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Rose SL, Ferroni FM, Horrell S, Brondino CD, Eady RR, Jaho S, Hough MA, Owen RL, Antonyuk SV, Hasnain SS. Spectroscopically Validated pH-dependent MSOX Movies Provide Detailed Mechanism of Copper Nitrite Reductases. J Mol Biol 2024; 436:168706. [PMID: 39002715 DOI: 10.1016/j.jmb.2024.168706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Copper nitrite reductases (CuNiRs) exhibit a strong pH dependence of their catalytic activity. Structural movies can be obtained by serially recording multiple structures (frames) from the same spot of a crystal using the MSOX serial crystallography approach. This method has been combined with on-line single crystal optical spectroscopy to capture the pH-dependent structural changes that accompany during turnover of CuNiRs from two Rhizobia species. The structural movies, initiated by the redox activation of a type-1 copper site (T1Cu) via X-ray generated photoelectrons, have been obtained for the substrate-free and substrate-bound states at low (high enzymatic activity) and high (low enzymatic activity) pH. At low pH, formation of the product nitric oxide (NO) is complete at the catalytic type-2 copper site (T2Cu) after a dose of 3 MGy (frame 5) with full bleaching of the T1Cu ligand-to-metal charge transfer (LMCT) 455 nm band (S(σ)Cys → T1Cu2+) which in itself indicates the electronic route of proton-coupled electron transfer (PCET) from T1Cu to T2Cu. In contrast at high pH, the changes in optical spectra are relatively small and the formation of NO is only observed in later frames (frame 15 in Br2DNiR, 10 MGy), consistent with the loss of PCET required for catalysis. This is accompanied by decarboxylation of the catalytic AspCAT residue, with CO2 trapped in the catalytic pocket.
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Affiliation(s)
- Samuel L Rose
- Molecular Biophysics Group, Life Sciences Building, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Felix Martín Ferroni
- Molecular Biophysics Group, Life Sciences Building, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), CONICET, Ciudad Universitaria, Paraje El Pozo, Santa Fe, Argentina.
| | - Sam Horrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - 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, Argentina
| | - Robert R Eady
- Molecular Biophysics Group, Life Sciences Building, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Sofia Jaho
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Michael A Hough
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Life Sciences Building, 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, Life Sciences Building, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
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2
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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [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: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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3
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Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
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Ferreira MP, Castro CB, Honorato J, He S, Gonçalves Guimarães Júnior W, Esmieu C, Castellano EE, de Moura AF, Truzzi DR, Nascimento OR, Simonneau A, Marques Netto CGC. Biomimetic catalysis of nitrite reductase enzyme using copper complexes in chemical and electrochemical reduction of nitrite. Dalton Trans 2023; 52:11254-11264. [PMID: 37526523 DOI: 10.1039/d3dt01091k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Copper nitrite reductase mimetics were synthesized using three new tridentate ligands sharing the same N,N,N motif of coordination. The ligands were based on L-proline modifications, attaching a pyridine and a triazole to the pyrrolidine ring, and differ by a pendant group (R = phenyl, n-butyl and n-propan-1-ol). All complexes coordinate nitrite, as evidenced by cyclic voltammetry, UV-Vis, FTIR and electron paramagnetic resonance (EPR) spectroscopies. The coordination mode of nitrite was assigned by FTIR and EPR as κ2O chelate mode. Upon acidification, EPR experiments indicated a shift from chelate to monodentate κO mode, and 15N NMR experiments of a Zn2+ analogue, suggested that the related Cu(II) nitrous acid complex may be reasonably stable in solution, but in equilibrium with free HONO under non catalytic conditions. Reduction of nitrite to NO was performed both chemically and electrocatalytically, observing the highest catalytic activities for the complex with n-propan-1-ol as pendant group. These results support the hypothesis that a hydrogen bond moiety in the secondary coordination sphere may aid the protonation step.
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Affiliation(s)
- Millena P Ferreira
- Department of Chemistry, Universidade Federal de São Carlos (UFSCar), Rod. Washington Luiz, km 235 s/n, CEP 13565905 São Carlos, SP, Brazil.
| | - Caio B Castro
- Department of Chemistry, Universidade Federal de São Carlos (UFSCar), Rod. Washington Luiz, km 235 s/n, CEP 13565905 São Carlos, SP, Brazil.
| | - João Honorato
- Insitututo de Química, Departamento de Bioquímica, Universidade de São Paulo (USP), Av. Prof. Dr. Lineu Prestes, 748, CEP 05513-970 São Paulo, SP, Brazil
- Instituto de Física, Universidade de São Paulo (USP), Av.João Dagnone, 1100, CEP 13563-120, São Carlos, SP, Brazil
| | - Sheng He
- Department of Chemistry, Emory University, 1515 Dickey Drive, 30322 Atlanta, GA, USA
| | - Walber Gonçalves Guimarães Júnior
- Department of Chemistry, Universidade Federal de São Carlos (UFSCar), Rod. Washington Luiz, km 235 s/n, CEP 13565905 São Carlos, SP, Brazil.
| | - Charlene Esmieu
- LCC-CNRS, Universite de Toulouse, CNRS, UPS, 205 route de Narbonne, F31077 Toulouse cedex 4, France
| | - Eduardo E Castellano
- Instituto de Física, Universidade de São Paulo (USP), Av.João Dagnone, 1100, CEP 13563-120, São Carlos, SP, Brazil
| | - André F de Moura
- Department of Chemistry, Universidade Federal de São Carlos (UFSCar), Rod. Washington Luiz, km 235 s/n, CEP 13565905 São Carlos, SP, Brazil.
| | - Daniela R Truzzi
- Insitututo de Química, Departamento de Bioquímica, Universidade de São Paulo (USP), Av. Prof. Dr. Lineu Prestes, 748, CEP 05513-970 São Paulo, SP, Brazil
| | - Otaciro R Nascimento
- Instituto de Física, Universidade de São Paulo (USP), Av.João Dagnone, 1100, CEP 13563-120, São Carlos, SP, Brazil
| | - Antoine Simonneau
- LCC-CNRS, Universite de Toulouse, CNRS, UPS, 205 route de Narbonne, F31077 Toulouse cedex 4, France
| | - Caterina G C Marques Netto
- Department of Chemistry, Universidade Federal de São Carlos (UFSCar), Rod. Washington Luiz, km 235 s/n, CEP 13565905 São Carlos, SP, Brazil.
- Department of Chemistry, Emory University, 1515 Dickey Drive, 30322 Atlanta, GA, USA
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5
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Barreiro DS, Oliveira RNS, Pauleta SR. Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae. Biomolecules 2023; 13:1215. [PMID: 37627281 PMCID: PMC10452240 DOI: 10.3390/biom13081215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/16/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5-6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.
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Affiliation(s)
- Daniela S. Barreiro
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ricardo N. S. Oliveira
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sofia R. Pauleta
- Microbial Stress Lab, UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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6
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Satvati S, Ghasemi Y, Najafipour S, Eskandari S, Mahmoodi S, Nezafat N, Hashemzaei M. Finding and engineering the newly found bacterial superoxide dismutase enzyme to increase its thermostability and decrease the immunogenicity: a computational and experimental research. Arch Microbiol 2023; 205:260. [PMID: 37291420 DOI: 10.1007/s00203-023-03601-0] [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: 04/03/2023] [Revised: 05/23/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023]
Abstract
Superoxide dismutase (SOD) is one of the most important antioxidant enzymes that can reduce oxidative stress in the cell environment. Nowadays, bacterial sources of enzyme are commercially applicable in the cosmetics and pharmaceutical industries, but the allergenic effect of proteins from non-human sources has been mentioned as disadvantage of these kinds of enzymes. In this study, to find the suitable bacterial SOD candidate for decreasing immunogenicity, the sequences of five thermophilic bacteria were selected as reference species. Then, linear and conformational B-cell epitopes of the SOD were analyzed by different servers. The stability and immunogenicity of mutant positions were also evaluated. The mutant gene was inserted into the pET-23a expression vector and transformed into E. Coli BL21 (DE3) for expression of the recombinant enzyme. Afterward, the expression of the mutant enzyme was evaluated by SDS-PAGE analysis and the recombinant enzyme activity was assessed. Anoxybacillus gonensis was selected as a reasonable SOD source according to BLAST search, physicochemical properties analysis, and prediction of allergenic features. Regarding our results, five residues including E84, E142, K144, G147, and M148 were predicted as candidates for mutagenesis. Finally, the K144A was chosen as the final modification due to the increase in the stability of the enzyme and decreased immunogenicity of the enzyme as well. The enzyme activity was 240 U/ml at room temperature. Alternation in K144 to alanine caused increased stability of the enzyme. In silico studies confirmed non-antigenic protein after mutation.
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Affiliation(s)
- Saha Satvati
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sohrab Najafipour
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Sedigheh Eskandari
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shirin Mahmoodi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Science Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Masoud Hashemzaei
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Computational vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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7
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Duré AB, Cristaldi JC, Guevara Cuasapud LA, Dalosto SD, Rivas MG, Ferroni FM, González PJ, Montich GG, Brondino CD. Molecular and kinetic properties of copper nitrite reductase from Sinorhizobium meliloti 2011 upon substituting the interfacial histidine ligand coordinated to the type 2 copper active site for glycine. J Inorg Biochem 2023; 241:112155. [PMID: 36739731 DOI: 10.1016/j.jinorgbio.2023.112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
A copper-containing nitrite reductase catalyzes the reduction of nitrite to nitric oxide in the denitrifier Sinorhizobium meliloti 2011 (SmNirK), a microorganism used as bioinoculant in alfalfa seeds. Wild type SmNirK is a homotrimer that contains two copper centers per monomer, one of type 1 (T1) and other of type 2 (T2). T2 is at the interface of two monomers in a distorted square pyramidal coordination bonded to a water molecule and three histidine side chains, H171 and H136 from one monomer and H342 from the other. We report the molecular, catalytic, and spectroscopic properties of the SmNirK variant H342G, in which the interfacial H342 T2 ligand is substituted for glycine. The molecular properties of H342G are similar to those of wild type SmNirK. Fluorescence-based thermal shift assays and FTIR studies showed that the structural effect of the mutation is only marginal. However, the kinetic reaction with the physiological electron donor was significantly affected, which showed a ∼ 100-fold lower turnover number compared to the wild type enzyme. UV-Vis, EPR and FTIR studies complemented with computational calculations indicated that the drop in enzyme activity are mainly due to the void generated in the protein substrate channel by the point mutation. The main structural changes involve the filling of the void with water molecules, the direct coordination to T2 copper ion of the second sphere aspartic acid ligand, a key residue in catalysis and nitrite sensing in NirK, and to the loss of the 3 N-O coordination of T2.
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Affiliation(s)
- Andrea B Duré
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Julio C Cristaldi
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina; Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende 5000, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Lorieth A Guevara Cuasapud
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Sergio D Dalosto
- Instituto de Física del Litoral, CONICET-UNL, Güemes 3450, S3000GLN, Santa Fe, Argentina
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Felix M Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Pablo J González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina
| | - Guillermo G Montich
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de la Torre y Medina Allende 5000, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina.
| | - Carlos D Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral and CONICET, S3000ZAA, Santa Fe, Argentina.
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8
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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] [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.
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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
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9
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Sun P, Chen Y, Liu J, Xu Y, Zhou L, Wu Y. Periphytic biofilms function as a double-edged sword influencing nitrogen cycling in paddy fields. Environ Microbiol 2022; 24:6279-6289. [PMID: 36335557 DOI: 10.1111/1462-2920.16277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/01/2022] [Indexed: 11/07/2022]
Abstract
It remains unclear whether periphytic biofilms are beneficial to N cycling in paddy fields. Here, based on a national-scale field investigation covering 220 rice fields in China, the N accumulation potential of periphytic biofilms was found to decrease from 8.8 ± 2.4 to 4.5 ± 0.7 g/kg and 3.1 ± 0.6 g/kg with increasing habitat latitude and longitude, respectively. The difference in abundant and rare subcommunities likely accounts for their geo-difference in N accumulation potential. The N cycling pathways involved in periphytic biofilms inferred that soil N and N2 were two potential sources for N accumulation in periphytic biofilms. Meanwhile, some of the accumulated N may be lost via N2 , N2 O, NO, or NH3 outputs. Superficially, periphytic biofilms are double-edged swords to N cycling by increasing soil N through biological N fixation but accelerating greenhouse gas emissions. Essentially, augmented periphytic biofilms increased change of TN (ΔTN) content in paddy soil from -231.9 to 31.9 mg/kg, indicating that periphytic biofilms overall benefit N content enhancement in paddy fields. This study highlights the contribution of periphytic biofilms to N cycling in rice fields, thus, drawing attention to their effect on rice production and environmental security.
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Affiliation(s)
- Pengfei Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Junzhuo Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Ying Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Lei Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China.,Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resource of the Peoples' Republic of China, Shuitianba, Zigui, Yichang, China
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10
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Sanz‐Martínez I, García‐García A, Tejero T, Hurtado‐Guerrero R, Merino P. The Essential Role of Water Molecules in the Reaction Mechanism of Protein O-Fucosyltransferase 2. Angew Chem Int Ed Engl 2022; 61:e202213610. [PMID: 36260536 PMCID: PMC9828666 DOI: 10.1002/anie.202213610] [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: 09/15/2022] [Indexed: 11/11/2022]
Abstract
Protein O-fucosyltransferase 2 (PoFUT2) is an inverting glycosyltransferase (GT) that fucosylates thrombospondin repeats (TSRs) from group 1 and 2. PoFUT2 recognizes a large and diverse number of TSRs through a dynamic network of water-mediated interactions. By X-ray structural studies of C. elegans PoFUT2 complexed to a TSR of group 2, we demonstrate that this GT recognizes similarly the 3D structure of TSRs from both groups 1 and 2. Its active site is highly exposed to the solvent, suggesting that water molecules might also play an essential role in the fucosylation mechanism. We applied QM/MM methods using human PoFUT2 as a model, and found that HsPoFUT2 follows a classical SN 2 reaction mechanism in which water molecules contribute to a great extent in facilitating the release of the leaving pyrophosphate unit, causing the H transfer from the acceptor nucleophile (Thr/Ser) to the catalytic base, which is the last event in the reaction. This demonstrates the importance of water molecules not only in recognition of the ligands but also in catalysis.
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Affiliation(s)
- Ignacio Sanz‐Martínez
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI).Universidad de Zaragoza50018ZaragozaSpain
| | - Ana García‐García
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI).Universidad de Zaragoza50018ZaragozaSpain
| | - Tomás Tejero
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH).Universidad de Zaragoza-CSIC50009ZaragozaSpain
| | - Ramón Hurtado‐Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI).Universidad de Zaragoza50018ZaragozaSpain,Copenhagen Center for GlycomicsDepartment of Cellular and Molecular MedicineUniversity of CopenhagenCopenhagenDK-2200Denmark,Fundación ARAIDZaragoza50018Spain
| | - Pedro Merino
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI).Universidad de Zaragoza50018ZaragozaSpain
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11
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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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12
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Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases. Proc Natl Acad Sci U S A 2022; 119:e2205664119. [PMID: 35862453 PMCID: PMC9335323 DOI: 10.1073/pnas.2205664119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
X-rays used to collect crystallographic data can change the redox states of transition metals utilized by many biological systems including metalloproteins. This disadvantage has been harnessed to drive a complex chemical reaction requiring the delivery of an electron to the active site and recording the structural changes accompanying catalysis, providing a real-time structural movie of an enzymatic reaction, which has been a dream of enzymologists for decades. By coupling the multiple-structures from one crystal technique with single-crystal and solution optical spectroscopy, we show that the electron transfer between the electron accepting type-1 Cu and catalytic type-2 Cu redox centers is gated in a recently characterized copper nitrite reductase. This combined structural/spectroscopic approach is applicable to many complex redox biological systems. Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.
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13
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Gopalasingam CC, Hasnain SS. Frontiers in metalloprotein crystallography and cryogenic electron microscopy. Curr Opin Struct Biol 2022; 75:102420. [PMID: 35841747 DOI: 10.1016/j.sbi.2022.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/03/2022]
Abstract
Metalloproteins comprise at least a third of all proteins that utilize redox properties of transition metals on their own or as parts of cofactors. The development of third generation storage ring sources and X-ray free-electron lasers with femtosecond pulses in the first decade of the 21st century has transformed metalloprotein crystallography. In the past decade, cryogenic-electron microscopy single-particle analysis, which does not require crystallization of biological samples has been extensively utilized, particularly for membrane-bound metalloprotein systems. Here, we explore recent frontiers in metalloprotein crystallography and cryogenic electron microscopy, organized for convenience under three metalloprotein-centered biological cycles, focusing on contributions from each technique, their synergy and the ability to preserve metals' redox states when subjected to a particular probe.
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Affiliation(s)
- Chai C Gopalasingam
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK; Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan. https://twitter.com/@Chai_Gopal
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, UK.
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14
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Eady RR, Samar Hasnain S. New horizons in structure-function studies of copper nitrite reductase. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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15
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Chang YL, Chen HY, Chen SH, Kao CL, Chiang MY, Hsu SCN. An investigation on catalytic nitrite reduction reaction by bioinspired Cu II complexes. Dalton Trans 2022; 51:7715-7722. [PMID: 35522169 DOI: 10.1039/d1dt04102a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic nitrite reductions by CuII complexes containing anionic Me2Tp, neutral Me2Tpm, or neutral iPrTIC ligands in the presence of L-ascorbic acid, which served as an electron donor and proton source, were investigated. The results showed that auxiliary ligands are important for copper-mediated catalytic nitrite reduction. Furthermore, the electronic effects of the ligand govern the nitrite reduction efficiency, which should be considered at two control points: one is the susceptibility of the LCuI-nitrite species to protonation and the other is the susceptibility of LCuII to reduction giving LCuI. In addition, an external strong acid leads to the production of nitrous acid, which may suggest that the reactivity of nitrous acid toward the LCuI species is a third control point.
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Affiliation(s)
- Yu-Lun Chang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Si-Hong Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan.
| | - Michael Y Chiang
- Department of Chemistry, National Sun Yat-Sen University No. 70, Lienhai Rd., Kaohsiung 804, Taiwan
| | - Sodio C N Hsu
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, 100 Shi-Chuan 1st Rd., San-Ming District, Kaohsiung 807, Taiwan. .,Department of Chemistry, National Sun Yat-Sen University No. 70, Lienhai Rd., Kaohsiung 804, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
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16
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Wilson MA. Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light. Annu Rev Biophys 2021; 51:79-98. [PMID: 34932909 PMCID: PMC9132212 DOI: 10.1146/annurev-biophys-100421-110959] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska, USA;
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17
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Nass K, Bacellar C, Cirelli C, Dworkowski F, Gevorkov Y, James D, Johnson PJM, Kekilli D, Knopp G, Martiel I, Ozerov D, Tolstikova A, Vera L, Weinert T, Yefanov O, Standfuss J, Reiche S, Milne CJ. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser. IUCRJ 2021; 8:905-920. [PMID: 34804544 PMCID: PMC8562661 DOI: 10.1107/s2052252521008046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 05/25/2023]
Abstract
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.
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Affiliation(s)
- Karol Nass
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Florian Dworkowski
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Daniel James
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | | | - Demet Kekilli
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Isabelle Martiel
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Laura Vera
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Tobias Weinert
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, Germany
| | - Jörg Standfuss
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
| | - Sven Reiche
- Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, Switzerland
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18
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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19
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Ramírez CS, Tolmie C, Opperman DJ, González PJ, Rivas MG, Brondino CD, Ferroni FM. Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator. Protein Sci 2021; 30:2310-2323. [PMID: 34562300 DOI: 10.1002/pro.4195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 11/08/2022]
Abstract
We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.
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Affiliation(s)
- Cintia Soledad Ramírez
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Carmien Tolmie
- Department of Microbiology and Biochemistry, University of the Free State (UFS), Bloemfontein, South Africa
| | - Diederik Johannes Opperman
- Department of Microbiology and Biochemistry, University of the Free State (UFS), Bloemfontein, South Africa
| | - Pablo Javier González
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - María Gabriela Rivas
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Carlos Dante Brondino
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
| | - Felix Martín Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL). CONICET, Ciudad Universitaria, Santa Fe, Argentina
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20
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Hough MA, Owen RL. Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis. Curr Opin Struct Biol 2021; 71:232-238. [PMID: 34455163 PMCID: PMC8667872 DOI: 10.1016/j.sbi.2021.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 11/24/2022]
Abstract
An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.
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Affiliation(s)
- Michael A Hough
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Robin L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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21
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2.85 and 2.99 Å resolution structures of 110 kDa nitrite reductase determined by 200 kV cryogenic electron microscopy. J Struct Biol 2021; 213:107768. [PMID: 34217801 DOI: 10.1016/j.jsb.2021.107768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/22/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022]
Abstract
Cu-containing nitrite reductases (NiRs) are 110 kDa enzymes that play central roles in denitrification. Although the NiRs have been well studied, with over 100 Protein Data Bank entries, such issues as crystal packing, photoreduction, and lack of high pH cases have impeded structural analysis of their catalytic mechanisms. Here we show the cryogenic electron microscopy (cryo-EM) structures of Achromobacter cycloclastes NiR (AcNiR) at pH 6.2 and 8.1. The optimization of 3D-reconstruction parameters achieved 2.99 and 2.85 Å resolution. Comprehensive comparisons with cryo-EM and 56 AcNiR crystal structures suggested crystallographic artifacts in residues 185-215 and His255' due to packing and photoreduction, respectively. We used a newly developed map comparison method to detect structural change around the type 2 Cu site. While the theoretical estimation of coordinate errors of cryo-EM structures remains difficult, combined analysis using X-ray and cryo-EM structures will allow deeper insight into the local structural changes of proteins.
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22
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Stauffer M, Sakhaei Z, Greene C, Ghosh P, Bertke JA, Warren TH. Mechanism of O-Atom Transfer from Nitrite: Nitric Oxide Release at Copper(II). Inorg Chem 2021; 60:15968-15974. [PMID: 34184870 DOI: 10.1021/acs.inorgchem.1c00625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nitric oxide (NO) is a key signaling molecule in health and disease. While nitrite acts as a reservoir of NO activity, mechanisms for NO release require further understanding. A series of electronically varied β-diketiminatocopper(II) nitrite complexes [CuII](κ2-O2N) react with a range of electronically tuned triarylphosphines PArZ3 that release NO with the formation of O═PArZ3. Second-order rate constants are largest for electron-poor copper(II) nitrite and electron-rich phosphine pairs. Computational analysis reveals a transition-state structure energetically matched with experimentally determined activation barriers. The production of NO follows a pathway that involves nitrite isomerization at CuII from κ2-O2N to κ1-NO2 followed by O-atom transfer (OAT) to form O═PArZ3 and [CuI]-NO that releases NO upon PArZ3 binding at CuI to form [CuI]-PArZ3. These findings illustrate important mechanistic considerations involved in NO formation from nitrite via OAT.
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Affiliation(s)
- Molly Stauffer
- Department of Chemistry, Georgetown University, Box 571227-1227, Washington, D.C. 20057, United States
| | - Zeinab Sakhaei
- Department of Chemistry, Georgetown University, Box 571227-1227, Washington, D.C. 20057, United States
| | - Christine Greene
- Department of Chemistry, Georgetown University, Box 571227-1227, Washington, D.C. 20057, United States
| | - Pokhraj Ghosh
- Department of Chemistry, Georgetown University, Box 571227-1227, Washington, D.C. 20057, United States
| | - Jeffery A Bertke
- Department of Chemistry, Georgetown University, Box 571227-1227, Washington, D.C. 20057, United States
| | - Timothy H Warren
- Department of Chemistry, Georgetown University, Box 571227-1227, Washington, D.C. 20057, United States
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