1
|
Kulbir, Das S, Devi T, Ghosh S, Chandra Sahoo S, Kumar P. Acid-induced nitrite reduction of nonheme iron(ii)-nitrite: mimicking biological Fe-NiR reactions. Chem Sci 2023; 14:2935-2942. [PMID: 36937601 PMCID: PMC10016336 DOI: 10.1039/d2sc06704h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Nitrite reductase (NiR) catalyzes nitrite (NO2 -) to nitric oxide (NO) transformation in the presence of an acid (H+ ions/pH) and serves as a critical step in NO biosynthesis. In addition to the NiR enzyme, NO synthases (NOSs) participate in NO production. The chemistry involved in the catalytic reduction of NO2 -, in the presence of H+, generates NO with a H2O molecule utilizing two H+ + one electron from cytochromes and is believed to be affected by the pH. Here, to understand the effect of H+ ions on NO2 - reduction, we report the acid-induced NO2 - reduction chemistry of a nonheme FeII-nitrito complex, [(12TMC)FeII(NO2 -)]+ (FeII-NO2 -, 2), with variable amounts of H+. FeII-NO2 - upon reaction with one-equiv. of acid (H+) generates [(12TMC)Fe(NO)]2+, {FeNO}7 (3) with H2O2 rather than H2O. However, the amount of H2O2 decreases with increasing equivalents of H+ and entirely disappears when H+ reaches ≅ two-equiv. and shows H2O formation. Furthermore, we have spectroscopically characterized and followed the formation of H2O2 (H+ = one-equiv.) and H2O (H+ ≅ two-equiv.) and explained why bio-driven NiR reactions end with NO and H2O. Mechanistic investigations, using 15N-labeled-15NO2 - and 2H-labeled-CF3SO3D (D+ source), revealed that the N atom in the {Fe14/15NO}7 is derived from the NO2 - ligand and the H atom in H2O or H2O2 is derived from the H+ source, respectively.
Collapse
Affiliation(s)
- Kulbir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| | - Sandip Das
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| | - Tarali Devi
- Humboldt-Universität zu Berlin, Institut für Chemie Brook-Taylor-Straße 2 D-12489 Berlin Germany
| | - Somnath Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| | | | - Pankaj Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati 517507 India
| |
Collapse
|
2
|
González PJ, Rivas MG, Ferroni FM, Rizzi AC, Brondino CD. Electron transfer pathways and spin–spin interactions in Mo- and Cu-containing oxidoreductases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
3
|
Frostegård Å, Vick SHW, Lim NYN, Bakken LR, Shapleigh JP. Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N 2O emissions and nitrite accumulation in soil. ISME J 2021. [PMID: 34211102 DOI: 10.1038/s41396-021-01045-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N2O reduction despite early transcription of nosZ (mainly clade I), encoding N2O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO2− reductase) in SoilA suggest that low NO2− concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO2− in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2− accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.
Collapse
|
4
|
Hedison TM, Shanmugam M, Heyes DJ, Edge R, Scrutton NS. Active Intermediates in Copper Nitrite Reductase Reactions Probed by a Cryotrapping-Electron Paramagnetic Resonance Approach. Angew Chem Int Ed Engl 2020; 59:13936-13940. [PMID: 32352195 PMCID: PMC7497095 DOI: 10.1002/anie.202005052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Indexed: 11/25/2022]
Abstract
Redox active metalloenzymes catalyse a range of biochemical processes essential for life. However, due to their complex reaction mechanisms, and often, their poor optical signals, detailed mechanistic understandings of them are limited. Here, we develop a cryoreduction approach coupled to electron paramagnetic resonance measurements to study electron transfer between the copper centers in the copper nitrite reductase (CuNiR) family of enzymes. Unlike alternative methods used to study electron transfer reactions, the cryoreduction approach presented here allows observation of the redox state of both metal centers, a direct read-out of electron transfer, determines the presence of the substrate/product in the active site and shows the importance of protein motion in inter-copper electron transfer catalyzed by CuNiRs. Cryoreduction-EPR is broadly applicable for the study of electron transfer in other redox enzymes and paves the way to explore transient states in multiple redox-center containing proteins (homo and hetero metal ions).
Collapse
Affiliation(s)
- Tobias M. Hedison
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
- BBSRC and EPSRC funded Future Biomanfacturing Research HubManchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| | - Ruth Edge
- Dalton Cumbrian FacilityThe University of ManchesterCumbriaUK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
- BBSRC and EPSRC funded Future Biomanfacturing Research HubManchester Institute of Biotechnology and School of ChemistryUniversity of ManchesterPrincess StreetManchesterM1 7DNUK
| |
Collapse
|
5
|
Hedison TM, Shanmugam M, Heyes DJ, Edge R, Scrutton NS. Active Intermediates in Copper Nitrite Reductase Reactions Probed by a Cryotrapping‐Electron Paramagnetic Resonance Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tobias M. Hedison
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
- BBSRC and EPSRC funded Future Biomanfacturing Research Hub Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| | - Derren J. Heyes
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| | - Ruth Edge
- Dalton Cumbrian Facility The University of Manchester Cumbria UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
- BBSRC and EPSRC funded Future Biomanfacturing Research Hub Manchester Institute of Biotechnology and School of Chemistry University of Manchester Princess Street Manchester M1 7DN UK
| |
Collapse
|
6
|
Pan H, Qin Y, Wang Y, Liu S, Yu B, Song Y, Wang X, Zhu G. Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) pathway dominates nitrate reduction processes in rhizosphere and non-rhizosphere of four fertilized farmland soil. Environ Res 2020; 186:109612. [PMID: 32668552 DOI: 10.1016/j.envres.2020.109612] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/26/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Nitrate (NO3-) reduction partitioning between denitrification, anaerobic ammonium oxidation (anammox), denitrifying anaerobic methane oxidation (DAMO), and dissimilatory nitrate reduction to ammonium (DNRA), can influence the nitrogen (N) use efficiency and crop production in arid farmland. The microbial structure, function and potential rates of denitrification, anammox, DAMO and DNRA, and their respective contributions to total NO3- reduction were investigated in rhizosphere and non-rhizosphere soil of four typical crops in north China by functional gene amplification, high-throughput sequencing, network analysis and isotopic tracing technique. The measured denitrification and DNRA rate varied from 0.0294 to 20.769 nmol N g-1 h-1and 2.4125-58.682 nmol N g-1 h-1, respectively, based on which DNRA pathway contributed to 84.44 ± 14.40% of dissimilatory NO3- reduction, hence dominated NO3- reduction processes compared to denitrification. Anammox and DAMO were not detected. High-throughput sequencing analysis on DNRA nrfA gene, and denitrification nirS and nirK genes demonstrated that these two processes did not correlate to corresponding gene abundance or dominant genus. RDA and Pearson's correlation analysis illustrated that DNRA rate was significantly correlated with the abundance of Chthiniobacter, as well as total organic matter (TOM); denitrification rate was significantly correlated with the abundance of Lautropia, so did TOM. Network analysis showed that the genus performed DNRA was the key connector in the microbial community of dissimilatory nitrate reducers. This study simultaneously investigated the dissimilatory nitrate reduction processes in rhizosphere and non-rhizosphere soils in arid farmland, highlighting that DNRA dominated NO3- reduction processes against denitrification. As denitrification results in N loss, whereas DNRA contributes to N retention, the relative contributions of DNRA versus denitrification activities should be considered appropriately when assessing N transformation processes and N fertilizer management in arid farmland fields.
Collapse
Affiliation(s)
- Huawei Pan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yu Qin
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuantao Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shiguang Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Bin Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Song
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
7
|
Halsted TP, Yamashita K, Gopalasingam CC, Shenoy RT, Hirata K, Ago H, Ueno G, Blakeley MP, Eady RR, Antonyuk SV, Yamamoto M, Hasnain SS. Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. IUCrJ 2019; 6:761-772. [PMID: 31316819 PMCID: PMC6608623 DOI: 10.1107/s2052252519008285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/12/2019] [Indexed: 05/31/2023]
Abstract
Copper-containing nitrite reductases (CuNiRs) that convert NO2 - to NO via a CuCAT-His-Cys-CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD-, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2 - a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.
Collapse
Affiliation(s)
- Thomas P. Halsted
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Chai C. Gopalasingam
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Rajesh T. Shenoy
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Hideo Ago
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Go Ueno
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - Matthew P. Blakeley
- Large-Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Robert R. Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| | - Masaki Yamamoto
- SR Life Science Instrumentation Unit, RIKEN SPring-8 Centre, Sayo 679-5148, Japan
| | - S. Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, England
| |
Collapse
|
8
|
Abstract
The development of redox-active metalloprotein catalysts is a challenging objective of de novo protein design. Within this Perspective we detail our efforts to create a redox-active Cu nitrite reductase (NiR) by incorporating Cu into the hydrophobic interior of well-defined three-stranded coiled coils (3SCCs). The scaffold contains three histidine residues that provide a layer of three nitrogen donors that mimic the type 2 catalytic site of NiR. We have found that this strategy successfully produces an active and stable CuNiR model that functions for over 1000 turnovers. Spectroscopic evidence indicates that the Cu(I) site has a lower coordination number in comparison to the enzyme, whereas the Cu(II) geometry may more faithfully reproduce the NiR type 2 center. Mutations at the helical interface successfully produce a hydrogen bond between an interfacial Glu residue and the Culigating His residue, which allows for the tuning of the redox potential over a 100 mV range. We successfully created constructs with as much as a 120-fold improvement from the original design by modifying the steric bulk above or below the Cu binding site. These systems are now the most active water-soluble and stable artificial NiR catalysts yet produced. Several avenues for improving the catalytic efficiency of later designs are detailed within this Perspective, including adjustment of their resting oxidation state, the use of asymmetric scaffolds to allow for single amino acid mutation within the second coordination sphere, and the design of hydrogen-bonding networks to tune residue orientation and electronics. Through these studies the TRI-H system has given insight into the difficulties that arise in creating a de novo redox active enzyme. Work to improve upon this model will provide strategies by which redox-active de novo enzymes may be tuned and detail how native enzymes accomplish catalytic efficiencies through proton gated redox catalysis.
Collapse
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan Ann Arbor, Michigan 48109, United States
| |
Collapse
|
9
|
Abstract
Electron transfer between two Cu sites in the enzyme induced by protonation of remote catalytic residues.
Collapse
Affiliation(s)
- Masami Lintuluoto
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
- Kyoto 606-8522
- Japan
| | | |
Collapse
|
10
|
Gao H, Li C, Ramesh B, Hu N. Cloning, purification and characterization of novel Cu-containing nitrite reductase from the Bacillus firmus GY-49. World J Microbiol Biotechnol 2018; 34. [DOI: 10.1007/s11274-017-2383-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 11/22/2017] [Indexed: 11/27/2022]
|
11
|
Cristaldi JC, Gómez MC, González PJ, Ferroni FM, Dalosto SD, Rizzi AC, Rivas MG, Brondino CD. 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 2018; 1862:752-60. [PMID: 29051066 DOI: 10.1016/j.bbagen.2017.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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
|
12
|
Qin X, Deng L, Hu C, Li L, Chen X. Copper-Containing Nitrite Reductase Employing Proton-Coupled Spin-Exchanged Electron-Transfer and Multiproton Synchronized Transfer to Reduce Nitrite. Chemistry 2017; 23:14900-14910. [DOI: 10.1002/chem.201703221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
|
13
|
Kim H, Park D, Yoon S. pH Control Enables Simultaneous Enhancement of Nitrogen Retention and N 2O Reduction in Shewanella loihica Strain PV-4. Front Microbiol 2017; 8:1820. [PMID: 28979255 PMCID: PMC5611402 DOI: 10.3389/fmicb.2017.01820] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/06/2017] [Indexed: 11/13/2022] Open
Abstract
pH has been recognized as one of the key environmental parameters with significant impacts on the nitrogen cycle in the environment. In this study, the effects of pH on NO3-/NO2- fate and N2O emission were examined with Shewanella loihica strain PV-4, an organism with complete denitrification and respiratory ammonification pathways. Strain PV-4 was incubated at varying pH with lactate as the electron donor and NO3-/NO2- and N2O as the electron acceptors. When incubated with NO3- and N2O at pH 6.0, transient accumulation of N2O was observed and no significant NH4+ production was observed. At pH 7.0 and 8.0, strain PV-4 served as a N2O sink, as N2O concentration decreased consistently without accumulation. Respiratory ammonification was upregulated in the experiments performed at these higher pH values. When NO2- was used in place of NO3-, neither growth nor NO2- reduction was observed at pH 6.0. NH4+ was the exclusive product from NO2- reduction at both pH 7.0 and 8.0 and neither production nor consumption of N2O was observed, suggesting that NO2- regulation superseded pH effects on the nitrogen-oxide dissimilation reactions. When NO3- was the electron acceptor, nirK transcription was significantly upregulated upon cultivation at pH 6.0, while nrfA transcription was significantly upregulated at pH 8.0. The highest level of nosZ transcription was observed at pH 6.0 and the lowest at pH 8.0. With NO2- as the electron acceptor, transcription profiles of nirK, nrfA, and nosZ were statistically indistinguishable between pH 7.0 and 8.0. The transcriptions of nirK and nosZ were severely downregulated regardless of pH. These observations suggested that the kinetic imbalance between N2O production and consumption, but neither decrease in expression nor activity of NosZ, was the major cause of N2O accumulation at pH 6.0. The findings also suggest that simultaneous enhancement of nitrogen retention and N2O emission reduction may be feasible through pH modulation, but only in environments where C:N or NO2-:NO3- ratio does not exhibit overarching control over the NO3-/NO2- reduction pathways.
Collapse
Affiliation(s)
- Hayeon Kim
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| | - Doyoung Park
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| |
Collapse
|
14
|
Lintuluoto M, Lintuluoto JM. DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase. Biochemistry 2016; 55:4697-707. [DOI: 10.1021/acs.biochem.6b00423] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho,
Sakyo, Kyoto 606-8522, Japan
| | - Juha M. Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
| |
Collapse
|
15
|
Weigand MA, Foriel J, Barnett B, Oleynik S, Sigman DM. Updates to instrumentation and protocols for isotopic analysis of nitrate by the denitrifier method. Rapid Commun Mass Spectrom 2016; 30:1365-1383. [PMID: 27197029 DOI: 10.1002/rcm.7570] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE The denitrifier method allows for highly sensitive measurement of the (15) N/(14) N (δ(15) N value) and (18) O/(16) O (δ(18) O value) of nitrate dissolved in natural waters and for highly sensitive δ(15) N measurement of other N forms (e.g., organic N) that can be converted into nitrate. Here, updates to instrumentation and protocols are described, and improvements in data quality are demonstrated. METHODS A 'heart cut' of the N2 O was implemented in the extraction system to (1) minimize introduction of contaminants into the mass spectrometer, reducing isotopic drift and (2) decrease the fraction of sample lost at the open split to improve sensitivity. Referencing protocols were updated, including a correction scheme for a weak dependence of nitrate δ(18) O values on nitrate concentration. Analyses of samples from the US GEOTRACES North Atlantic Program and of reference solutions from the same analysis batches were used to characterize performance. RESULTS The drift is typically <0.1‰ for both δ(15) N and δ(18) O values. Within-batch and inter-batch replication yields 1 standard deviation (SD) of ≤0.06‰ for δ(15) N values and ≤0.14‰ for δ(18) O values down to 5 μM nitrate and ≤0.08‰ and ≤0.23‰ at 2 and 1 μM. The blank is typically 0.06 nmol N, 0.3% of the N in a 20 nmol N sample. Differences between reference materials in seawater are indistinguishable from reported differences for δ(15) N values, with a contraction for δ(18) O values of ≤5%. CONCLUSIONS The new instrumentation and protocols yield nitrate isotopic data with external precision of ≤0.1‰ for large sample sets such as those derived from oceanographic sections. Further study should investigate the causes of (1) the weak dependence of nitrate δ(18) O values on nitrate concentration and (2) the inter-batch variation in the δ(18) O contraction (due mostly to oxygen atom exchange with water). Nevertheless, comprehensive correction schemes are in place for the measurement of both the δ(15) N and δ(18) O values of nitrate. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- M Alexandra Weigand
- Department of Geosciences, Princeton University, Guyot Hall, Princeton, NJ, 08544, USA
| | - Julien Foriel
- Department of Geosciences, Princeton University, Guyot Hall, Princeton, NJ, 08544, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-1E-1 Ookayayama Meguro-ku, Tokyo, 152-8550, Japan
| | - Bruce Barnett
- Department of Geosciences, Princeton University, Guyot Hall, Princeton, NJ, 08544, USA
- W. M. Keck Paleoenvironmental and Environmental Stable Isotope Laboratory, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Sergey Oleynik
- Department of Geosciences, Princeton University, Guyot Hall, Princeton, NJ, 08544, USA
| | - Daniel M Sigman
- Department of Geosciences, Princeton University, Guyot Hall, Princeton, NJ, 08544, USA
| |
Collapse
|
16
|
Abstract
Nitrite reductase (NiR) activity was examined in a series of dicopper P.a. azurin variants in which a surface binding copper site was added through site-directed mutagenesis. Four variants were synthesized with copper binding motifs inspired by the catalytic type 2 copper binding sites found in the native noncoupled dinuclear copper enzymes nitrite reductase and peptidylglycine α-hydroxylating monooxygenase. The four azurin variants, denoted Az-NiR, Az-NiR3His, Az-PHM, and Az-PHM3His, maintained the azurin electron transfer copper center, with the second designed copper site located over 13 Å away and consisting of mutations Asn10His,Gln14Asp,Asn16His-azurin, Asn10His,Gln14His,Asn16His-azurin, Gln8Met,Gln14His,Asn16His-azurin, and Gln8His,Gln14His,Asn16His-azurin, respectively. UV-visible absorption spectroscopy, EPR spectroscopy, and electrochemistry of the sites demonstrate copper binding as well as interaction with small exogenous ligands. The nitrite reduction activity of the variants was determined, including the catalytic Michaelis-Menten parameters. The variants showed activity (0.34-0.59 min(-1)) that was slower than that of native NiRs but comparable to that of other model systems. There were small variations in activity of the four variants that correlated with the number of histidines in the added copper site. Catalysis was found to be reversible, with nitrite produced from NO. Reactions starting with reduced azurin variants demonstrated that electrons from both copper centers were used to reduce nitrite, although steady-state catalysis required the T2 copper center and did not require the T1 center. Finally, experiments separating rates of enzyme reduction from rates of reoxidation by nitrite demonstrated that the reaction with nitrite was rate limiting during catalysis.
Collapse
Affiliation(s)
- Steven M Berry
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Jacob N Strange
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Erika L Bladholm
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Balabhadra Khatiwada
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Christine G Hedstrom
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| | - Alexandra M Sauer
- Department of Chemistry and Biochemistry, University of Minnesota Duluth , 1039 University Drive, Duluth, Minnesota 55812, United States
| |
Collapse
|
17
|
Yoon S, Cruz-García C, Sanford R, Ritalahti KM, Löffler FE. Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3(-)/NO2(-) reduction pathways in Shewanella loihica strain PV-4. ISME J 2015; 9:1093-104. [PMID: 25350157 PMCID: PMC4409154 DOI: 10.1038/ismej.2014.201] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 08/30/2014] [Accepted: 09/05/2014] [Indexed: 11/09/2022]
Abstract
Denitrification and respiratory ammonification are two competing, energy-conserving NO3(-)/NO2(-) reduction pathways that have major biogeochemical consequences for N retention, plant growth and climate. Batch and continuous culture experiments using Shewanella loihica strain PV-4, a bacterium possessing both the denitrification and respiratory ammonification pathways, revealed factors that determine NO3(-)/NO2(-) fate. Denitrification dominated at low carbon-to-nitrogen (C/N) ratios (that is, electron donor-limiting growth conditions), whereas ammonium was the predominant product at high C/N ratios (that is, electron acceptor-limiting growth conditions). pH and temperature also affected NO3(-)/NO2(-) fate, and incubation above pH 7.0 and temperatures of 30 °C favored ammonium formation. Reverse-transcriptase real-time quantitative PCR analyses correlated the phenotypic observations with nirK and nosZ transcript abundances that decreased up to 1600-fold and 27-fold, respectively, under conditions favoring respiratory ammonification. Of the two nrfA genes encoded on the strain PV-4 genome, nrfA0844 transcription decreased only when the chemostat reactor received medium with the lowest C/N ratio of 1.5, whereas nrfA0505 transcription occurred at low levels (≤3.4 × 10(-2) transcripts per cell) under all growth conditions. At intermediate C/N ratios, denitrification and respiratory ammonification occurred concomitantly, and both nrfA0844 (5.5 transcripts per cell) and nirK (0.88 transcripts per cell) were transcribed. Recent findings suggest that organisms with both the denitrification and respiratory ammonification pathways are not uncommon in soil and sediment ecosystems, and strain PV-4 offers a tractable experimental system to explore regulation of dissimilatory NO3(-)/NO2(-) reduction pathways.
Collapse
Affiliation(s)
- Sukhwan Yoon
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Claribel Cruz-García
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert Sanford
- Department of Geology, University of Illinois, Urbana, IL, USA
| | - Kirsti M Ritalahti
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS) and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| |
Collapse
|
18
|
Tabares LC, Gupta A, Aartsma TJ, Canters GW. Tracking electrons in biological macromolecules: from ensemble to single molecule. Molecules 2014; 19:11660-78. [PMID: 25102116 PMCID: PMC6271485 DOI: 10.3390/molecules190811660] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 11/29/2022] Open
Abstract
Nature utilizes oxido-reductases to cater to the energy demands of most biochemical processes in respiratory species. Oxido-reductases are capable of meeting this challenge by utilizing redox active sites, often containing transition metal ions, which facilitate movement and relocation of electrons/protons to create a potential gradient that is used to energize redox reactions. There has been a consistent struggle by researchers to estimate the electron transfer rate constants in physiologically relevant processes. This review provides a brief background on the measurements of electron transfer rates in biological molecules, in particular Cu-containing enzymes, and highlights the recent advances in monitoring these electron transfer events at the single molecule level or better to say, at the individual event level.
Collapse
Affiliation(s)
- Leandro C Tabares
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies de Saclay, Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Gif-sur-Yvette Cedex 91191, France
| | - Ankur Gupta
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands
| | - Thijs J Aartsma
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands
| | - Gerard W Canters
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, PO Box 9504, RA Leiden 2300, The Netherlands.
| |
Collapse
|
19
|
Leferink NGH, Antonyuk SV, Houwman JA, Scrutton NS, Eady RR, Hasnain SS. Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase. Nat Commun 2014; 5:4395. [PMID: 25022223 PMCID: PMC4104443 DOI: 10.1038/ncomms5395] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/13/2014] [Indexed: 11/29/2022] Open
Abstract
Enzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of catalysis. Evidence for long-range effects on enzyme mechanism resulting from mutations remains sparse, limiting the design/redesign of synthetic catalysts in a predictable way. Here we show that improving the accessibility of the active site pocket of copper nitrite reductase by mutation of a surface-exposed phenylalanine residue (Phe306), located 12 Å away from the catalytic site type-2 Cu (T2Cu), profoundly affects intra-molecular electron transfer, substrate-binding and catalytic activity. Structures and kinetic studies provide an explanation for the lower affinity for the substrate and the alteration of the rate-limiting step in the reaction. Our results demonstrate that distant residues remote from the active site can have marked effects on enzyme catalysis, by driving mechanistic change through relatively minor structural perturbations. Residues within the catalytic site of enzymes are important for activity, but whether more distant residues are also sensitive to mutation is unclear. Here, Leferink et al. show that mutation of residues in copper nitrate reductase that are 12Å away from the active site perturb enzyme function.
Collapse
Affiliation(s)
- Nicole G H Leferink
- 1] Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK [2]
| | - Svetlana V Antonyuk
- 1] Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK [2]
| | - Joseline A Houwman
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
| | - Robert R Eady
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| |
Collapse
|
20
|
Affiliation(s)
- Luisa B. Maia
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento
de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| |
Collapse
|
21
|
Fukuda Y, Tse KM, Lintuluoto M, Fukunishi Y, Mizohata E, Matsumura H, Takami H, Nojiri M, Inoue T. Structural insights into the function of a thermostable copper-containing nitrite reductase. ACTA ACUST UNITED AC 2013; 155:123-35. [DOI: 10.1093/jb/mvt107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
22
|
Ferroni FM, Guerrero SA, Rizzi AC, Brondino CD. Overexpression, purification, and biochemical and spectroscopic characterization of copper-containing nitrite reductase from Sinorhizobium meliloti 2011. Study of the interaction of the catalytic copper center with nitrite and NO. J Inorg Biochem 2012; 114:8-14. [DOI: 10.1016/j.jinorgbio.2012.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 11/28/2022]
|
23
|
Leferink NGH, Eady RR, Hasnain SS, Scrutton NS. Laser-flash photolysis indicates that internal electron transfer is triggered by proton uptake by Alcaligenes xylosoxidans copper-dependent nitrite reductase. FEBS J 2012; 279:2174-81. [DOI: 10.1111/j.1742-4658.2012.08601.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
24
|
Han C, Wright G, Fisher K, Rigby S, Eady R, Hasnain S. Characterization of a novel copper-haem c dissimilatory nitrite reductase from Ralstonia pickettii. Biochem J 2012; 444:219-26. [DOI: 10.1042/bj20111623] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
NiRs (nitrite reductases) convert nitrite into NO in the denitrification process. RpNiR (Ralstonia pickettii NiR), a new type of dissimilatory Cu-containing NiR with a C-terminal haem c domain from R. pickettii, has been cloned, overexpressed in Escherichia coli and purified to homogeneity. The enzyme has a subunit molecular mass of 50515 Da, consistent with sequence data showing homology to the well-studied two-domain Cu NiRs, but with an attached C-terminal haem c domain. Gel filtration and combined SEC (size-exclusion chromatography)-SAXS (small angle X-ray scattering) analysis shows the protein to be trimeric. The metal content of RpNiR is consistent with each monomer having a single haem c group and the two Cu sites being metallated by Cu2+ ions. The absorption spectrum of the oxidized as-isolated recombinant enzyme is dominated by the haem c. X-band EPR spectra have clear features arising from both type 1 Cu and type 2 Cu centres in addition to those of low-spin ferric haem. The requirements for activity and low apparent Km for nitrite are similar to other CuNiRs (Cu-centre NiRs). However, EPR and direct binding measurements of nitrite show that oxidized RpNiR binds nitrite very weakly, suggesting that substrate binds to the reduced type 2 Cu site during turnover. Analysis of SEC-SAXS data suggests that the haem c domains in RpNiR form extensions into the solvent, conferring a high degree of conformational flexibility in solution. SAXS data yield Rg (gyration radius) and Dmax (maximum particle diameter) values of 43.4 Å (1 Å=0.1 nm) and 154 Å compared with 28 Å and 80 Å found for the two-domain CuNiR of Alcaligenes xylosoxidans.
Collapse
|
25
|
Hira D, Toh H, Migita CT, Okubo H, Nishiyama T, Hattori M, Furukawa K, Fujii T. Anammox organism KSU-1 expresses a NirK-type copper-containing nitrite reductase instead of a NirS-type with cytochromecd1. FEBS Lett 2012; 586:1658-63. [DOI: 10.1016/j.febslet.2012.04.041] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 10/28/2022]
|
26
|
Tabares LC, Kostrz D, Elmalk A, Andreoni A, Dennison C, Aartsma TJ, Canters GW. Fluorescence lifetime analysis of nitrite reductase from Alcaligenes xylosoxidans at the single-molecule level reveals the enzyme mechanism. Chemistry 2011; 17:12015-9. [PMID: 21922585 DOI: 10.1002/chem.201102063] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Leandro C Tabares
- Leiden Institute of Physics, Huygens Laboratory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
27
|
Krzemiński Ł, Ndamba L, Canters GW, Aartsma TJ, Evans SD, Jeuken LJC. Spectroelectrochemical Investigation of Intramolecular and Interfacial Electron-Transfer Rates Reveals Differences Between Nitrite Reductase at Rest and During Turnover. J Am Chem Soc 2011; 133:15085-93. [DOI: 10.1021/ja204891v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Lionel Ndamba
- Leiden Institute of Physics, Leiden University, P.O. Box 9504, 2300 RA, Leiden, The Netherlands
| | - Gerard W. Canters
- Leiden Institute of Physics, Leiden University, P.O. Box 9504, 2300 RA, Leiden, The Netherlands
| | - Thijs J. Aartsma
- Leiden Institute of Physics, Leiden University, P.O. Box 9504, 2300 RA, Leiden, The Netherlands
| | | | | |
Collapse
|
28
|
Leferink NGH, Han C, Antonyuk SV, Heyes DJ, Rigby SEJ, Hough MA, Eady RR, Scrutton NS, Hasnain SS. Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry 2011; 50:4121-31. [DOI: 10.1021/bi200246f] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicole G. H. Leferink
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Cong Han
- 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
| | - Derren J. Heyes
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Stephen E. J. Rigby
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Michael A. Hough
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, 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
| | - Nigel S. Scrutton
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, 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
| |
Collapse
|
29
|
Brenner S, Heyes DJ, Hay S, Hough MA, Eady RR, Hasnain SS, Scrutton NS. Demonstration of proton-coupled electron transfer in the copper-containing nitrite reductases. J Biol Chem 2009; 284:25973-83. [PMID: 19586913 DOI: 10.1074/jbc.m109.012245] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reduction of nitrite (NO2-) into nitric oxide (NO), catalyzed by nitrite reductase, is an important reaction in the denitrification pathway. In this study, the catalytic mechanism of the copper-containing nitrite reductase from Alcaligenes xylosoxidans (AxNiR) has been studied using single and multiple turnover experiments at pH 7.0 and is shown to involve two protons. A novel steady-state assay was developed, in which deoxyhemoglobin was employed as an NO scavenger. A moderate solvent kinetic isotope effect (SKIE) of 1.3 +/- 0.1 indicated the involvement of one protonation to the rate-limiting catalytic step. Laser photoexcitation experiments have been used to obtain single turnover data in H2O and D2O, which report on steps kinetically linked to inter-copper electron transfer (ET). In the absence of nitrite, a normal SKIE of approximately 1.33 +/- 0.05 was obtained, suggesting a protonation event that is kinetically linked to ET in substrate-free AxNiR. A nitrite titration gave a normal hyperbolic behavior for the deuterated sample. However, in H2O an unusual decrease in rate was observed at low nitrite concentrations followed by a subsequent acceleration in rate at nitrite concentrations of >10 mM. As a consequence, the observed ET process was faster in D2O than in H2O above 0.1 mM nitrite, resulting in an inverted SKIE, which featured a significant dependence on the substrate concentration with a minimum value of approximately 0.61 +/- 0.02 between 3 and 10 mM. Our work provides the first experimental demonstration of proton-coupled electron transfer in both the resting and substrate-bound AxNiR, and two protons were found to be involved in turnover.
Collapse
Affiliation(s)
- Sibylle Brenner
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | | | | | | | | | | | | |
Collapse
|
30
|
Chi Q, Jensen PS, Ulstrup J. Electrochemical Biosensing of Redox Proteins and Enzymes. In: Offenhäusser A, Rinaldi R, editors. Nanobioelectronics - for Electronics, Biology, and Medicine. New York: Springer; 2009. pp. 182-209. [DOI: 10.1007/978-0-387-09459-5_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
31
|
Hough MA, Eady RR, Hasnain SS. Identification of the Proton Channel to the Active Site Type 2 Cu Center of Nitrite Reductase: Structural and Enzymatic Properties of the His254Phe and Asn90Ser Mutants,. Biochemistry 2008; 47:13547-53. [DOI: 10.1021/bi801369y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael A. Hough
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, U.K., and STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K
| | - Robert R. Eady
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, U.K., and STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K
| | - S. Samar Hasnain
- Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, U.K., and STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, U.K
| |
Collapse
|
32
|
Stefanelli P, Colotti G, Neri A, Salucci ML, Miccoli R, Di Leandro L, Ippoliti R. Molecular characterization of nitrite reductase gene (aniA) and gene product inNeisseria meningitidisisolates: IsaniA essential for meningococcal survival? IUBMB Life 2008; 60:629-36. [DOI: 10.1002/iub.95] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
33
|
Tocheva EI, Eltis LD, Murphy MEP. Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite Reductase by Small Molecules. Biochemistry 2008; 47:4452-60. [DOI: 10.1021/bi7020537] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elitza I. Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada
| |
Collapse
|
34
|
Kuznetsova S, Zauner G, Aartsma TJ, Engelkamp H, Hatzakis N, Rowan AE, Nolte RJ, Christianen PC, Canters GW. The enzyme mechanism of nitrite reductase studied at single-molecule level. Proc Natl Acad Sci U S A 2008; 105:3250-5. [PMID: 18303118 DOI: 10.1073/pnas.0707736105] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A generic method is described for the fluorescence "readout" of the activity of single redox enzyme molecules based on Förster resonance energy transfer from a fluorescent label to the enzyme cofactor. The method is applied to the study of copper-containing nitrite reductase from Alcaligenes faecalis S-6 immobilized on a glass surface. The parameters extracted from the single-molecule fluorescence time traces can be connected to and agree with the macroscopic ensemble averaged kinetic constants. The rates of the electron transfer from the type 1 to the type 2 center and back during turnover exhibit a distribution related to disorder in the catalytic site. The described approach opens the door to single-molecule mechanistic studies of a wide range of redox enzymes and the precise investigation of their internal workings.
Collapse
|
35
|
Kohzuma T, Kikuchi M, Horikoshi N, Nagatomo S, Kitagawa T, Czernuszewicz RS. Intersite structural rearrangement of the blue copper site induced by substrate binding: spectroscopic studies of a copper-containing nitrite reductase from Alcaligenes xylosoxidans NCIMB 11015. Inorg Chem 2007; 45:8474-6. [PMID: 17029353 DOI: 10.1021/ic0609195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A copper-containing nitrite reductase from Alcaligenes xylosoxidans NCIMB 11015 has its own unique blue or type 1 copper protein resonance Raman spectrum in the usual Cu-S(Cys) stretching region, nu(Cu-S(Cys)), with a pair of strong peaks at 412 and 420 cm(-1) and a weak peak at 364 cm(-1). The predominantly nu(Cu-S(Cys)) Raman bands at 412, 420, and 364 cm(-1) of the type 1 copper site all shifted to higher frequencies upon binding of nitrite to the type 2 copper site, and the resonance Raman difference spectra progressively intensified with the increments of nitrite ion concentration. Positive support for substrate binding to the type 2 copper is provided by the nu(Cu-S(Cys)) bands in the resonance Raman spectrum of a type 2 copper-depleted enzyme, which is insensitive to the presence of NO2-. The shift to higher frequency of the Raman bands of the type 1 copper center with the addition of nitrite ions suggests a stronger Cu-S(Cys) interaction in the substrate-bound A. xylosoxidans nitrite reductase.
Collapse
Affiliation(s)
- Takamitsu Kohzuma
- Institute of Applied Beam Science, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki 310-8512, Japan.
| | | | | | | | | | | |
Collapse
|
36
|
Jacobson F, Pistorius A, Farkas D, De Grip W, Hansson O, Sjölin L, Neutze R. pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase. J Biol Chem 2007; 282:6347-55. [PMID: 17148448 DOI: 10.1074/jbc.m605746200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity.
Collapse
Affiliation(s)
- Frida Jacobson
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Box 462, SE-40530 Göteborg, Sweden
| | | | | | | | | | | | | |
Collapse
|
37
|
Harris RL, Eady RR, Hasnain SS, Sawers RG. Coordinate synthesis of azurin I and copper nitrite reductase in Alcaligenes xylosoxidans during denitrification. Arch Microbiol 2006; 186:241-9. [PMID: 16832626 DOI: 10.1007/s00203-006-0139-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/07/2006] [Accepted: 06/19/2006] [Indexed: 11/27/2022]
Abstract
The denitrifying bacterium Alcaligenes xylosoxidans synthesises two azurins (Az), which are termed Az I and Az 2. Both function as effective electron donors to copper nitrite reductase (NiR) in vitro. As a first step towards identifying the physiological relevance of these electron transfer proteins in the denitrification process, the gene (azuA) encoding Az I was characterised and its expression with respect to denitrification determined. We show that the azuA gene from A. xylosoxidans is monocistronic and its expression is increased when cells are grown under denitrifying conditions in the presence of nitrate or nitrite. The expression pattern of azuA was similar, though not identical, to that of the monocistronic nirK gene, which encodes copper NiR, and is in accord with both gene products being synthesised when the bacterium denitrifies. Recombinant Az I was exported to the periplasm of the heterologous host Escherichia coli, was synthesised at very high levels (80 mg purified protein per litre) and was fully loaded with copper. Electron donation from reduced recombinant Az to NiR was indistinguishable from the activity determined with the native protein. Taken together, these findings indicate that in A. xylosoxidans azuA expression is coordinated with denitrification and recombinant Az I is processed and matured in the periplasm of E. coli in the same way it is in A. xylosoxidans.
Collapse
Affiliation(s)
- Roger L Harris
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | | | | |
Collapse
|
38
|
Wijma HJ, Jeuken LJC, Verbeet MP, Armstrong FA, Canters GW. A Random-sequential Mechanism for Nitrite Binding and Active Site Reduction in Copper-containing Nitrite Reductase. J Biol Chem 2006; 281:16340-6. [PMID: 16613859 DOI: 10.1074/jbc.m601610200] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The homotrimeric copper-containing nitrite reductase (NiR) contains one type-1 and one type-2 copper center per monomer. Electrons enter through the type-1 site and are shuttled to the type-2 site where nitrite is reduced to nitric oxide. To investigate the catalytic mechanism of NiR the effects of pH and nitrite on the turnover rate in the presence of three different electron donors at saturating concentrations were measured. The activity of NiR was also measured electrochemically by exploiting direct electron transfer to the enzyme immobilized on a graphite rotating disk electrode. In all cases, the steady-state kinetics fitted excellently to a random-sequential mechanism in which electron transfer from the type-1 to the type-2 site is rate-limiting. At low [NO(-)(2)] reduction of the type-2 site precedes nitrite binding, at high [NO(-)(2)] the reverse occurs. Below pH 6.5, the catalytic activity diminished at higher nitrite concentrations, in agreement with electron transfer being slower to the nitrite-bound type-2 site than to the water-bound type-2 site. Above pH 6.5, substrate activation is observed, in agreement with electron transfer to the nitrite-bound type-2 site being faster than electron transfer to the hydroxyl-bound type-2 site. To study the effect of slower electron transfer between the type-1 and type-2 site, NiR M150T was used. It has a type-1 site with a 125-mV higher midpoint potential and a 0.3-eV higher reorganization energy leading to an approximately 50-fold slower intramolecular electron transfer to the type-2 site. The results confirm that NiR employs a random-sequential mechanism.
Collapse
Affiliation(s)
- Hein J Wijma
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | | | | | | | | |
Collapse
|
39
|
Chi Q, Zhang J, Jensen PS, Christensen HEM, Ulstrup J. Long-range interfacial electron transfer of metalloproteins based on molecular wiring assemblies. Faraday Discuss 2006; 131:181-95; discussion 205-20. [PMID: 16512372 DOI: 10.1039/b506136a] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We address some physical features associated with long-range interfacial electron transfer (ET) of metalloproteins in both electrochemical and electrochemical scanning tunneling microscopy (ECSTM) configurations, which offer a brief foundation for understanding of the ET mechanisms. These features are illustrated experimentally by new developments of two systems with the blue copper protein azurin and enzyme nitrite reductase as model metalloproteins. Azurin and nitrite reductase were assembled on Au(111) surfaces by molecular wiring to establish effective electronic coupling between the redox centers in the proteins and the electrode surface for ET and biological electrocatalysis. With such assemblies, interfacial ET proceeds through chemically defined and well oriented sites and parallels biological ET. In the case of azurin, the ET properties can be characterized comprehensively and even down to the single-molecule level with direct observation of redox-gated electron tunnelling resonance. Molecular wiring using a pi-conjugated thiol is suitable for assembling monolayers of the enzyme with catalytic activity well-retained. The catalytic mechanism involves multiple-ET steps including both intramolecular and interfacial processes. Interestingly, ET appears to exhibit a substrate-gated pattern observed preliminarily in both voltammetry and ECSTM.
Collapse
Affiliation(s)
- Qijin Chi
- Department of Chemistry and Nano . DTU, Building 207, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | | | | | | | | |
Collapse
|
40
|
Antonyuk SV, Strange RW, Sawers G, Eady RR, Hasnain SS. Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism. Proc Natl Acad Sci U S A 2005; 102:12041-6. [PMID: 16093314 PMCID: PMC1189323 DOI: 10.1073/pnas.0504207102] [Citation(s) in RCA: 144] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Indexed: 11/18/2022] Open
Abstract
Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.
Collapse
Affiliation(s)
- Svetlana V Antonyuk
- Molecular Biophysics Group, Council for the Central Laboratory of the Research Councils Daresbury Laboratory, Warrington WA4 4AD, United Kingdom
| | | | | | | | | |
Collapse
|
41
|
Hough MA, Ellis MJ, Antonyuk S, Strange RW, Sawers G, Eady RR, Samar Hasnain S. High Resolution Structural Studies of Mutants Provide Insights into Catalysis and Electron Transfer Processes in Copper Nitrite Reductase. J Mol Biol 2005; 350:300-9. [PMID: 15927201 DOI: 10.1016/j.jmb.2005.04.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2005] [Revised: 04/01/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
We present high-resolution crystal structures and functional analysis of T1Cu centre mutants of nitrite reductase that perturb the redox potential and the Cys130-His129 "hard-wired" bridge through which electron transfer to the catalytic T2Cu centre occurs. These data provide insight into how activity can be altered through mutational manipulation of the electron delivery centre (T1Cu). The alteration of Cys to Ala results in loss of T1Cu and enzyme inactivation with azurin as electron donor despite the mutant enzyme retaining full nitrite-binding capacity. These data establish unequivocally that no direct transfer of electrons occurs from azurin to the catalytic type 2 Cu centre. The mutation of the axial ligand Met144 to Leu increases both the redox potential and catalytic activity, establishing that the rate-determining step of catalysis is the intermolecular electron transfer from azurin to nitrite reductase.
Collapse
Affiliation(s)
- Michael A Hough
- Molecular Biophysics Group, CCLRC Daresbury Laboratory, Warrington WA4 4AD, UK
| | | | | | | | | | | | | |
Collapse
|
42
|
Hansen AG, Zhang J, Christensen HEM, Welinder AC, Wackerbarth H, Ulstrup J. Electron Transfer and Redox Metalloenzyme Catalysis at the Single-Molecule Level. Isr J Chem 2004. [DOI: 10.1560/wy97-q5pq-f6vj-nln8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
43
|
Yousafzai FK, Eady RR. Dithionite reduction kinetics of the dissimilatory copper-containing nitrite reductase of Alcalegenes xylosoxidans. The SO(2)(.-) radical binds to the substrate binding type 2 copper site before the type 2 copper is reduced. J Biol Chem 2002; 277:34067-73. [PMID: 12082116 DOI: 10.1074/jbc.m204305200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report here the first detailed study of the dithionite reduction kinetics of a copper-containing dissimilatory nitrite reductase (NiR). The reduction of the blue type 1 copper (T1Cu) center of NiR preparations that contained both type 1 and type 2 copper atoms, followed biphasic kinetics. In contrast, NiR that was deficient in type 2 copper (T2DNiR), followed monophasic kinetics with a second-order rate constant (T2D)k = 3.06 x 10(6) m(-1) s(-1). In all cases the SO(2)(.-) radical rather than S(2)O(4)(2-) was the effective reductant. The observed kinetics were compatible with a reaction mechanism in which the T1Cu of the fully loaded protein is reduced both directly by dithionite and indirectly by the type 2 Cu (T2Cu) site via intramolecular electron transfer. Reduction kinetics of the T2Cu were consistent with SO(2)(.-) binding first to the T2Cu center and then transferring electrons (112 s(-1)) to reduce it. As SO(2)(.-) is a homologue of NO(2)(-), the NiR substrate, it is not unlikely that it binds to the catalytic T2Cu site. Effects on the catalytic activity of the enzyme using dithionite as a reducing agent are discussed. Reduction of the semireduced T1Cu(I)T2Cu(II) state followed either second-order kinetics with k(2) = 3.33 x 10(7) m(-1) s(-1) or first-order kinetics with 52.6 s(-1) < (T1red)k(1) < 112 s(-1). Values of formation constants of the T1Cu(II)T2Cu(II)-SO(2)(.-) and T1Cu(I)T2Cu(II)-SO(2)(.-) adducts showed that the redox state of T1Cu affected binding of SO(2)(.-) at the catalytic T2Cu center. Analysis of the kinetics required the development of a mathematical protocol that could be applied to a system with two intercommunicating sites but only one of which can be monitored. This novel protocol, reported for the first time, is of general application.
Collapse
Affiliation(s)
- Faridoon K Yousafzai
- Department of Biological Chemistry, John Innes Center, Colney, Norwich NR4 7UH, United Kingdom.
| | | |
Collapse
|
44
|
Murphy LM, Dodd FE, Yousafzai FK, Eady RR, Hasnain SS. Electron donation between copper containing nitrite reductases and cupredoxins: the nature of protein-protein interaction in complex formation. J Mol Biol 2002; 315:859-71. [PMID: 11812153 DOI: 10.1006/jmbi.2001.5253] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In denitrifying organisms with copper containing dissimilatory nitrite reductases, electron donation from a reduced cupredoxin is an essential step in the reduction of nitrite to nitric oxide. Copper nitrite reductases are categorised into two subgroups based on their colour, green and blue, which are found in organisms where the cupredoxins are pseudoazurins and azurins, respectively. In view of this and some in vitro electron donation experiments, it has been suggested that copper nitrite reductases have specific electron donors and that electron transfer takes place in a specific complex of the two proteins. We report results from the first comprehensive electron donation experiments using three copper nitrite reductases, one green and two blue, and five cupredoxins, one pseudoazurin and four azurins. Our data show that pseudoazurin can readily donate electrons to both blue and green copper nitrite reductases. In contrast, all of the azurins react very sluggishly as electron donors to the green nitrite reductase. These results are discussed in terms of surface compatibility of the component proteins, complex formation, overall charges, charge distribution, hydrophobic patches and redox potentials. A docking model for the complexes is proposed.
Collapse
|
45
|
Skipper L, Campbell WH, Mertens JA, Lowe DJ. Pre-steady-state kinetic analysis of recombinant Arabidopsis NADH:nitrate reductase: rate-limiting processes in catalysis. J Biol Chem 2001; 276:26995-7002. [PMID: 11356830 DOI: 10.1074/jbc.m100356200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recombinant Arabidopsis NADH:nitrate reductase was expressed in Pichia pastoris using fermentation. Large enzyme quantities were purified for pre-steady-state kinetic analysis, which had not been done before with any eukaryotic nitrate reductase. Basic biochemical properties of recombinant nitrate reductase were similar to natural enzyme forms. Molybdenum content was lower than expected, which was compensated for by activity calculation on molybdenum basis. Stopped-flow rapid-scan spectrophotometry showed that the enzyme FAD and heme were rapidly reduced by NADH with and without nitrate present. NADPH reduced FAD at less than one-tenth of NADH rate. Reaction of NADH-reduced enzyme with nitrate yielded rapid initial oxidation of heme with slower oxidation of flavin. Rapid-reaction freeze-quench EPR spectra revealed molybdenum was maintained in a partially reduced state during turnover. Rapid-reaction chemical quench for quantifying nitrite production showed that the rate of nitrate reduction was initially greater than the steady-state rate, but rapidly decreased to near steady-state turnover rate. However, rates of internal electron transfer and nitrate reduction were similar in magnitude with no one step in the catalytic process appearing to be much slower than the others. This leads to the conclusion that the catalytic rate is determined by a combination of rates with no overall rate-limiting individual process.
Collapse
Affiliation(s)
- L Skipper
- Biological Chemistry Department, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | | | | |
Collapse
|
46
|
Prudêncio M, Eady RR, Sawers G. Catalytic and spectroscopic analysis of blue copper-containing nitrite reductase mutants altered in the environment of the type 2 copper centre: implications for substrate interaction. Biochem J 2001; 353:259-66. [PMID: 11139389 PMCID: PMC1221567 DOI: 10.1042/0264-6021:3530259] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The blue dissimilatory nitrite reductase (NiR) from Alcaligenes xylosoxidans is a trimer containing two types of Cu centre, three type 1 electron transfer centres and three type 2 centres. The latter have been implicated in the binding and reduction of nitrite. The Cu ion of the type 2 centre of the oxidized enzyme is ligated by three His residues, and additionally has a co-ordinated water molecule that is also hydrogen-bonded to the carboxyl of Asp(92) [Dodd, Van Beeumen, Eady and Hasnain (1998), J. Mol. Biol. 282, 369-382]. Two mutations of this residue have been made, one to a glutamic acid residue and a second to an asparagine residue; the effects of both mutations on the spectroscopic and catalytic properties of the enzyme have been analysed. EPR spectroscopy revealed that both mutants retained intact type 1 Cu centres with g( parallel)=2.12 (A( parallel)=0 mT) and g( perpendicular)=2.30 (A( perpendicular)=6.4 mT), which was consistent with their blue colour, but differed in their activities and in the spectroscopic properties of the type 2 centres. The D92E mutant had an altered geometry of its type 2 centre such that nitrite was no longer capable of binding to elicit changes in the EPR parameters of this centre. Accordingly, this mutation resulted in a form of NiR that had very low enzyme activity with the artificial electron donors reduced Methyl Viologen and sodium dithionite. As isolated, the EPR spectrum of the Asp(92)-->Asn (D92N) mutant showed no characteristic type 2 hyperfine lines. However, oxidation with iridium hexachloride partly restored a type 2 EPR signal, suggesting that type 2 copper is present in the enzyme but in a reduced, EPR-silent form. Like the Asp(92)-->Glu mutant, D92N had very low enzyme activities with either Methyl Viologen or dithionite. Remarkably, when the physiological electron donor reduced azurin I was used, both mutant proteins exhibited restoration of enzyme activity. The degree of restoration differed for the two mutants, with the D92N derivative exhibiting approx. 60% of the activity seen for the wild-type NiR. These findings suggest that on formation of an electron transfer complex with azurin, a conformational change in NiR occurs that returns the catalytic Cu centre to a functionally active state capable of binding and reducing nitrite.
Collapse
Affiliation(s)
- M Prudêncio
- Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich NR4 7UH, U.K
| | | | | |
Collapse
|
47
|
Affiliation(s)
- Haoming Zhang
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin J. Boulanger
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - A. Grant Mauk
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michael E. P. Murphy
- Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
48
|
|
49
|
Strange RW, Murphy LM, Dodd FE, Abraham ZH, Eady RR, Smith BE, Hasnain SS. Structural and kinetic evidence for an ordered mechanism of copper nitrite reductase. J Mol Biol 1999; 287:1001-9. [PMID: 10222206 DOI: 10.1006/jmbi.1999.2648] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystallographic structures of several copper-containing nitrite reductases are now available. Despite this wealth of structural data, no definitive information is available as to whether the reaction proceeds by an ordered mechanism where nitrite binds to the oxidised type 2 site, followed by an internal electron transfer from the type 1 Cu, or whether binding occurs to the reduced type 2 Cu centre, or a random mechanism operates. We present here the first structural information on both types of Cu centres for the reduced form of NiR from Alcaligenes xylosoxidans (AxNiR) using X-ray absorption spectroscopy. The reduced type 2 Cu site EXAFS shows striking similarity to the EXAFS data for reduced bovine superoxide dismutase (Cu2Zn2 SOD), providing strong evidence for the loss of the water molecule from the catalytic Cu site in NiR on reduction resulting in a tri-coordinate Cu site similar to that in Cu2Zn2 SOD. The reduced type 2 Cu site of AxNiR is shown to be unable to bind inhibitory ligands such as azide, and to react very sluggishly with nitrite leading to only a slow re-oxidation of the the type 1 centre. These observations provide strong evidence that turnover of AxNiR proceeds by an ordered mechanism in which nitrite binds to the oxidised type 2 Cu centres before electron transfer from the reduced type 1 centre occurs. We propose that the two links between the Cu sites of AxNiR, namely His129-Cys130 and His89-Asp92-His94 are utilised for electron transfer and for communicating the status of the type 2 Cu site, respectively. Nitrite binding at type 2 Cu is sensed by the proton abstracting group Asp92 and the type 2 Cu ligand His94, and relayed to the type 1 Cu site via His89 thus triggering an internal electron transfer. The similarity of the type 2 Cu NiR catalytic site to the reduced Cu site of SOD is examined in some detail together with the biochemical evidence for the SOD activity of AxNiR.
Collapse
Affiliation(s)
- R W Strange
- CCLRC Daresbury Laboratory, Warrington, Cheshire, WA4 4AD, UK
| | | | | | | | | | | | | |
Collapse
|
50
|
Prudêncio M, Eady RR, Sawers G. The blue copper-containing nitrite reductase from Alcaligenes xylosoxidans: cloning of the nirA gene and characterization of the recombinant enzyme. J Bacteriol 1999; 181:2323-9. [PMID: 10197991 PMCID: PMC93653 DOI: 10.1128/jb.181.8.2323-2329.1999] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nirA gene encoding the blue dissimilatory nitrite reductase from Alcaligenes xylosoxidans has been cloned and sequenced. To our knowledge, this is the first report of the characterization of a gene encoding a blue copper-containing nitrite reductase. The deduced amino acid sequence exhibits a high degree of similarity to other copper-containing nitrite reductases from various bacterial sources. The full-length protein included a 24-amino-acid leader peptide. The nirA gene was overexpressed in Escherichia coli and was shown to be exported to the periplasm. Purification was achieved in a single step, and analysis of the recombinant Nir enzyme revealed that cleavage of the signal peptide occurred at a position identical to that for the native enzyme isolated from A. xylosoxidans. The recombinant Nir isolated directly was blue and trimeric and, on the basis of electron paramagnetic resonance spectroscopy and metal analysis, possessed only type 1 copper centers. This type 2-depleted enzyme preparation also had a low nitrite reductase enzyme activity. Incubation of the periplasmic fraction with copper sulfate prior to purification resulted in the isolation of an enzyme with a full complement of type 1 and type 2 copper centers and a high specific activity. The kinetic properties of the recombinant enzyme were indistinguishable from those of the native nitrite reductase isolated from A. xylosoxidans. This rapid isolation procedure will greatly facilitate genetic and biochemical characterization of both wild-type and mutant derivatives of this protein.
Collapse
Affiliation(s)
- M Prudêncio
- Nitrogen Fixation Laboratory, John Innes Centre, Norwich, United Kingdom
| | | | | |
Collapse
|