107768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/22/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022]
Abstract
Cu-containing nitrite reductases (NiRs) are 110 kDa enzymes that play central roles in denitrification. Although the NiRs have been well studied, with over 100 Protein Data Bank entries, such issues as crystal packing, photoreduction, and lack of high pH cases have impeded structural analysis of their catalytic mechanisms. Here we show the cryogenic electron microscopy (cryo-EM) structures of Achromobacter cycloclastes NiR (AcNiR) at pH 6.2 and 8.1. The optimization of 3D-reconstruction parameters achieved 2.99 and 2.85 Å resolution. Comprehensive comparisons with cryo-EM and 56 AcNiR crystal structures suggested crystallographic artifacts in residues 185-215 and His255' due to packing and photoreduction, respectively. We used a newly developed map comparison method to detect structural change around the type 2 Cu site. While the theoretical estimation of coordinate errors of cryo-EM structures remains difficult, combined analysis using X-ray and cryo-EM structures will allow deeper insight into the local structural changes of proteins.
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12
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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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13
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Rose SL, Antonyuk SV, Sasaki D, Yamashita K, Hirata K, Ueno G, Ago H, Eady RR, Tosha T, Yamamoto M, Hasnain SS. An unprecedented insight into the catalytic mechanism of copper nitrite reductase from atomic-resolution and damage-free structures. SCIENCE ADVANCES 2021; 7:eabd8523. [PMID: 33523860 PMCID: PMC7775769 DOI: 10.1126/sciadv.abd8523] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/27/2020] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs), encoded by nirK gene, are found in all kingdoms of life with only 5% of CuNiR denitrifiers having two or more copies of nirK Recently, we have identified two copies of nirK genes in several α-proteobacteria of the order Rhizobiales including Bradyrhizobium sp. ORS 375, encoding a four-domain heme-CuNiR and the usual two-domain CuNiR (Br 2DNiR). Compared with two of the best-studied two-domain CuNiRs represented by the blue (AxNiR) and green (AcNiR) subclasses, Br 2DNiR, a blue CuNiR, shows a substantially lower catalytic efficiency despite a sequence identity of ~70%. Advanced synchrotron radiation and x-ray free-electron laser are used to obtain the most accurate (atomic resolution with unrestrained SHELX refinement) and damage-free (free from radiation-induced chemistry) structures, in as-isolated, substrate-bound, and product-bound states. This combination has shed light on the protonation states of essential catalytic residues, additional reaction intermediates, and how catalytic efficiency is modulated.
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Affiliation(s)
- Samuel L Rose
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Daisuke Sasaki
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kunio Hirata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Go Ueno
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Robert R Eady
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Takehiko Tosha
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Masaki Yamamoto
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
| | - S Samar Hasnain
- Molecular Biophysics Group, Life Sciences Building and Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.
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14
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Hough MA, Conradie J, Strange RW, Antonyuk SV, Eady RR, Ghosh A, Hasnain SS. Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis. Chem Sci 2020; 11:12485-12492. [PMID: 34094452 PMCID: PMC8163067 DOI: 10.1039/d0sc04797j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The design and synthesis of copper complexes that can reduce nitrite to NO has attracted considerable interest. They have been guided by the structural information on the catalytic Cu centre of the widespread enzymes Cu nitrite reductases but the chemically novel side-on binding of NO observed in all crystallographic studies of these enzymes has been questioned in terms of its functional relevance. We show conversion of NO2− to NO in the crystal maintained at 170 K and present ‘molecular movies’ defining events during enzyme turnover including the formation of side-on Cu-NO intermediate. DFT modelling suggests that both true {CuNO}11 and formal {CuNO}10 states may occur as side-on forms in an enzymatic active site with the stability of the {CuNO}10 side-on form governed by the protonation state of the histidine ligands. Formation of a copper-nitrosyl intermediate thus needs to be accommodated in future design templates for functional synthetic Cu-NiR complexes. Observation of side-on copper-nitrosyl intermediate and its confirmation by DFT during catalysis of copper nitrite reductases.![]()
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Affiliation(s)
- Michael A Hough
- School of Life Sciences, University of Essex Wivenhoe Park Colchester CO4 3SQW UK
| | - Jeanet Conradie
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of the Free State PO Box 339 Bloemfontein South Africa.,Department of Chemistry, UiT, The Arctic University of Tromsø 9037 Tromsø Norway
| | - Richard W Strange
- School of Life Sciences, University of Essex Wivenhoe Park Colchester CO4 3SQW UK
| | - 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 UK
| | - 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 UK
| | - Abhik Ghosh
- Department of Chemistry, UiT, The Arctic University of Tromsø 9037 Tromsø Norway
| | - 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 UK
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15
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Dissanayake DMMM, Petel BE, Brennessel WW, Bren KL, Matson EM. Hydrogen bonding promotes diversity in nitrite coordination modes at a single iron(II) center. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1821373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Brittney E. Petel
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | - Ellen M. Matson
- Department of Chemistry, University of Rochester, Rochester, NY, USA
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16
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First-principles study on the structure and optical spectroscopy of the redox-active center of blue copper proteins. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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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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Pinter TBJ, Koebke KJ, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Helical Scaffolds. Angew Chem Int Ed Engl 2020; 59:7678-7699. [PMID: 31441170 PMCID: PMC7035182 DOI: 10.1002/anie.201907502] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Indexed: 12/31/2022]
Abstract
The relationship between protein structure and function is one of the greatest puzzles within biochemistry. De novo metalloprotein design is a way to wipe the board clean and determine what is required to build in function from the ground up in an unrelated structure. This Review focuses on protein design efforts to create de novo metalloproteins within alpha-helical scaffolds. Examples of successful designs include those with carbonic anhydrase or nitrite reductase activity by incorporating a ZnHis3 or CuHis3 site, or that recapitulate the spectroscopic properties of unique electron-transfer sites in cupredoxins (CuHis2 Cys) or rubredoxins (FeCys4 ). This work showcases the versatility of alpha helices as scaffolds for metalloprotein design and the progress that is possible through careful rational design. Our studies cover the invariance of carbonic anhydrase activity with different site positions and scaffolds, refinement of our cupredoxin models, and enhancement of nitrite reductase activity up to 1000-fold.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States, 48109-1055
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20
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Pinter TBJ, Koebke KJ, Pecoraro VL. Katalyse und Elektronentransfer in helikalen De‐novo‐Gerüststrukturen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201907502] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
| | - Vincent L. Pecoraro
- Department of Chemistry University of Michigan Ann Arbor Michigan 48109-1055 USA
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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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Andring JT, Kim CU, McKenna R. Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase. IUCRJ 2020; 7:287-293. [PMID: 32148856 PMCID: PMC7055381 DOI: 10.1107/s2052252520000986] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2020] [Indexed: 05/06/2023]
Abstract
Nitric oxide (NO) promotes vasodilation through the activation of guanylate cyclase, resulting in the relaxation of the smooth muscle vasculature and a subsequent decrease in blood pressure. Therefore, its regulation is of interest for the treatment and prevention of heart disease. An example is pulmonary hypertension which is treated by targeting this NO/vasodilation pathway. In bacteria, plants and fungi, nitrite (NO2 -) is utilized as a source of NO through enzymes known as nitrite reductases. These enzymes reduce NO2 - to NO through a catalytic metal ion, often copper. Recently, several studies have shown nitrite reductase activity of mammalian carbonic anhydrase II (CAII), yet the molecular basis for this activity is unknown. Here we report the crystal structure of copper-bound human CAII (Cu-CAII) in complex with NO2 - at 1.2 Å resolution. The structure exhibits Type 1 (T-1) and 2 (T-2) copper centers, analogous to bacterial nitrite reductases, both required for catalysis. The copper-substituted CAII active site is penta-coordinated with a 'side-on' bound NO2 -, resembling a T-2 center. At the N terminus, several residues that are normally disordered form a porphyrin ring-like configuration surrounding a second copper, acting as a T-1 center. A structural comparison with both apo- (without metal) and zinc-bound CAII (Zn-CAII) provides a mechanistic picture of how, in the presence of copper, CAII, with minimal conformational changes, can function as a nitrite reductase.
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Affiliation(s)
- Jacob T. Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
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24
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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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25
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High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase. Proc Natl Acad Sci U S A 2020; 117:4071-4077. [PMID: 32041886 PMCID: PMC7049163 DOI: 10.1073/pnas.1918125117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
X-ray crystallography often fails to determine the positions of hydrogen atoms, which play crucial roles in enzymatic reactions. Despite many X-ray crystallographic studies, the reaction mechanism of copper-containing nitrite reductases (CuNIRs), which reduce nitrite using two protons, has been controversial. The high-resolution neutron structure of a CuNIR reveals the protonation states of catalytic residues and key water molecules, thus providing insights into the catalytic mechanism. The catalytic Cu is shown to be coordinated by a hydroxide ion and not water. Furthermore, the hydrogen-deuterium exchange ratio suggests that intramolecular electron transfer is involved in a hydrogen-bond jump. These observations are consistent with previous computational chemistry; therefore, our study forms a bridge between the structural biology and quantum chemistry of CuNIRs. Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.
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26
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Mondal A, Reddy KP, Bertke JA, Kundu S. Phenol Reduces Nitrite to NO at Copper(II): Role of a Proton-Responsive Outer Coordination Sphere in Phenol Oxidation. J Am Chem Soc 2020; 142:1726-1730. [PMID: 31910624 DOI: 10.1021/jacs.9b11597] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the view of physiological significance, the transition-metal-mediated routes for nitrite (NO2-) to nitric oxide (NO) conversion and phenol oxidation are of prime importance. Probing the reactivity of substituted phenols toward the nitritocopper(II) cryptate complex [mC]Cu(κ2-O2N)(ClO4) (1a), this report illustrates NO release from nitrite at copper(II) following a proton-coupled electron transfer (PCET) pathway. Moreover, a different protonated state of 1a with a proton hosted in the outer coordination sphere, [mCH]Cu(κ2-O2N)(ClO4)2 (3), also reacts with substituted phenols via primary electron transfer from the phenol. Intriguingly, the alternative mechanism operative because of the presence of a proton at the remote site in 3 facilitates an unusual anaerobic pathway for phenol nitration.
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Affiliation(s)
- Aditesh Mondal
- School of Chemistry , Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM) , Thiruvananthapuram 695551 , India
| | - Kiran P Reddy
- School of Chemistry , Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM) , Thiruvananthapuram 695551 , India
| | - Jeffery A Bertke
- Department of Chemistry , Georgetown University , Box 571227-1227, Washington , D.C. 20057 , United States
| | - Subrata Kundu
- School of Chemistry , Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM) , Thiruvananthapuram 695551 , India
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27
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Cheng R, Wu C, Cao Z, Wang B. QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase. Phys Chem Chem Phys 2020; 22:20922-20928. [DOI: 10.1039/d0cp03053h] [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
The nitrite reduction in copper nitrite reductase is found to proceed through an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer from T1-Cu to T2-Cu preceding the proton transfer from Asp98 to nitrite.
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Affiliation(s)
- Ronny Cheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- P. R. China
| | - Chun Wu
- College of Science and Mathematics
- Rowan University
- Glassboro
- 08028 USA
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen 361005
- P. R. China
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28
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Moreno-Chicano T, Ebrahim A, Axford D, Appleby MV, Beale JH, Chaplin AK, Duyvesteyn HME, Ghiladi RA, Owada S, Sherrell DA, Strange RW, Sugimoto H, Tono K, Worrall JAR, Owen RL, Hough MA. High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. IUCRJ 2019; 6:1074-1085. [PMID: 31709063 PMCID: PMC6830213 DOI: 10.1107/s2052252519011655] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/21/2019] [Indexed: 05/09/2023]
Abstract
High-throughput X-ray crystal structures of protein-ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein-ligand complexes using SFX.
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Affiliation(s)
- Tadeo Moreno-Chicano
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Ali Ebrahim
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - John H. Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Amanda K. Chaplin
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Helen M. E. Duyvesteyn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology (STRUBI), University of Oxford, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, England
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA
| | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Richard W. Strange
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | | | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Jonathan A. R. Worrall
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Michael A. Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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29
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Bower JK, Sokolov AY, Zhang S. Four‐Coordinate Copper Halonitrosyl {CuNO}
10
Complexes. Angew Chem Int Ed Engl 2019; 58:10225-10229. [DOI: 10.1002/anie.201904732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Jamey K. Bower
- Department of Chemistry and BiochemistryThe Ohio State University 100 W. 18th Ave Columbus OH USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and BiochemistryThe Ohio State University 100 W. 18th Ave Columbus OH USA
| | - Shiyu Zhang
- Department of Chemistry and BiochemistryThe Ohio State University 100 W. 18th Ave Columbus OH USA
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30
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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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31
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Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. IUCRJ 2019; 6:761-772. [PMID: 31316819 PMCID: PMC6608623 DOI: 10.1107/s2052252519008285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) that convert NO2 - to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD-, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 - a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.
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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
| | - Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rajesh T. Shenoy
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - 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
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - 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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32
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Bower JK, Sokolov AY, Zhang S. Four‐Coordinate Copper Halonitrosyl {CuNO}
10
Complexes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jamey K. Bower
- Department of Chemistry and BiochemistryThe Ohio State University 100 W. 18th Ave Columbus OH USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and BiochemistryThe Ohio State University 100 W. 18th Ave Columbus OH USA
| | - Shiyu Zhang
- Department of Chemistry and BiochemistryThe Ohio State University 100 W. 18th Ave Columbus OH USA
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33
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Shi K, Mathivathanan L, Boudalis AK, Turek P, Chakraborty I, Raptis RG. Nitrite Reduction by Trinuclear Copper Pyrazolate Complexes: An Example of a Catalytic, Synthetic Polynuclear NO Releasing System. Inorg Chem 2019; 58:7537-7544. [DOI: 10.1021/acs.inorgchem.9b00748] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kaige Shi
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Logesh Mathivathanan
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Athanassios K. Boudalis
- Institut de Chimie UMR 7177/Université de Strasbourg 4, rue Blaise Pascal/CS 90032, F-67081 Strasbourg CEDEX, France
| | - Philippe Turek
- Institut de Chimie UMR 7177/Université de Strasbourg 4, rue Blaise Pascal/CS 90032, F-67081 Strasbourg CEDEX, France
| | - Indranil Chakraborty
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Raphael G. Raptis
- Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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34
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Ebrahim A, Appleby MV, Axford D, Beale J, Moreno-Chicano T, Sherrell DA, Strange RW, Hough MA, Owen RL. Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2019; 75:151-159. [PMID: 30821704 PMCID: PMC6400251 DOI: 10.1107/s2059798318010240] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/16/2018] [Indexed: 11/11/2022] Open
Abstract
The ability to determine high-quality, artefact-free structures is a challenge in micro-crystallography, and the rapid onset of radiation damage and requirement for a high-brilliance X-ray beam mean that a multi-crystal approach is essential. However, the combination of crystal-to-crystal variation and X-ray-induced changes can make the formation of a final complete data set challenging; this is particularly true in the case of metalloproteins, where X-ray-induced changes occur rapidly and at the active site. An approach is described that allows the resolution, separation and structure determination of crystal polymorphs, and the tracking of radiation damage in microcrystals. Within the microcrystal population of copper nitrite reductase, two polymorphs with different unit-cell sizes were successfully separated to determine two independent structures, and an X-ray-driven change between these polymorphs was followed. This was achieved through the determination of multiple serial structures from microcrystals using a high-throughput high-speed fixed-target approach coupled with robust data processing.
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Affiliation(s)
- Ali Ebrahim
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - John Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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35
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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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36
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Chuang WJ, Narwane M, Chen HY, Kao CL, Huang B, Hsu KM, Wang YM, Hsu SCN. Nitric oxide-release study of a bio-inspired copper(i)-nitrito complex under chemical and biological conditions. Dalton Trans 2018; 47:13151-13157. [PMID: 30175363 DOI: 10.1039/c8dt02281j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The selective and efficient nitrite reduction process is ubiquitous in biological systems. To understand copper-mediated nitrite reduction, we developed a bio-inspired model system to investigate the mechanism of copper-containing nitrite reductase. A well-characterized copper(i)-nitrate complex with amino functionalized 2-(diphenylphosphino)aniline ligands, [(Ph2PC6H4(o-NH2))2Cu(ONO)], demonstrated the aniline protonation will cause NO release in an acidic environment. To further understand NO releasing ability, we also performed pH-dependency experiments and confocal imaging to release NO under physiological buffer conditions. According to titration and spectroscopic studies on the protonation reaction of complex [(Ph2PC6H4(o-NH2))2Cu(ONO)], we proposed a mechanistic pathway for proton transfer and NO release. Furthermore, DFT calculations predicted that the release of NO takes place via aniline in both organic and aqueous media. These results highlight the importance of the proton-rich microenvironment around the copper(i)-nitrite core to induce nitrate reduction in a chemical and biological environment.
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Affiliation(s)
- Wan-Jung Chuang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Manmath Narwane
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan. and Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Bin Huang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Kuang-Mei Hsu
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - Yun-Ming Wang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan and Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - Sodio C N Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan. and Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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37
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Koebke KJ, Pecoraro VL. Development of de Novo Copper Nitrite Reductases: Where We Are and Where We Need To Go. ACS Catal 2018; 8:8046-8057. [PMID: 30294504 DOI: 10.1021/acscatal.8b02153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of redox-active metalloprotein catalysts is a challenging objective of de novo protein design. Within this Perspective we detail our efforts to create a redox-active Cu nitrite reductase (NiR) by incorporating Cu into the hydrophobic interior of well-defined three-stranded coiled coils (3SCCs). The scaffold contains three histidine residues that provide a layer of three nitrogen donors that mimic the type 2 catalytic site of NiR. We have found that this strategy successfully produces an active and stable CuNiR model that functions for over 1000 turnovers. Spectroscopic evidence indicates that the Cu(I) site has a lower coordination number in comparison to the enzyme, whereas the Cu(II) geometry may more faithfully reproduce the NiR type 2 center. Mutations at the helical interface successfully produce a hydrogen bond between an interfacial Glu residue and the Culigating His residue, which allows for the tuning of the redox potential over a 100 mV range. We successfully created constructs with as much as a 120-fold improvement from the original design by modifying the steric bulk above or below the Cu binding site. These systems are now the most active water-soluble and stable artificial NiR catalysts yet produced. Several avenues for improving the catalytic efficiency of later designs are detailed within this Perspective, including adjustment of their resting oxidation state, the use of asymmetric scaffolds to allow for single amino acid mutation within the second coordination sphere, and the design of hydrogen-bonding networks to tune residue orientation and electronics. Through these studies the TRI-H system has given insight into the difficulties that arise in creating a de novo redox active enzyme. Work to improve upon this model will provide strategies by which redox-active de novo enzymes may be tuned and detail how native enzymes accomplish catalytic efficiencies through proton gated redox catalysis.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
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38
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Fukuda Y, Matsusaki T, Tse KM, Mizohata E, Murphy MEP, Inoue T. Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:769-777. [PMID: 30082512 DOI: 10.1107/s2059798318010082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 07/12/2018] [Indexed: 11/10/2022]
Abstract
Copper-containing nitrite reductases (CuNIRs) are multifunctional enzymes that catalyse the one-electron reduction of nitrite (NO2-) to nitric oxide (NO) and the two-electron reduction of dioxygen (O2) to hydrogen peroxide (H2O2). In contrast to the mechanism of nitrite reduction, that of dioxygen reduction is poorly understood. Here, results from anaerobic synchrotron-radiation crystallography (SRX) and aerobic in-house radiation crystallography (iHRX) with a CuNIR from the thermophile Geobacillus thermodenitrificans (GtNIR) support the hypothesis that the dioxygen present in an aerobically manipulated crystal can bind to the catalytic type 2 copper (T2Cu) site of GtNIR during SRX experiments. The anaerobic SRX structure showed a dual conformation of one water molecule as an axial ligand in the T2Cu site, while previous aerobic SRX GtNIR structures were refined as diatomic molecule-bound states. Moreover, an SRX structure of the C135A mutant of GtNIR with peroxide bound to the T2Cu atom was determined. The peroxide molecule was mainly observed in a side-on binding manner, with a possible minor end-on conformation. The structures provide insights into dioxygen chemistry in CuNIRs and hence help to unmask the other face of CuNIRs.
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Affiliation(s)
- Yohta Fukuda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takuro Matsusaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ka Man Tse
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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39
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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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40
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Horrell S, Kekilli D, Sen K, Owen RL, Dworkowski FSN, Antonyuk SV, Keal TW, Yong CW, Eady RR, Hasnain SS, Strange RW, Hough MA. Enzyme catalysis captured using multiple structures from one crystal at varying temperatures. IUCRJ 2018; 5:283-292. [PMID: 29755744 PMCID: PMC5929374 DOI: 10.1107/s205225251800386x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/05/2018] [Indexed: 05/24/2023]
Abstract
High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.
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Affiliation(s)
- Sam Horrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Kakali Sen
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | | | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Thomas W. Keal
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Chin W. Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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41
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Chang YL, Lin YF, Chuang WJ, Kao CL, Narwane M, Chen HY, Chiang MY, Hsu SCN. Structure and nitrite reduction reactivity study of bio-inspired copper(i)-nitro complexes in steric and electronic considerations of tridentate nitrogen ligands. Dalton Trans 2018; 47:5335-5341. [PMID: 29589010 DOI: 10.1039/c7dt03843g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Two copper(i)-nitro complexes [Tpm3-tBuCu(NO2)] (1) and [(Ph3P)2N][Tp3-tBuCu(NO2)] (2), containing steric bulky neutral tris(3-tert-butylpyrazolyl)methane and anionic hydrotris(3-tert-butylpyrazolyl)borate ligands, have been synthesized and characterized. Complex 2 adopts a unique κ2-binding mode of Tp3-tBu around the copper(i)-nitro environment in the solid state and shows a four-coordinated tetrahedral geometry surrounded by a nitro and three pz3-tBu groups in solution. Both complexes 1 and 2 allow for the stoichiometric reduction of NO2- to NO with H+ addition. The results of this effort show that increasing steric bulk and electron donation properties on the nitrogen ancillary ligand will improve the nitrite reduction ability of the copper(i)-nitro model complexes.
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Affiliation(s)
- Yu-Lun Chang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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42
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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: 149] [Impact Index Per Article: 24.8] [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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43
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Chandra Maji R, Mishra S, Bhandari A, Singh R, Olmstead MM, Patra AK. A Copper(II) Nitrite That Exhibits Change of Nitrite Binding Mode and Formation of Copper(II) Nitrosyl Prior to Nitric Oxide Evolution. Inorg Chem 2018; 57:1550-1561. [DOI: 10.1021/acs.inorgchem.7b02897] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ram Chandra Maji
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
| | - Saikat Mishra
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
| | - Anirban Bhandari
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
| | - Ravindra Singh
- Department of Chemistry, Indian Institute of Technology (IIT) Kanpur, Kanpur 208 016, India
| | - Marilyn M. Olmstead
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Apurba K. Patra
- Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713 209, India
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44
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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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45
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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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46
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Mizohata E, Nakane T, Fukuda Y, Nango E, Iwata S. Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology. Biophys Rev 2017; 10:209-218. [PMID: 29196935 DOI: 10.1007/s12551-017-0344-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Abstract
X-ray crystallography visualizes the world at the atomic level. It has been used as the most powerful technique for observing the three-dimensional structures of biological macromolecules and has pioneered structural biology. To determine a crystal structure with high resolution, it was traditionally required to prepare large crystals (> 200 μm). Later, synchrotron radiation facilities, such as SPring-8, that produce powerful X-rays were built. They enabled users to obtain good quality X-ray diffraction images even with smaller crystals (ca. 200-50 μm). In recent years, one of the most important technological innovations in structural biology has been the development of X-ray free electron lasers (XFELs). The SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan generates the XFEL beam by accelerating electrons to relativistic speeds and directing them through in-vacuum, short-period undulators. Since user operation started in 2012, we have been involved in the development of serial femtosecond crystallography (SFX) measurement systems using XFEL at the SACLA. The SACLA generates X-rays a billion times brighter than SPring-8. The extremely bright XFEL pulses enable data collection with microcrystals (ca. 50-1 μm). Although many molecular analysis techniques exist, SFX is the only technique that can visualize radiation-damage-free structures of biological macromolecules at room temperature in atomic resolution and fast time resolution. Here, we review the achievements of the SACLA-SFX Project in the past 5 years. In particular, we focus on: (1) the measurement system for SFX; (2) experimental phasing by SFX; (3) enzyme chemistry based on damage-free room-temperature structures; and (4) molecular movie taken by time-resolved SFX.
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Affiliation(s)
- Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 OQH, UK
| | - Yohta Fukuda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
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47
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Study of the Cys-His bridge electron transfer pathway in a copper-containing nitrite reductase by site-directed mutagenesis, spectroscopic, and computational methods. Biochim Biophys Acta Gen Subj 2017; 1862:752-760. [PMID: 29051066 DOI: 10.1016/j.bbagen.2017.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/06/2017] [Accepted: 10/12/2017] [Indexed: 11/22/2022]
Abstract
The Cys-His bridge as electron transfer conduit in the enzymatic catalysis of nitrite to nitric oxide by nitrite reductase from Sinorhizobium meliloti 2011 (SmNir) was evaluated by site-directed mutagenesis, steady state kinetic studies, UV-vis and EPR spectroscopic measurements as well as computational calculations. The kinetic, structural and spectroscopic properties of the His171Asp (H171D) and Cys172Asp (C172D) SmNir variants were compared with the wild type enzyme. Molecular properties of H171D and C172D indicate that these point mutations have not visible effects on the quaternary structure of SmNir. Both variants are catalytically incompetent using the physiological electron donor pseudoazurin, though C172D presents catalytic activity with the artificial electron donor methyl viologen (kcat=3.9(4) s-1) lower than that of wt SmNir (kcat=240(50) s-1). QM/MM calculations indicate that the lack of activity of H171D may be ascribed to the Nδ1H…OC hydrogen bond that partially shortcuts the T1-T2 bridging Cys-His covalent pathway. The role of the Nδ1H…OC hydrogen bond in the pH-dependent catalytic activity of wt SmNir is also analyzed by monitoring the T1 and T2 oxidation states at the end of the catalytic reaction of wt SmNir at pH6 and 10 by UV-vis and EPR spectroscopies. These data provide insight into how changes in Cys-His bridge interrupts the electron transfer between T1 and T2 and how the pH-dependent catalytic activity of the enzyme are related to pH-dependent structural modifications of the T1-T2 bridging chemical pathway.
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48
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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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49
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Sen K, Horrell S, Kekilli D, Yong CW, Keal TW, Atakisi H, Moreau DW, Thorne RE, Hough MA, Strange RW. Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase. IUCRJ 2017; 4:495-505. [PMID: 28875036 PMCID: PMC5571812 DOI: 10.1107/s2052252517007527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/21/2017] [Indexed: 06/07/2023]
Abstract
Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site 'capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.
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Affiliation(s)
- Kakali Sen
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Sam Horrell
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Demet Kekilli
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Chin W. Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Thomas W. Keal
- Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, England
| | - Hakan Atakisi
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | - David W. Moreau
- Physics Department, Cornell University, Ithaca, NY 14853, USA
| | | | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
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50
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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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