1
|
Ramírez CS, Tolmie C, Rivas MG, Gonzalez PJ, Murgida DH, Opperman DJ, Brondino CD, Ferroni FM. Structural insights into the copper-containing nitrite reductase from Bradyrhizobium japonicum USDA110 and its role in the low nitrite reductase activity of rhizobia. Arch Biochem Biophys 2025; 770:110467. [PMID: 40381977 DOI: 10.1016/j.abb.2025.110467] [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: 03/07/2025] [Revised: 04/25/2025] [Accepted: 05/12/2025] [Indexed: 05/20/2025]
Abstract
Bradyrhizobium japonicum USDA110 is a widely used microorganism in the formulation of bioinoculants for soybean crops, harboring a copper-containing nitrite reductase with low enzymatic activity. The activity of BjNirK at pH 6.5 was higher compared to that at pH 8.0, regardless of the presence of either physiological or artificial electron donors. Thermal shift assays reveal that the enzyme is more stable at pH 6.5 than at pH 8.0. X-ray structural data reveals that the funnel for substrate entry shows a wider cavity when compared to other class I NirK structures. Furthermore, the presence of an additional channel for proton provision is observed, in addition to the primary and secondary proton channels. The T2Cu active site can accommodate one or two water molecules, resulting in a tetra- or pentacoordinated metal site, respectively. The structural data correlates well with both optical visible and resonance Raman spectroscopies, denoting a strong blue character of the T1Cu site in both solid and solution states. Furthermore, EPR-monitored redox titration reveals that the catalytic rate is not constrained by T1Cu-T2Cu intraprotein electron transfer reaction at either pH 6.5 or pH 8.0. Additionally, bioinformatics studies indicate that the interaction between the enzyme and the electron donor is not pH dependent. These two observations suggest that the low activity of BjNirK is not caused by inefficient donor-enzyme interaction or impaired electron transfer. The present results suggest that the structural architecture and enzyme properties in rhizobia are designed to ensure low activity, a trait that is particularly advantageous for symbiosis.
Collapse
Affiliation(s)
- Cintia Soledad Ramírez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas. Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe, S300ZAA, Argentina
| | - Carmien Tolmie
- Department of Microbiology and Biochemistry, University of the Free State (UFS), 205 Nelson Mandela Drive, Bloemfontein, Free State, 9300, South Africa
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas. Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe, S300ZAA, Argentina
| | - Pablo Javier Gonzalez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas. Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe, S300ZAA, Argentina
| | - Daniel Horacio Murgida
- Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2 piso 1, Buenos Aires, Buenos Aires, C1428EHA, Argentina
| | - Diederik Johannes Opperman
- Department of Microbiology and Biochemistry, University of the Free State (UFS), 205 Nelson Mandela Drive, Bloemfontein, Free State, 9300, South Africa
| | - Carlos Dante Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas. Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe, S300ZAA, Argentina
| | - Felix Martín Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas. Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Santa Fe, S300ZAA, Argentina.
| |
Collapse
|
2
|
Morimoto Y, Inoue K, Itoh S. Reactivity of copper(I) complexes supported by tripodal nitrogen-containing tetradentate ligands toward gaseous diatomic molecules, NO, CO and O 2. Dalton Trans 2025; 54:5327-5333. [PMID: 40012511 DOI: 10.1039/d4dt03001j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2025]
Abstract
Series of Cu(I) complexes supported by nitrogen-based tetradentate ligands were examined for their reactivity toward nitric oxide (NO). The copper complexes generated the corresponding Cu(II)-nitrite complexes in the presence of an excess molar amount of NO. A higher reactivity of the Cu(I) complexes toward NO was observed with a more negative Cu(I/II) redox potential, same as their reactivity toward O2 and CO, while [CuI(tepa)]+ with the most positive oxidation potential only reacted with NO among the diatomic gaseous molecules (NO, O2, and CO) examined in this study. DFT studies explained that the reactivity of the Cu-NO complex was the key to its selectivity rather than its coordination bond stability.
Collapse
Affiliation(s)
- Yuma Morimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Keisuke Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Shinobu Itoh
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
| |
Collapse
|
3
|
Guevara Cuasapud LA, González PJ, Ferroni FM, Duré AB, Dalosto SD, Rivas MG, Brondino CD. Replacement of the essential catalytic aspartate with serine leads to an active form of copper-containing nitrite reductase from the denitrifier Sinorhizobium meliloti 2011. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2025; 1873:141062. [PMID: 39743188 DOI: 10.1016/j.bbapap.2024.141062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/15/2024] [Accepted: 12/26/2024] [Indexed: 01/04/2025]
Abstract
We report the molecular, biochemical and spectroscopic characterization and computational calculations of a variant of the copper-containing nitrite reductase from the rhizobial microorganism S. meliloti (SmNirK), in which the catalytic aspartate residue (AspCAT) has been replaced with serine (SerCAT, D134S) by site-directed mutagenesis. Like the wild-type enzyme, D134S is a homotrimer with the typical catalytic pocket of two-domain NirK containing two copper centers, one of type 1 (T1) and another of type 2 (T2). The T1 electron transfer center is similar to that of the wild-type enzyme but the electronic and covalent properties of T2 active site are altered by the mutation. As for the wild-type enzyme, the enzymatic activity of D134S is pH-dependent, i.e. it is higher at lower pH values, but the kcat is an order of magnitude lower. EPR studies showed a decrease in g‖ and an increase in A‖ of D134S relative to wild-type enzyme. This indicates changes in the electronic and covalent properties of T2 upon mutation, which affects the reduction potential of T2 and the T1-T2 reduction potential gap. Taken together, this evidence points to the importance of the ligands of the second coordination sphere of T2 in controlling critical parameters in catalysis. The possibility that AspCAT/SerCAT is the switch that triggers T1 → T2 electron transfer upon T2 nitrite binding and the importance of HisCAT for the pH-dependent catalytic activity of NirK are discussed.
Collapse
Affiliation(s)
- Lorieth A Guevara Cuasapud
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina
| | - Pablo J González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina
| | - Félix M Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina
| | - Andrea B Duré
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina
| | - Sergio D Dalosto
- Instituto de Física del Litoral, CONICET-UNL, Güemes 3450, S3000GLN Santa Fe, Argentina
| | - Maria G Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina.
| | - Carlos D Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA Santa Fe, Argentina.
| |
Collapse
|
4
|
Biswas J, Sanden S, Bhardwaj P, Siegmund D, Kumar P, Apfel UP. A terpyridine-based copper complex for electrochemical reduction of nitrite to nitric oxide. Dalton Trans 2025; 54:1815-1826. [PMID: 39670725 DOI: 10.1039/d4dt02777a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2024]
Abstract
In biological systems, nitrite reductase enzymes (NIRs) are responsible for reduction of nitrite (NO2-) to nitric oxide (NO). These NIRs have mostly Cu- or Fe-containing active sites, surrounded by amine-containing ligands. Therefore, mononuclear Cu complexes with N-donor ligands are highly relevant in the development of NIR model systems and in the mechanistic investigation of the nitrite reduction reaction. Herein, we report on a terpyridine-based CuII complex with square planar geometry for H+-assisted electrochemical reduction of NO2-. Through electrochemical measurements, spectroscopic characterization and isotope-labelling experiments we propose a mechanistic reaction pathway involving an unstable HNO2 state. The CuI intermediate, formed electrochemically, was isolated and its molecular structure was deduced, showing linkage isomerism of the nitrite ligand. Moreover, qualitative and quantitative product analysis by GC-MS shows N2O formed as a side product along with the main product NO. Furthermore, by obtaining single crystals and conducting structural analysis we were able to determine the structural arrangement and redox state of the complex after electrochemical treatment.
Collapse
Affiliation(s)
- Jyotiprokash Biswas
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Sebastian Sanden
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
| | - Prabhakar Bhardwaj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Daniel Siegmund
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
- Department of Electrosynthesis, Fraunhofer UMSICHT, Osterfelder Str. 3, 46047 Oberhausen, Germany
| | - Pankaj Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Ulf-Peter Apfel
- Inorganic Chemistry I, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany.
- Department of Electrosynthesis, Fraunhofer UMSICHT, Osterfelder Str. 3, 46047 Oberhausen, Germany
| |
Collapse
|
5
|
Martinez Fernandez J, Haji Seyed Javadi A, Teat SJ, Cundari TR, Tilley TD. Synthetically Reversible, Proton-Mediated Nitrite N-O Bond Cleavage at a Dicopper Site. J Am Chem Soc 2024; 146:34962-34969. [PMID: 39655620 DOI: 10.1021/jacs.4c14642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2024]
Abstract
A monocationic dicopper(I,I) nitrite complex [Cu2(μ-κ1:κ1-O2N)DPFN][NTf2] (2) (DPFN = 2,7-bis(fluoro-di(2-pyridyl)methyl)-1,8-naphthyridine, NTf2- = N(SO2CF3)2-), was synthesized by treatment of a dicopper acetonitrile complex, [Cu2(μ-MeCN)DPFN][NTf2]2 (1), with tetrabutylammonium nitrite ([nBu4N][NO2]). DFT calculations indicate that 2 is one of three linkage isomers that are close in energy and presumably accessible in solution. Reaction of the μ-κ1:κ1-O2N complex with p-TolSH produces nitrous acid (HONO) and the corresponding dicopper thiolate species via an acid-base exchange reaction. Notably, treatment of 2 with HNTf2 results in N-O bond cleavage in the putative, HONO-ligated complex to form the more thermodynamically favorable nitrosyl-bridged dicopper complex [Cu2(μ-NO)(μ-OH)DPFN][NTf2]2 (4). This scission can be reversed via deprotonation of the hydroxy ligand with KOtBu. X-ray diffraction studies confirmed the solid-state molecular structures of 2 and 4. DFT calculations were used to construct a reaction coordinate diagram detailing formation of the μ-NO complex and to describe its electronic structure. The nitrosyl ligand in 4 is chemically labile, as demonstrated by its ready displacement in reactions with CO or NO2-.
Collapse
Affiliation(s)
- Jose Martinez Fernandez
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Alireza Haji Seyed Javadi
- Department of Chemistry, Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203, United States
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Thomas R Cundari
- Department of Chemistry, Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203, United States
| | - T Don Tilley
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
6
|
Kametani Y, Shiota Y. Mechanistic studies of NO x reduction reactions involving copper complexes: encouragement of DFT calculations. Dalton Trans 2024; 53:19081-19087. [PMID: 39530191 DOI: 10.1039/d4dt02420f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
The reduction of nitrogen oxides (NOx), which is mainly mediated by metalloenzymes and metal complexes, is a critical process in the nitrogen cycle and environmental remediation. This Frontier article highlights the importance of density functional theory (DFT) calculations to gain mechanistic insights into nitrite (NO2-) and nitric oxide (NO) reduction reactions facilitated by copper complexes by focusing on two key processes: the reduction of NO2- to NO by a monocopper complex, with special emphasis on the concerted proton-electron transfer, and the reduction of NO to N2O by a dicopper complex, which involves N-N bond formation, N2O2 isomerization, and N-O bond cleavage. These findings underscore the utility of DFT calculations in unraveling complicated reaction mechanisms and offer a foundation for future research aimed at improving the reactivity of transition metal complexes in NOx reduction reactions.
Collapse
Affiliation(s)
- Yohei Kametani
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering and IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| |
Collapse
|
7
|
Yamada M. Molecular basis and functional development of membrane-based microbial metabolism. Biosci Biotechnol Biochem 2024; 88:461-474. [PMID: 38366612 DOI: 10.1093/bbb/zbae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/18/2024]
Abstract
My research interest has so far been focused on metabolisms related to the "membrane" of microorganisms, such as the respiratory chain, membrane proteins, sugar uptake, membrane stress and cell lysis, and fermentation. These basic metabolisms are important for the growth and survival of cell, and their knowledge can be used for efficient production of useful materials. Notable achievements in research on metabolisms are elucidation of the structure and function of membrane-bound glucose dehydrogenase as a primary enzyme in the respiratory chain, elucidation of ingenious expression regulation of several operons or by divergent promoters, elucidation of stress-induced programed-cell lysis and its requirement for survival during a long-term stationary phase, elucidation of molecular mechanism of survival at a critical high temperature, elucidation of thermal adaptation and its limit, isolation of thermotolerant fermenting yeast strains, and development of high-temperature fermentation and green energy production technologies. These achievements are described together in this review.
Collapse
Affiliation(s)
- Mamoru Yamada
- Graduate School of Sciences and Technology for Innovation, and Research Center for Thermotolerant Microbial Resources, Yamaguchi University, Yamaguchi, Japan
| |
Collapse
|
8
|
Chang J, Peng P, Farhan Ul-Haque M, Hira A, DiSpirito AA, Semrau JD. Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin. Environ Microbiol 2023; 25:2338-2350. [PMID: 37395163 DOI: 10.1111/1462-2920.16456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.
Collapse
Affiliation(s)
- Jin Chang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Peng Peng
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Abid Hira
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
9
|
Sarkar A, Bhakta S, Chattopadhyay S, Dey A. Role of distal arginine residue in the mechanism of heme nitrite reductases. Chem Sci 2023; 14:7875-7886. [PMID: 37502318 PMCID: PMC10370594 DOI: 10.1039/d3sc01777j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023] Open
Abstract
Heme nitrite reductases reduce NO2- by 1e-/2H+ to NO or by 6e-/8H+ to NH4+ which are key steps in the global nitrogen cycle. Second-sphere residues, such as arginine (with a guanidine head group), are proposed to play a key role in the reaction by assisting substrate binding and hydrogen bonding and by providing protons to the active site for the reaction. The reactivity of an iron porphyrin with a NO2- covalently attached to a guanidinium arm in its 2nd sphere was investigated to understand the role of arginine residues in the 2nd sphere of heme nitrite reductases. The presence of the guanidinium residue allows the synthetic ferrous porphyrin to reduce NO2- and produce a ferrous nitrosyl species ({FeNO}7), where the required protons are provided by the guanidinium group in the 2nd sphere. However, in the presence of additional proton sources in solution, the reaction of ferrous porphyrin with NO2- results in the formation of ferric porphyrin and the release of NO. Spectroscopic and kinetic data indicated that re-protonation of the guanidine group in the 2nd sphere by an external proton source causes NO to dissociate from a ferric nitrosyl species ({FeNO}6) at rates similar to those observed for enzymatic sites. This re-protonation of the guanidine group mimics the proton recharge mechanism in the active site of NiR. DFT calculations indicated that the lability of the Fe-NO bond in the {FeNO}6 species is derived from the greater binding affinity of anions (e.g. NO2-) to the ferric center relative to neutral NO due to hydrogen bonding and electrostatic interaction of these bound anions with the protonated guanidium group in the 2nd sphere. The reduced {FeNO}7 species, once formed, is not affected significantly by the re-protonation of the guanidine residue. These results provide direct insight into the role of the 2nd sphere arginine residue present in the active sites of heme-based NiRs in determining the fate of NO2- reduction. Specifically, the findings using the synthetic model suggest that rapid re-protonation of these arginine residues may trigger the dissociation of NO from the {FeNO}6, which may also be the case in the protein active site.
Collapse
Affiliation(s)
- Ankita Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| | - Snehadri Bhakta
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| | - Samir Chattopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| | - Abhishek Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science 2A & 2B Raja S.C. Mullick Road Kolkata WB 700032 India
| |
Collapse
|
10
|
Duré AB, Cristaldi JC, Guevara Cuasapud LA, Dalosto SD, Rivas MG, Ferroni FM, González PJ, Montich GG, Brondino CD. Molecular and kinetic properties of copper nitrite reductase from Sinorhizobium meliloti 2011 upon substituting the interfacial histidine ligand coordinated to the type 2 copper active site for glycine. J Inorg Biochem 2023; 241:112155. [PMID: 36739731 DOI: 10.1016/j.jinorgbio.2023.112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
A copper-containing nitrite reductase catalyzes the reduction of nitrite to nitric oxide in the denitrifier Sinorhizobium meliloti 2011 (SmNirK), a microorganism used as bioinoculant in alfalfa seeds. Wild type SmNirK is a homotrimer that contains two copper centers per monomer, one of type 1 (T1) and other of type 2 (T2). T2 is at the interface of two monomers in a distorted square pyramidal coordination bonded to a water molecule and three histidine side chains, H171 and H136 from one monomer and H342 from the other. We report the molecular, catalytic, and spectroscopic properties of the SmNirK variant H342G, in which the interfacial H342 T2 ligand is substituted for glycine. The molecular properties of H342G are similar to those of wild type SmNirK. Fluorescence-based thermal shift assays and FTIR studies showed that the structural effect of the mutation is only marginal. However, the kinetic reaction with the physiological electron donor was significantly affected, which showed a ∼ 100-fold lower turnover number compared to the wild type enzyme. UV-Vis, EPR and FTIR studies complemented with computational calculations indicated that the drop in enzyme activity are mainly due to the void generated in the protein substrate channel by the point mutation. The main structural changes involve the filling of the void with water molecules, the direct coordination to T2 copper ion of the second sphere aspartic acid ligand, a key residue in catalysis and nitrite sensing in NirK, and to the loss of the 3 N-O coordination of T2.
Collapse
Affiliation(s)
- Andrea B Duré
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Julio C Cristaldi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende 5000, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lorieth A Guevara Cuasapud
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Sergio D Dalosto
- Instituto de Física del Litoral, CONICET-UNL, Güemes 3450, S3000GLN, Santa Fe, Argentina
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Felix M Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Pablo J González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Guillermo G Montich
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende 5000, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Carlos D Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina.
| |
Collapse
|
11
|
Li X, Zou H. A molecular dynamics and quantum mechanical investigation of intermolecular interaction and electron-transfer mechanism between copper-containing nitrite reductase and redox partner pseudoazurin. Phys Chem Chem Phys 2023; 25:7783-7793. [PMID: 36857651 DOI: 10.1039/d2cp05534a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Much of biological electron transfer occurs between proteins. These molecular processes usually involve molecular recognition and intermolecular electron transfer (inter-ET). The inter-ET reaction between copper-containing nitrite reductase (CuNiR) and partner protein pseudoazurin (PAz) is the first step in denitrification, which is affected by intermolecular association. However, the transient interaction between CuNiR and PAz and the indistinct inter-ET pathway pose challenges for people to understand the biological functions of the CuNiR-PAz complex. Thus, molecular dynamics simulation and quantum mechanical calculation were used to investigate the question in this study. The interaction of the interface residues was determined through hydrogen bonds, root-mean-square deviation, root-mean-square fluctuation, the dynamics cross-correlation matrix, and molecular mechanics Poisson-Boltzmann surface area of molecular dynamics simulations. The interactions among the residues Glu89, Gly200, Asp205, Asn91, Glu204, Thr92, and Met141 on CuNiR and the residues Lys109, Ala15, Lys10, Asn9, Ile110, Met84, and Met16 on PAz are responsible for the stabilization of the complex. The binding free energy is up to -25.33 kcal mol-1. We compared the wild-type and mutant (M84A) interfacial optimized complex models at the CAM-B3LYP level with Grimme dispersion corrections (GD3) to confirm Met84 as a relay station for promoting the inter-ET. Additionally, to test whether Met84 may combine with the adjacent Met141 to form a special two-center, three-electron (S∴S)+ structure to promote the inter-ET, QM/MM was further performed to discuss the possibility of generating an electron stepping stone. Our study will promote a deep understanding of the stable protein-protein interaction, and the identified inter-residue interaction will be theoretical guidance for enhancing the catalytic activity of CuNiR in denitrification.
Collapse
Affiliation(s)
- Xin Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China.
| | - Hang Zou
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| |
Collapse
|
12
|
Wang P, Li T, Wu Q, Du R, Zhang Q, Huang WH, Chen CL, Fan Y, Chen H, Jia Y, Dai S, Qiu Y, Yan K, Meng Y, Waterhouse GIN, Gu L, Zhao Y, Zhao WW, Chen G. Molecular Assembled Electrocatalyst for Highly Selective CO 2 Fixation to C 2+ Products. ACS NANO 2022; 16:17021-17032. [PMID: 36223163 DOI: 10.1021/acsnano.2c07138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In certain metalloenzymes, multimetal centers with appropriate primary/secondary coordination environments allow carbon-carbon coupling reactions to occur efficiently and with high selectivity. This same function is seldom realized in molecular electrocatalysts. Herein we synthesized rod-shaped nanocatalysts with multiple copper centers through the molecular assembly of a triphenylphosphine copper complex (CuPPh). The assembled molecular CuPPh catalyst demonstrated excellent electrochemical CO2 fixation performance in aqueous solution, yielding high-value C2+ hydrocarbons (ethene) and oxygenates (ethanol) as the main products. Using density functional theory (DFT) calculations, in situ X-ray absorption spectroscopy (XAS) and quasi-in situ X-ray photoelectron spectroscopy (XPS), and reaction intermediate capture, we established that the excellent catalytic performance originated from the large number of double copper centers in the rod-shaped assemblies. Cu-Cu distances in the absence of CO2 were as long as 7.9 Å, decreasing substantially after binding CO2 molecules indicating dynamic and cooperative function. The double copper centers were shown to promote carbon-carbon coupling via a CO2 transfer-coupling mechanism involving an oxalate (OOC-COO) intermediate, allowing the efficient production of C2+ products. The assembled CuPPh nanorods showed high activity, excellent stability, and a high Faradaic efficiency (FE) to C2+ products (65.4%), with performance comparable to state-of-the-art copper oxide-based catalysts. To our knowledge, our findings demonstrate that harnessing metalloenzyme-like properties in molecularly assembled catalysts can greatly improve the selectivity of CO2RR, promoting the rational design of improved CO2 reduction catalysts.
Collapse
Affiliation(s)
- Peng Wang
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Tan Li
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Qiqi Wu
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Ruian Du
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Qinghua Zhang
- Institute of Physics, Chinese Academy of Sciences, Beijing100190, China
| | - Wei-Hsiang Huang
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu30076, Taiwan
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology (NTUST), Taipei10607, Taiwan
| | - Chi-Liang Chen
- National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu30076, Taiwan
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology (NTUST), Taipei10607, Taiwan
| | - Yan Fan
- Medical Device Research & Testing Center, South China University of Technology, Guangzhou510006, China
| | - Haonan Chen
- Medical Device Research & Testing Center, South China University of Technology, Guangzhou510006, China
| | - Yanyan Jia
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Centre, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology, Shanghai200237, China
| | - Sheng Dai
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Centre, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology, Shanghai200237, China
| | - Yongcai Qiu
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Keyou Yan
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Yuanyuan Meng
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan030002, China
| | | | - Lin Gu
- Institute of Physics, Chinese Academy of Sciences, Beijing100190, China
| | - Yun Zhao
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing210023, China
| | - Guangxu Chen
- School of Environment and Energy, State Key Laboratory of Luminescent Materials and Devices, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou510006, China
| |
Collapse
|
13
|
Braley SE, Kwon HY, Xu S, Dalton EZ, Jakubikova E, Smith JM. Buffer Assists Electrocatalytic Nitrite Reduction by a Cobalt Macrocycle Complex. Inorg Chem 2022; 61:12998-13006. [PMID: 35948065 DOI: 10.1021/acs.inorgchem.2c00909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work reports a combined experimental and computational study of the activation of an otherwise catalytically inactive cobalt complex, [Co(TIM)Br2]+, for aqueous nitrite reduction. The presence of phosphate buffer leads to efficient electrocatalysis, with rapid reduction to ammonium occurring close to the thermodynamic potential and with high Faradaic efficiency. At neutral pH, increasing buffer concentrations increase catalytic current while simultaneously decreasing overpotential, although high concentrations have an inhibitory effect. Controlled potential electrolysis and rotating ring-disk electrode experiments indicate that ammonium is directly produced from nitrite by [Co(TIM)Br2]+, along with hydroxylamine. Mechanistic investigations implicate a vital role for the phosphate buffer, specifically as a proton shuttle, although high buffer concentrations inhibit catalysis. These results indicate a role for buffer in the design of electrocatalysts for nitrogen oxide conversion.
Collapse
Affiliation(s)
- Sarah E Braley
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Hyuk-Yong Kwon
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Song Xu
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Evan Z Dalton
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Elena Jakubikova
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Jeremy M Smith
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47401, United States
| |
Collapse
|
14
|
|
15
|
Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
Collapse
Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
16
|
Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin. Appl Environ Microbiol 2022; 88:e0234621. [PMID: 35285718 DOI: 10.1128/aem.02346-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N2O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N2O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N2O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N2O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.
Collapse
|
17
|
Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
Collapse
Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| |
Collapse
|
18
|
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: 2.3] [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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
|
21
|
Kono F, Tamada T. Neutron crystallography for the elucidation of enzyme catalysis. Curr Opin Struct Biol 2021; 71:36-42. [PMID: 34214927 DOI: 10.1016/j.sbi.2021.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/08/2021] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Hydrogen atoms and hydration water molecules in proteins are indispensable for many biochemical processes, especially enzymatic catalysis. The locations of hydrogen atoms in proteins are usually predicted based on X-ray structures, but it is still very difficult to know the ionization states of the catalytic residues, the hydration structure of the protein, and the characteristics of hydrogen-bonding interactions. Neutron crystallography allows the direct observation of hydrogen atoms that play crucial roles in molecular recognition and the catalytic reactions of enzymes. In this review, we present the current status of neutron crystallography in structural biology and recent neutron structural analyses of three enzymes: ascorbate peroxidase, the main protease of severe acute respiratory syndrome coronavirus 2, and copper-containing nitrite reductase.
Collapse
Affiliation(s)
- Fumiaki Kono
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan.
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Enhancement of nitrous oxide emissions in soil microbial consortia via copper competition between proteobacterial methanotrophs and denitrifiers. Appl Environ Microbiol 2020; 87:e0230120. [PMID: 33355098 DOI: 10.1128/aem.02301-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Unique means of copper scavenging have been identified in proteobacterial methanotrophs, particularly the use of methanobactin, a novel ribosomally synthesized post-translationally modified polypeptide that binds copper with very high affinity. The possibility that copper sequestration strategies of methanotrophs may interfere with copper uptake of denitrifiers in situ and thereby enhance N2O emissions was examined using a suite of laboratory experiments performed with rice paddy microbial consortia. Addition of purified methanobactin from Methylosinus trichosporium OB3b to denitrifying rice paddy soil microbial consortia resulted in substantially increased N2O production, with more pronounced responses observed for soils with lower copper content. The N2O emission-enhancing effect of the soil's native mbnA-expressing Methylocystaceae methanotrophs on the native denitrifiers was then experimentally verified with a Methylocystaceae-dominant chemostat culture prepared from a rice paddy microbial consortium as the inoculum. Lastly, with microcosms amended with varying cell numbers of methanobactin-producing Methylosinus trichosporium OB3b before CH4 enrichment, microbiomes with different ratios of methanobactin-producing Methylocystaceae to gammaproteobacterial methanotrophs incapable of methanobactin production were simulated. Significant enhancement of N2O production from denitrification was evident in both Methylocystaceae-dominant and Methylococcaceae-dominant enrichments, albeit to a greater extent in the former, signifying the comparative potency of methanobactin-mediated copper sequestration while implying the presence of alternative copper abstraction mechanisms for Methylococcaceae These observations support that copper-mediated methanotrophic enhancement of N2O production from denitrification is plausible where methanotrophs and denitrifiers cohabit.IMPORTANCE Proteobacterial methanotrophs, groups of microorganisms that utilize methane as source of energy and carbon, have been known to utilize unique mechanisms to scavenge copper, namely utilization of methanobactin, a polypeptide that binds copper with high affinity and specificity. Previously the possibility that copper sequestration by methanotrophs may lead to alteration of cuproenzyme-mediated reactions in denitrifiers and consequently increase emission of potent greenhouse gas N2O has been suggested in axenic and co-culture experiments. Here, a suite of experiments with rice paddy soil slurry cultures with complex microbial compositions were performed to corroborate that such copper-mediated interplay may actually take place in environments co-habited by diverse methanotrophs and denitrifiers. As spatial and temporal heterogeneity allow for spatial coexistence of methanotrophy (aerobic) and denitrification (anaerobic) in soils, the results from this study suggest that this previously unidentified mechanism of N2O production may account for significant proportion of N2O efflux from agricultural soils.
Collapse
|
24
|
Pinter TBJ, Manickas EC, Tolbert AE, Koebke KJ, Deb A, Penner-Hahn JE, Pecoraro VL. Making or Breaking Metal-Dependent Catalytic Activity: The Role of Stammers in Designed Three-Stranded Coiled Coils. Angew Chem Int Ed Engl 2020; 59:20445-20449. [PMID: 32748510 PMCID: PMC7722090 DOI: 10.1002/anie.202008356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/21/2020] [Indexed: 12/31/2022]
Abstract
While many life-critical reactions would be infeasibly slow without metal cofactors, a detailed understanding of how protein structure can influence catalytic activity remains elusive. Using de novo designed three-stranded coiled coils (TRI and Grand peptides formed using a heptad repeat approach), we examine how the insertion of a three residue discontinuity, known as a stammer insert, directly adjacent to a (His)3 metal binding site alters catalytic activity. The stammer, which locally alters the twist of the helix, significantly increases copper-catalyzed nitrite reductase activity (CuNiR). In contrast, the well-established zinc-catalyzed carbonic anhydrase activity (p-nitrophenyl acetate, pNPA) is effectively ablated. This study illustrates how the perturbation of the protein sequence using non-coordinating and non-acid base residues in the helical core can perturb metalloenzyme activity through the simple expedient of modifying the helical pitch adjacent to the catalytic center.
Collapse
Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | | | - Audrey E. Tolbert
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Karl J. Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA, 48109
| |
Collapse
|
25
|
Pinter TBJ, Manickas EC, Tolbert AE, Koebke KJ, Deb A, Penner‐Hahn JE, Pecoraro VL. Making or Breaking Metal‐Dependent Catalytic Activity: The Role of Stammers in Designed Three‐Stranded Coiled Coils. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Audrey E. Tolbert
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Aniruddha Deb
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | | | | |
Collapse
|
26
|
Yang J, Feng L, Pi S, Cui D, Ma F, Zhao HP, Li A. A critical review of aerobic denitrification: Insights into the intracellular electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139080. [PMID: 32417477 DOI: 10.1016/j.scitotenv.2020.139080] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/04/2020] [Accepted: 04/26/2020] [Indexed: 05/23/2023]
Abstract
Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.
Collapse
Affiliation(s)
- Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Di Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China; Engineering Research Center for Medicine, College of Pharmacy, Harbin University of Commerce, Harbin 150076, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China.
| |
Collapse
|
27
|
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: 0.8] [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.
Collapse
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
| |
Collapse
|
28
|
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: 2.0] [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.
Collapse
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
| |
Collapse
|
29
|
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: 19] [Impact Index Per Article: 3.8] [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.
Collapse
|
30
|
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: 2.3] [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.
Collapse
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
| |
Collapse
|
31
|
Cioncoloni G, Wilson C, Roger I, Symes MD. Crystal structure of catena-poly[[(μ-6-{[bis-(pyridin-2-ylmeth-yl)amino]-meth-yl}pyridine-2-carboxyl-ato)copper(II)] perchlorate aceto-nitrile monosolvate]. Acta Crystallogr E Crystallogr Commun 2019; 75:789-793. [PMID: 31391967 PMCID: PMC6658946 DOI: 10.1107/s2056989019006285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/03/2019] [Indexed: 11/11/2022]
Abstract
The crystal structure of the title compound, {[Cu(C19H17N4O2)]ClO4·C2H3N} n , is reported and compared to similar structures in the literature. The compound crystallizes in the monoclinic space group P21. The unit cell contains one complex mol-ecule in addition to perchlorate as the counter-ion and solvent (aceto-nitrile). The crystal packing evinces extended chains whereby the carboxyl-ate moiety on the 6-carboxyl-ato-2-(pyridyl-meth-yl)bis-(pyridin-2-ylmeth-yl)amine ligand bridges between two different copper centers in adjacent mol-ecules. This packing arrangement for the title compound appears to be unique when compared to allied structures in the literature. The perchlorate anion showed signs of disorder and its oxygen atoms were modelled over two sets of partially occupied sites, the occupancy of which was competitively refined to 0.564 (12)/0.436 (12). The crystal studied was refined as a two-component inversion twin.
Collapse
Affiliation(s)
- Giacomo Cioncoloni
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Claire Wilson
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Isolda Roger
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, United Kingdom
| | - Mark D. Symes
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow, G12 8QQ, United Kingdom
| |
Collapse
|
32
|
Wang SY, Yang XY, Meng HS, Zhang YC, Li XY, Xu J. Enhanced denitrification by nano ɑ-Fe 2O 3 induced self-assembled hybrid biofilm on particle electrodes of three-dimensional biofilm electrode reactors. ENVIRONMENT INTERNATIONAL 2019; 125:142-151. [PMID: 30716574 DOI: 10.1016/j.envint.2019.01.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/16/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Three-dimensional biofilm electrode reactors (3D-BERs) represent a novel technology for wastewater denitrification. Formation of mature electroactive biofilm on particle electrodes is crucial to realize successful denitrification in 3D-BERs. However, long start-up time and low electroactivity of the biofilm formed on particle electrodes limit the further application of 3D-BERs in wastewater treatment. In this work, self-assembled hybrid biofilms (SAHB) was cultivated on granular activate carbon particle electrodes of the 3D-BER by assembling nano ɑ-Fe2O3 into the biofilm. ɑ-Fe2O3 was selected due to its high affinity to bacterial outer-membrane cytochromes, an important mediator for microbial electron transfer. SAHB formed on particle electrodes were characterized and the denitrification performance of 3D-BERs was also investigated. Results indicate that nano ɑ-Fe2O3 plays positive roles in the start-up of 3D-BER, which captures more microbes into SAHB and constructs thick biofilm on particle electrodes. Special microorganisms with denitrification function related with genera of Hydrogenophaga and Opitutus are distinctively enriched in SAHB. Nano ɑ-Fe2O3 induced SAHB exhibit superior denitrification performance compared to natural biofilm. The average denitrification rate increases from 0.62 mg total nitrogen/L/h for natural biofilm to 1.73 mg total nitrogen/L/h for SAHB, mainly ascribed to accelerated nitrites reduction. Our work provides new technical solution to enhance nitrates removal in 3D-BERs and brings deep insights into application of bio-electrochemical system in wastewater treatment.
Collapse
Affiliation(s)
- Si-Yuan Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Xue-Yuan Yang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Hui-Shan Meng
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Yan-Chen Zhang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Xiu-Yan Li
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Juan Xu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China; Institute of Eco-Chongming, East China Normal University, Shanghai, China.
| |
Collapse
|
33
|
Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| |
Collapse
|
34
|
Guo Y, Stroka JR, Kandemir B, Dickerson CE, Bren KL. Cobalt Metallopeptide Electrocatalyst for the Selective Reduction of Nitrite to Ammonium. J Am Chem Soc 2018; 140:16888-16892. [PMID: 30457856 DOI: 10.1021/jacs.8b09612] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A cobalt-tripeptide complex (CoGGH) is developed as an electrocatalyst for the selective six-electron, eight-proton reduction of nitrite to ammonium in aqueous buffer near neutral pH. The onset potential for nitrite reduction occurs at -0.65 V vs Ag/AgCl (1 M KCl). Controlled potential electrolysis at -0.90 V generates ammonium with a faradaic efficiency of 90 ± 3% and a turnover number of 3550 ± 420 over 5.5 h. CoGGH also catalyzes the reduction of the proposed intermediates nitric oxide and hydroxylamine to ammonium. These results reveal that a simple metallopeptide is an active functional mimic of the complex enzymes cytochrome c nitrite reductase and siroheme-containing nitrite reductase.
Collapse
Affiliation(s)
- Yixing Guo
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , United States
| | - Jesse R Stroka
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , United States
| | - Banu Kandemir
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , United States.,Department of Chemistry , Middle East Technical University , North Cyprus via Mersin 10 , Turkey
| | - Claire E Dickerson
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , United States
| | - Kara L Bren
- Department of Chemistry , University of Rochester , Rochester , New York 14627-0216 , United States
| |
Collapse
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
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: 1.0] [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.
Collapse
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
| |
Collapse
|
37
|
Yamaguchi T, Wood K, Taborosi A, Akao K, Kohzuma T. Solution Structure Determination of a Copper-containing Nitrite Reductase of Achromobacter cycloclastes by Small Angle Neutron Scattering. CHEM LETT 2018. [DOI: 10.1246/cl.180152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Attila Taborosi
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Kouhei Akao
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
38
|
Cioncoloni G, Roger I, Wheatley PS, Wilson C, Morris RE, Sproules S, Symes MD. Proton-Coupled Electron Transfer Enhances the Electrocatalytic Reduction of Nitrite to NO in a Bioinspired Copper Complex. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00361] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Giacomo Cioncoloni
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Isolda Roger
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Paul S. Wheatley
- EaStCHEM School of Chemistry, University of St Andrews, Purdie Building, St Andrews KY16 9ST, United Kingdom
| | - Claire Wilson
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Russell E. Morris
- EaStCHEM School of Chemistry, University of St Andrews, Purdie Building, St Andrews KY16 9ST, United Kingdom
| | - Stephen Sproules
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| | - Mark D. Symes
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, United Kingdom
| |
Collapse
|
39
|
Blum JM, Su Q, Ma Y, Valverde-Pérez B, Domingo-Félez C, Jensen MM, Smets BF. The pH dependency of N-converting enzymatic processes, pathways and microbes: effect on net N2O production. Environ Microbiol 2018; 20:1623-1640. [DOI: 10.1111/1462-2920.14063] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/31/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Jan-Michael Blum
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Qingxian Su
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Yunjie Ma
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Borja Valverde-Pérez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Carlos Domingo-Félez
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark, Miljøvej Building 115; Kongens Lyngby 2800 Denmark
| |
Collapse
|
40
|
Tsutsui Y, Kobayashi K, Takeuchi F, Tsubaki M, Kozawa T. Reaction Intermediates of Nitric Oxide Synthase from Deinococcus radiodurans as Revealed by Pulse Radiolysis: Evidence for Intramolecular Electron Transfer from Biopterin to Fe II-O 2 Complex. Biochemistry 2018; 57:1611-1619. [PMID: 29320163 DOI: 10.1021/acs.biochem.7b00887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nitric oxide synthase (NOS) is a cytochrome P450-type mono-oxygenase that catalyzes the oxidation of l-arginine (Arg) to nitric oxide (NO) through a reaction intermediate N-hydroxy-l-arginine (NHA). The mechanism underlying the reaction catalyzed by NOS from Deinococcus radiodurans was investigated using pulse radiolysis. Radiolytically generated hydrated electrons reduced the heme iron of NOS within 2 μs. Subsequently, ferrous heme reacted with O2 to form a ferrous-dioxygen intermediate with a second-order rate constant of 2.8 × 108 M-1 s-1. In the tetrahydrofolate (H4F)-bound enzyme, the ferrous-dioxygen intermediate was found to decay an another intermediate with a first-order rate constant of 2.2 × 103 s-1. The spectrum of the intermediate featured an absorption maximum at 440 nm and an absorption minimum at 390 nm. In the absence of H4F, this step did not proceed, suggesting that H4F was reduced with the ferrous-dioxygen intermediate to form a second intermediate. The intermediate further converted to the original ferric form with a first-order rate constant of 4 s-1. A similar intermediate could be detected after pulse radiolysis in the presence of NHA, although the intermediate decayed more slowly (0.5 s-1). These data suggested that a common catalytically active intermediate involved in the substrate oxidation of both Arg and NHA may be formed during catalysis. In addition, we investigated the solvent isotope effects on the kinetics of the intermediate after pulse radiolysis. Our experiments revealed dramatic kinetic solvent isotope effects on the conversion of the intermediate to the ferric form, of 10.5 and 2.5 for Arg and NHA, respectively, whereas the faster phases were not affected. These data suggest that the proton transfer in DrNOS is the rate-limiting reaction of the intermediate with the substrates.
Collapse
Affiliation(s)
- Yuko Tsutsui
- The Institute of Scientific and Industrial Research , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan
| | - Kazuo Kobayashi
- The Institute of Scientific and Industrial Research , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan
| | - Fusako Takeuchi
- Institute for Promotion of Higher Education , Kobe University , 1-2-1 Tsurukabuto , Nada-ku, Kobe , Hyogo 657-8501 , Japan
| | - Motonari Tsubaki
- Graduate School of Science, Department of Chemistry , Kobe University , 1-1 Rokkodai-cho , Nada-ku, Kobe , Hyogo 657-8501 , Japan
| | - Takahiro Kozawa
- The Institute of Scientific and Industrial Research , Osaka University , Mihogaoka 8-1 , Ibaraki , Osaka 567-0047 , Japan
| |
Collapse
|
41
|
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: 1.3] [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
| |
Collapse
|
42
|
Cloning, purification and characterization of novel Cu-containing nitrite reductase from the Bacillus firmus GY-49. World J Microbiol Biotechnol 2017; 34:10. [DOI: 10.1007/s11274-017-2383-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/22/2017] [Indexed: 11/27/2022]
|
43
|
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: 0.6] [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.
Collapse
|
44
|
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: 1.0] [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
| |
Collapse
|
45
|
Roger I, Wilson C, Senn HM, Sproules S, Symes MD. An investigation into the unusual linkage isomerization and nitrite reduction activity of a novel tris(2-pyridyl) copper complex. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170593. [PMID: 28879000 PMCID: PMC5579116 DOI: 10.1098/rsos.170593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/18/2017] [Indexed: 05/05/2023]
Abstract
The copper-containing nitrite reductases (CuNIRs) are a class of enzymes that mediate the reduction of nitrite to nitric oxide in biological systems. Metal-ligand complexes that reproduce the salient features of the active site of CuNIRs are therefore of fundamental interest, both for elucidating the possible mode of action of the enzymes and for developing biomimetic catalysts for nitrite reduction. Herein, we describe the synthesis and characterization of a new tris(2-pyridyl) copper complex ([Cu1(NO2)2]) that binds two molecules of nitrite, and displays all three of the common binding modes for [Formula: see text], with one nitrite bound in an asymmetric quasi-bidentate κ2-ONO manner and the other bound in a monodentate fashion with a linkage isomerism between the κ1-ONO and κ1-NO2 binding modes. We use density functional theory to help rationalize the presence of all three of these linkage isomers in one compound, before assessing the redox activity of [Cu1(NO2)2]. These latter studies show that the complex is not a competent nitrite reduction electrocatalyst in non-aqueous solvent, even in the presence of additional proton donors, a finding which may have implications for the design of biomimetic catalysts for nitrite reduction.
Collapse
Affiliation(s)
| | | | | | | | - Mark D. Symes
- WestCHEM, School of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| |
Collapse
|
46
|
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: 1.6] [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
| |
Collapse
|
47
|
Horrell S, Kekilli D, Strange RW, Hough MA. Recent structural insights into the function of copper nitrite reductases. Metallomics 2017; 9:1470-1482. [DOI: 10.1039/c7mt00146k] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Copper nitrite reductases (CuNiRs) catalyse the reduction of nitrite to nitric oxide as part of the denitrification pathway. In this review, we describe insights into CuNiR function from structural studies.
Collapse
Affiliation(s)
- Sam Horrell
- School of Biological Sciences
- University of Essex
- Colchester
- UK
| | - Demet Kekilli
- School of Biological Sciences
- University of Essex
- Colchester
- UK
| | | | | |
Collapse
|
48
|
Milton RD, Minteer SD. Enzymatic Bioelectrosynthetic Ammonia Production: Recent Electrochemistry of Nitrogenase, Nitrate Reductase, and Nitrite Reductase. Chempluschem 2016; 82:513-521. [PMID: 31961593 DOI: 10.1002/cplu.201600442] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/19/2016] [Indexed: 11/06/2022]
Abstract
As an essential component of amino acids and nucleic acids, nitrogen (N) is a key element of life. For atmospheric (dinitrogen, N2 ) and environmental (nitrate and nitrite, NO3 - and NO2 - ) sources of N to be utilized in amino acid synthesis in various forms of life, it must first be reduced to ammonia (NH3 ). The Haber-Bosch process, in which N2 is reduced to NH3 at elevated temperature and pressure, represents a major NH3 production process that has had a great impact on the agricultural crop industry. This Minireview discusses the recent electrochemistry of three key enzymes of the global biogeochemical N cycle (nitrogenase, nitrate reductase, and nitrite reductase), in view of moving toward the creation of alternative NH3 production biotechnologies.
Collapse
Affiliation(s)
- Ross D Milton
- Departments of Chemistry and Materials Science and Engineering, University of Utah, 315 S 1400 E, Room 2020, Salt Lake City, Utah, 84112, USA
| | - Shelley D Minteer
- Departments of Chemistry and Materials Science and Engineering, University of Utah, 315 S 1400 E, Room 2020, Salt Lake City, Utah, 84112, USA
| |
Collapse
|
49
|
Fujii H, Yamaki D, Ogura T, Hada M. The functional role of the structure of the dioxo-isobacteriochlorin in the catalytic site of cytochrome cd 1 for the reduction of nitrite. Chem Sci 2016; 7:2896-2906. [PMID: 30090283 PMCID: PMC6054029 DOI: 10.1039/c5sc04825g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Cytochrome cd1 is a key enzyme in bacterial denitrification and catalyzes one-electron reduction of nitrite (NO2-) to nitric oxide (NO) at the heme d1 center under anaerobic conditions. The heme d1 has a unique dioxo-isobacteriochlorin structure and is present only in cytochrome cd1. To reveal the functional role of the unique heme d1 in the catalytic nitrite reduction, we studied effect of the porphyrin macrocycle on each reaction step of the catalytic cycle of cytochrome cd1 using synthetic model complexes. The complexes investigated are iron complexes of dioxo-octaethylisobacteriochlorin (1), mono-oxo-octaethylchlorin (2) and octaethylporphyrin (3). We show here that the reduction potential for the transition from the ferric state to the ferrous state and the binding constant for binding of NO2- to the ferrous complex increases with a trend of 3 < 2 < 1. However, the reactivity of the ferrous nitrite complex with protons increases in the reversed order, 1 < 2 < 3. We also show that the iron bound NO of the ferric NO complex is readily replaced by addition of 1 equiv. of p-nitrophenolate. These results indicate that the dioxo-isobacteriochlorin structure is superior to porphyrin and mono-oxo-chlorin structures in the first iron reduction step, the second nitrite binding step, and the NO dissociation step, but inferior in the third nitrite reduction step. These results suggest that the heme d1 has evolved as the catalytic site of cytochrome cd1 to catalyze the nitrite reduction at the highest possible redox potential while maintaining its catalytic activity.
Collapse
Affiliation(s)
- Hiroshi Fujii
- Department of Chemistry, Biology and Environmental Science , Faculty of Science , Nara Women's University , Kitauoyanishi , Nara 630-8506 , Japan .
| | - Daisuke Yamaki
- Department of Chemistry , Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-Osawa , Hachioji , Tokyo 192-0397 , Japan
| | - Takashi Ogura
- Department of Life Science and Picobiology Institute , Graduate School of Life Science , University of Hyogo , RSC-UH Leading Program Center , 1-1-1 Koto, Sayo-cho, Sayo-gun , Hyogo 679-5148 , Japan
| | - Masahiko Hada
- Department of Chemistry , Graduate School of Science , Tokyo Metropolitan University , 1-1 Minami-Osawa , Hachioji , Tokyo 192-0397 , Japan
| |
Collapse
|
50
|
Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. Proc Natl Acad Sci U S A 2016; 113:2928-33. [PMID: 26929369 DOI: 10.1073/pnas.1517770113] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proton-coupled electron transfer (PCET), a ubiquitous phenomenon in biological systems, plays an essential role in copper nitrite reductase (CuNiR), the key metalloenzyme in microbial denitrification of the global nitrogen cycle. Analyses of the nitrite reduction mechanism in CuNiR with conventional synchrotron radiation crystallography (SRX) have been faced with difficulties, because X-ray photoreduction changes the native structures of metal centers and the enzyme-substrate complex. Using serial femtosecond crystallography (SFX), we determined the intact structures of CuNiR in the resting state and the nitrite complex (NC) state at 2.03- and 1.60-Å resolution, respectively. Furthermore, the SRX NC structure representing a transient state in the catalytic cycle was determined at 1.30-Å resolution. Comparison between SRX and SFX structures revealed that photoreduction changes the coordination manner of the substrate and that catalytically important His255 can switch hydrogen bond partners between the backbone carbonyl oxygen of nearby Glu279 and the side-chain hydroxyl group of Thr280. These findings, which SRX has failed to uncover, propose a redox-coupled proton switch for PCET. This concept can explain how proton transfer to the substrate is involved in intramolecular electron transfer and why substrate binding accelerates PCET. Our study demonstrates the potential of SFX as a powerful tool to study redox processes in metalloenzymes.
Collapse
|