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Giri NC, Mintmier B, Radhakrishnan M, Mielke JW, Wilcoxen J, Basu P. The critical role of a conserved lysine residue in periplasmic nitrate reductase catalyzed reactions. J Biol Inorg Chem 2024; 29:395-405. [PMID: 38782786 DOI: 10.1007/s00775-024-02057-x] [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: 11/06/2023] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Periplasmic nitrate reductase NapA from Campylobacter jejuni (C. jejuni) contains a molybdenum cofactor (Moco) and a 4Fe-4S cluster and catalyzes the reduction of nitrate to nitrite. The reducing equivalent required for the catalysis is transferred from NapC → NapB → NapA. The electron transfer from NapB to NapA occurs through the 4Fe-4S cluster in NapA. C. jejuni NapA has a conserved lysine (K79) between the Mo-cofactor and the 4Fe-4S cluster. K79 forms H-bonding interactions with the 4Fe-4S cluster and connects the latter with the Moco via an H-bonding network. Thus, it is conceivable that K79 could play an important role in the intramolecular electron transfer and the catalytic activity of NapA. In the present study, we show that the mutation of K79 to Ala leads to an almost complete loss of activity, suggesting its role in catalytic activity. The inhibition of C. jejuni NapA by cyanide, thiocyanate, and azide has also been investigated. The inhibition studies indicate that cyanide inhibits NapA in a non-competitive manner, while thiocyanate and azide inhibit NapA in an uncompetitive manner. Neither inhibition mechanism involves direct binding of the inhibitor to the Mo-center. These results have been discussed in the context of the loss of catalytic activity of NapA K79A variant and a possible anion binding site in NapA has been proposed.
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Affiliation(s)
- Nitai C Giri
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Breeanna Mintmier
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Manohar Radhakrishnan
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA
| | - Jonathan W Mielke
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, IN, USA.
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2
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Wu Q, Zhang J, Pan X, Huang Z, Zhang H, Guo J, Xue Y, Shi R, Liu H. Vacancy Augmented Piezo-Sonosensitizer for Cancer Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301152. [PMID: 37395638 PMCID: PMC10502820 DOI: 10.1002/advs.202301152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Indexed: 07/04/2023]
Abstract
Sonodynamic therapy (SDT) has been widely reported as a noninvasive and high-penetration therapy for cancer; however, the design of an efficient sonosensitizer remains an urgent need. To address this issue, molybdenum disulfide nanoflowers (MoS2 NF) as piezo-sonosensitizers and introduced sulfur vacancies on the MoS2 NF (Sv-MoS2 NF) to improve their piezoelectric property for cancer therapy are designed. Under ultrasonic mechanical stress, the Sv-MoS2 NF resulted in piezoelectric polarization and band tilting, which enhanced the charge carrier separation and migration. This resulted in an improved catalytic reaction for reactive oxygen species (ROS) production, ultimately enhancing the SDT performance. Thanks to the high efficiency of ROS generation, the Sv-MoS2 NF have demonstrated a good anticancer effect in vitro and in vivo. Following a systematic evaluation, Sv-MoS2 NF also demonstrated good biocompatibility. This novel piezo-sonosensitizer and vacancy engineering strategy provides a promising new approach for achieving efficient SDT.
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Affiliation(s)
- Qingyuan Wu
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringState Key Laboratory of Organic‐Inorganic CompositesBeijing Laboratory of Biomedical MaterialsBionanomaterials & Translational Engineering LaboratoryBeijing Key Laboratory of BioprocessBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringState Key Laboratory of Organic‐Inorganic CompositesBeijing Laboratory of Biomedical MaterialsBionanomaterials & Translational Engineering LaboratoryBeijing Key Laboratory of BioprocessBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Xueting Pan
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringState Key Laboratory of Organic‐Inorganic CompositesBeijing Laboratory of Biomedical MaterialsBionanomaterials & Translational Engineering LaboratoryBeijing Key Laboratory of BioprocessBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Zhijun Huang
- Beijing National Laboratory of Molecular Sciences, Beijing National Laboratory of Molecular SciencesInstitute of Chemistry, Chinese Academy of SciencesBeijing100190P. R. China
| | - Haoyuan Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringState Key Laboratory of Organic‐Inorganic CompositesBeijing Laboratory of Biomedical MaterialsBionanomaterials & Translational Engineering LaboratoryBeijing Key Laboratory of BioprocessBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Juan Guo
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringState Key Laboratory of Organic‐Inorganic CompositesBeijing Laboratory of Biomedical MaterialsBionanomaterials & Translational Engineering LaboratoryBeijing Key Laboratory of BioprocessBeijing University of Chemical TechnologyBeijing100029P. R. China
| | - Yun Xue
- National Center for OrthopaedicsBeijing Research Institute of Traumatology and OrthopaedicsBeijing Jishuitan HospitalBeijing100035P. R. China
| | - Rui Shi
- National Center for OrthopaedicsBeijing Research Institute of Traumatology and OrthopaedicsBeijing Jishuitan HospitalBeijing100035P. R. China
| | - Huiyu Liu
- Beijing Advanced Innovation Center for Soft Matter Science and EngineeringState Key Laboratory of Organic‐Inorganic CompositesBeijing Laboratory of Biomedical MaterialsBionanomaterials & Translational Engineering LaboratoryBeijing Key Laboratory of BioprocessBeijing University of Chemical TechnologyBeijing100029P. R. China
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3
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González PJ, Rivas MG, Ferroni FM, Rizzi AC, Brondino CD. Electron transfer pathways and spin–spin interactions in Mo- and Cu-containing oxidoreductases. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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The Effect of Gamma Irradiation on the Physiochemical Properties of Caesium-Selective Ammonium Phosphomolybdate–Polyacrylonitrile (AMP–PAN) Composites. CLEAN TECHNOLOGIES 2019. [DOI: 10.3390/cleantechnol1010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Managing certain by-products of the nuclear fuel cycle, such as the radioactive isotopes of caesium: 134Cs, 135Cs and 137Cs is challenging due to their environmental mobility and radioactivity. While a great many materials can isolate Cs+ ions from neutral or basic aqueous solutions via ion exchange, few of these, with the exception of ammonium phosphomolybdate (AMP), function effectively in acidic media. The use of AMP, and its porous composite in polyacrylonitrile (PAN) for management of Cs radioisotopes in various nuclear wastes have been known for decades and are well studied, yet the effects of radiation on the physiochemical properties of such composites have only received limited attention to date. In a previous publication, we demonstrated that a 100 kGy gamma irradiation dose has negligible effect on the ion exchange performance of AMP and AMP–PAN with respect to capacity or kinetics under the Cs+ concentrations and acidity found in spent nuclear fuel (SNF) recycling. As a continuation of this prior study, in this publication we explore the effects of gamma irradiation on the physiochemical properties of AMP and AMP–PAN using a range of characterisation methods. The effects of the same gamma dose on the oxidation state of Mo in AMP and AMP–PAN, the thermal degradation of both AMP and AMP–PAN, combined with a first study into the high-temperature degradation AMP, are reported. The implications of irradiation, its possible mechanism, the conditions present in SNF recycling, and for the end-of-life disposal or recycling of these materials are also discussed.
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6
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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7
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Maia LB, Moura I, Moura JJ. EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Cerqueira NMFSA, Gonzalez PJ, Fernandes PA, Moura JJG, Ramos MJ. Periplasmic nitrate reductase and formate dehydrogenase: similar molecular architectures with very different enzymatic activities. Acc Chem Res 2015; 48:2875-84. [PMID: 26509703 DOI: 10.1021/acs.accounts.5b00333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It is remarkable how nature has been able to construct enzymes that, despite sharing many similarities, have simple but key differences that tune them for completely different functions in living cells. Periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh) from the DMSOr family are representative examples of this. Both enzymes share almost identical three-dimensional protein foldings and active sites, in terms of coordination number, geometry and nature of the ligands. The substrates of both enzymes (nitrate and formate) are polyatomic anions that also share similar charge and stereochemistry. In terms of the catalytic mechanism, both enzymes have a common activation mechanism (the sulfur-shift mechanism) that ensures a constant coordination number around the metal ion during the catalytic cycle. In spite of these similarities, they catalyze very different reactions: Nap abstracts an oxygen atom from nitrate releasing nitrite, whereas FdH catalyzes a hydrogen atom transfer from formate and releases carbon dioxide. In this Account, a critical analysis of structure, function, and catalytic mechanism of the molybdenum enzymes periplasmic nitrate reductase (Nap) and formate dehydrogenase (Fdh) is presented. We conclude that the main structural driving force that dictates the type of reaction, catalyzed by each enzyme, is a key difference on one active site residue that is located in the top region of the active sites of both enzymes. In both enzymes, the active site is centered on the metal ion of the cofactor (Mo in Nap and Mo or W in Fdh) that is coordinated by four sulfur atoms from two pyranopterin guanosine dinucleotide (PGD) molecules and by a sulfido. However, while in Nap there is a Cys directly coordinated to the Mo ion, in FdH there is a SeCys instead. In Fdh there is also an important His that interacts very closely with the SeCys, whereas in Nap the same position is occupied by a Met. The role of Cys in Nap and SeCys in FdH is similar in both enzymes; however, Met and His have different roles. His participates directly on catalysis, and it is therefore detrimental for the catalytic cycle of FdH. Met only participates in substrate binding. We concluded that this small but key difference dictates the type of reaction that is catalyzed by each enzyme. In addition, it allows explaining why formate can bind in the Nap active site in the same way as the natural substrate (nitrate), but the reaction becomes stalled afterward.
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Affiliation(s)
- Nuno M. F. S. A. Cerqueira
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pablo J. Gonzalez
- REQUIMTE/UCIBIO,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Pedro A. Fernandes
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - José J. G. Moura
- REQUIMTE/UCIBIO,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| | - Maria João Ramos
- REQUIMTE/UCIBIO,
Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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9
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Srivastava AP, Allen JP, Vaccaro BJ, Hirasawa M, Alkul S, Johnson MK, Knaff DB. Identification of Amino Acids at the Catalytic Site of a Ferredoxin-Dependent Cyanobacterial Nitrate Reductase. Biochemistry 2015; 54:5557-68. [PMID: 26305228 DOI: 10.1021/acs.biochem.5b00511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An in silico model of the ferredoxin-dependent nitrate reductase from the cyanobacterium Synechococcus sp. PCC 7942, and information about active sites in related enzymes, had identified Cys148, Met149, Met306, Asp163, and Arg351 as amino acids likely to be involved in either nitrate binding, prosthetic group binding, or catalysis. Site-directed mutagenesis was used to alter each of these residues, and differences in enzyme activity and substrate binding of the purified variants were analyzed. In addition, the effects of these replacements on the assembly and properties of the Mo cofactor and [4Fe-4S] centers were investigated using Mo and Fe determinations, coupled with electron paramagnetic resonance spectroscopy. The C148A, M149A, M306A, D163N, and R351Q variants were all inactive with either the physiological electron donor, reduced ferredoxin, or the nonphysiological electron donor, reduced methyl viologen, as the source of electrons, and all exhibited changes in the properties of the Mo cofactor. Charge-conserving D163E and R351K variants were also inactive, suggesting that specific amino acids are required at these two positions. The implications for the role of these five conserved active-site residues in light of these new results and previous structural, spectroscopic, and mutagenesis studies for related periplasmic nitrate reductases are discussed.
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Affiliation(s)
- Anurag P Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
| | - James P Allen
- Department of Chemistry and Biochemistry, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Brian J Vaccaro
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602-2556, United States
| | - Masakazu Hirasawa
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
| | - Suzanne Alkul
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States
| | - Michael K Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia , Athens, Georgia 30602-2556, United States
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409-1061, United States.,Center for Biotechnology and Genomics, Texas Tech University , Lubbock, Texas 79409-3132, United States
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10
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Cerqueira NMFSA, Pakhira B, Sarkar S. Theoretical studies on mechanisms of some Mo enzymes. J Biol Inorg Chem 2015; 20:323-35. [DOI: 10.1007/s00775-015-1237-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 01/05/2015] [Indexed: 11/30/2022]
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11
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Changes in metabolic pathways of Desulfovibrio alaskensis G20 cells induced by molybdate excess. J Biol Inorg Chem 2014; 20:311-22. [PMID: 25488518 DOI: 10.1007/s00775-014-1224-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/25/2014] [Indexed: 01/06/2023]
Abstract
The activity of sulfate-reducing bacteria (SRB) intensifies the problems associated to corrosion of metals and the solution entails significant economic costs. Although molybdate can be used to control the negative effects of these organisms, the mechanisms triggered in the cells exposed to Mo-excess are poorly understood. In this work, the effects of molybdate ions on the growth and morphology of the SRB Desulfovibrio alaskensis G20 (DaG20) were investigated. In addition, the cellular localization, ion uptake and regulation of protein expression were studied. We found that molybdate concentrations ranging between 50 and 150 µM produce a twofold increase in the doubling time with this effect being more significant at 200 µM molybdate (five times increase in the doubling time). It was also observed that 500 µM molybdate completely inhibits the cellular growth. On the context of protein regulation, we found that several enzymes involved in energy metabolism, cellular division and metal uptake processes were particularly influenced under the conditions tested. An overall description of some of the mechanisms involved in the DaG20 adaptation to molybdate-stress conditions is discussed.
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12
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Jacques JG, Burlat B, Arnoux P, Sabaty M, Guigliarelli B, Léger C, Pignol D, Fourmond V. Kinetics of substrate inhibition of periplasmic nitrate reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1801-9. [DOI: 10.1016/j.bbabio.2014.05.357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/14/2014] [Accepted: 05/22/2014] [Indexed: 11/26/2022]
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13
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Sparacino-Watkins C, Stolz JF, Basu P. Nitrate and periplasmic nitrate reductases. Chem Soc Rev 2014; 43:676-706. [PMID: 24141308 DOI: 10.1039/c3cs60249d] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. Although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. In this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. Many bacteria readily reduce nitrate to nitrite via nitrate reductases. Classified into three distinct types--periplasmic nitrate reductase (Nap), respiratory nitrate reductase (Nar) and assimilatory nitrate reductase (Nas), they are defined by their cellular location, operon organization and active site structure. Of these, Nap proteins are the focus of this review. Despite similarities in the catalytic and spectroscopic properties Nap from different Proteobacteria are phylogenetically distinct. This review has two major sections: in the first section, nitrate in the nitrogen cycle and human health, taxonomy of nitrate reductases, assimilatory and dissimilatory nitrate reduction, cellular locations of nitrate reductases, structural and redox chemistry are discussed. The second section focuses on the features of periplasmic nitrate reductase where the catalytic subunit of the Nap and its kinetic properties, auxiliary Nap proteins, operon structure and phylogenetic relationships are discussed.
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14
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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15
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Ferroni FM, Marangon J, Neuman NI, Cristaldi JC, Brambilla SM, Guerrero SA, Rivas MG, Rizzi AC, Brondino CD. Pseudoazurin from Sinorhizobium meliloti as an electron donor to copper-containing nitrite reductase: influence of the redox partner on the reduction potentials of the enzyme copper centers. J Biol Inorg Chem 2014; 19:913-21. [DOI: 10.1007/s00775-014-1124-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
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16
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Reductive activation in periplasmic nitrate reductase involves chemical modifications of the Mo-cofactor beyond the first coordination sphere of the metal ion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:277-86. [PMID: 24212053 DOI: 10.1016/j.bbabio.2013.10.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 11/24/2022]
Abstract
In Rhodobacter sphaeroides periplasmic nitrate reductase NapAB, the major Mo(V) form (the "high g" species) in air-purified samples is inactive and requires reduction to irreversibly convert into a catalytically competent form (Fourmond et al., J. Phys. Chem., 2008). In the present work, we study the kinetics of the activation process by combining EPR spectroscopy and direct electrochemistry. Upon reduction, the Mo (V) "high g" resting EPR signal slowly decays while the other redox centers of the protein are rapidly reduced, which we interpret as a slow and gated (or coupled) intramolecular electron transfer between the [4Fe-4S] center and the Mo cofactor in the inactive enzyme. Besides, we detect spin-spin interactions between the Mo(V) ion and the [4Fe-4S](1+) cluster which are modified upon activation of the enzyme, while the EPR signatures associated to the Mo cofactor remain almost unchanged. This shows that the activation process, which modifies the exchange coupling pathway between the Mo and the [4Fe-4S](1+) centers, occurs further away than in the first coordination sphere of the Mo ion. Relying on structural data and studies on Mo-pyranopterin and models, we propose a molecular mechanism of activation which involves the pyranopterin moiety of the molybdenum cofactor that is proximal to the [4Fe-4S] cluster. The mechanism implies both the cyclization of the pyran ring and the reduction of the oxidized pterin to give the competent tricyclic tetrahydropyranopterin form.
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17
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Srivastava AP, Hirasawa M, Bhalla M, Chung JS, Allen JP, Johnson MK, Tripathy JN, Rubio LM, Vaccaro B, Subramanian S, Flores E, Zabet-Moghaddam M, Stitle K, Knaff DB. Roles of four conserved basic amino acids in a ferredoxin-dependent cyanobacterial nitrate reductase. Biochemistry 2013; 52:4343-53. [PMID: 23692082 DOI: 10.1021/bi400354n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The roles of four conserved basic amino acids in the reaction catalyzed by the ferredoxin-dependent nitrate reductase from the cyanobacterium Synechococcus sp. PCC 7942 have been investigated using site-directed mutagenesis in combination with measurements of steady-state kinetics, substrate-binding affinities, and spectroscopic properties of the enzyme's two prosthetic groups. Replacement of either Lys58 or Arg70 by glutamine leads to a complete loss of activity, both with the physiological electron donor, reduced ferredoxin, and with a nonphysiological electron donor, reduced methyl viologen. More conservative, charge-maintaining K58R and R70K variants were also completely inactive. Replacement of Lys130 by glutamine produced a variant that retained 26% of the wild-type activity with methyl viologen as the electron donor and 22% of the wild-type activity with ferredoxin as the electron donor, while replacement by arginine produces a variant that retains a significantly higher percentage of the wild-type activity with both electron donors. In contrast, replacement of Arg146 by glutamine had minimal effect on the activity of the enzyme. These results, along with substrate-binding and spectroscopic measurements, are discussed in terms of an in silico structural model for the enzyme.
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Affiliation(s)
- Anurag P Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Gonzalez PJ, Rivas MG, Mota CS, Brondino CD, Moura I, Moura JJ. Periplasmic nitrate reductases and formate dehydrogenases: Biological control of the chemical properties of Mo and W for fine tuning of reactivity, substrate specificity and metabolic role. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Weinberg DR, Gagliardi CJ, Hull JF, Murphy CF, Kent CA, Westlake BC, Paul A, Ess DH, McCafferty DG, Meyer TJ. Proton-Coupled Electron Transfer. Chem Rev 2012; 112:4016-93. [DOI: 10.1021/cr200177j] [Citation(s) in RCA: 1125] [Impact Index Per Article: 93.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- David R. Weinberg
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
- Department of Physical and Environmental
Sciences, Colorado Mesa University, 1100 North Avenue, Grand Junction,
Colorado 81501-3122, United States
| | - Christopher J. Gagliardi
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Jonathan F. Hull
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Christine Fecenko Murphy
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Caleb A. Kent
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Brittany C. Westlake
- The American Chemical Society,
1155 Sixteenth Street NW, Washington, District of Columbia 20036,
United States
| | - Amit Paul
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Daniel H. Ess
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
| | - Dewey Granville McCafferty
- Department
of Chemistry, B219
Levine Science Research Center, Box 90354, Duke University, Durham,
North Carolina 27708-0354, United States
| | - Thomas J. Meyer
- Department
of Chemistry, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290,
United States
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Substrate-dependent modulation of the enzymatic catalytic activity: reduction of nitrate, chlorate and perchlorate by respiratory nitrate reductase from Marinobacter hydrocarbonoclasticus 617. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1072-82. [PMID: 22561116 DOI: 10.1016/j.bbabio.2012.04.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/23/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
Abstract
The respiratory nitrate reductase complex (NarGHI) from Marinobacter hydrocarbonoclasticus 617 (Mh, formerly Pseudomonas nautica 617) catalyzes the reduction of nitrate to nitrite. This reaction is the first step of the denitrification pathway and is coupled to the quinone pool oxidation and proton translocation to the periplasm, which generates the proton motive force needed for ATP synthesis. The Mh NarGH water-soluble heterodimer has been purified and the kinetic and redox properties have been studied through in-solution enzyme kinetics, protein film voltammetry and spectropotentiometric redox titration. The kinetic parameters of Mh NarGH toward substrates and inhibitors are consistent with those reported for other respiratory nitrate reductases. Protein film voltammetry showed that at least two catalytically distinct forms of the enzyme, which depend on the applied potential, are responsible for substrate reduction. These two forms are affected differentially by the oxidizing substrate, as well as by pH and inhibitors. A new model for the potential dependence of the catalytic efficiency of Nars is proposed.
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22
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Biaso F, Burlat B, Guigliarelli B. DFT Investigation of the Molybdenum Cofactor in Periplasmic Nitrate Reductases: Structure of the Mo(V) EPR-Active Species. Inorg Chem 2012; 51:3409-19. [DOI: 10.1021/ic201533p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frédéric Biaso
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bénédicte Burlat
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique
et Ingénierie des Protéines, UMR 7281, Centre National
de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée,
and Aix-Marseille University, 31 Chemin
Joseph Aiguier, 13402 Marseille Cedex 20, France
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23
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Wang TH, Chen YH, Huang JY, Liu KC, Ke SC, Chu HA. Enzyme kinetics, inhibitors, mutagenesis and electron paramagnetic resonance analysis of dual-affinity nitrate reductase in unicellular N(2)-fixing cyanobacterium Cyanothece sp. PCC 8801. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2011; 49:1369-1376. [PMID: 21821424 DOI: 10.1016/j.plaphy.2011.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/12/2011] [Indexed: 05/31/2023]
Abstract
The assimilatory nitrate reductase (NarB) of N(2)-fixing cyanobacterium Cyanothece sp. PCC 8801 is a monomeric enzyme with dual affinity for substrate nitrate. We purified the recombinant NarB of Cyanothece sp. PCC 8801 and further investigated it by enzyme kinetics analysis, site-directed mutagenesis, inhibitor kinetics analysis, and electron paramagnetic resonance (EPR) spectroscopy. The NarB showed 2 kinetic regimes at pH 10.5 or 8 and electron-donor conditions methyl viologen or ferredoxin (Fd). Fd-dependent NR assay revealed NarB with very high affinity for nitrate (K(m)1, ∼1μM; K(m)2, ∼270μM). Metal analysis and EPR results showed that NarB contains a Mo cofactor and a [4Fe-4S] cluster. In addition, the R352A mutation on the proposed nitrate-binding site of NarB greatly altered both high- and low-affinity kinetic components. Furthermore, the effect of azide on the NarB of Cyanothece sp. PCC 8801 was more complex than that on the NarB of Synechococcus sp. PCC 7942 with its single kinetic regime. With 1mM azide, the kinetics of the wild-type NarB was transformed from 2 kinetic regimes to hyperbolic kinetics, and its activity was enhanced significantly under medium nitrate concentrations. Moreover, EPR results also suggested a structural difference between the two NarBs. Taken together, our results show that the NarB of Cyanothece sp. PCC 8801 contains only a single Mo-catalytic center, and we rule out that the enzyme has 2 independent, distinct catalytic sites. In addition, the NarB of Cyanothece sp. PCC 8801 may have a regulatory nitrate-binding site.
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Affiliation(s)
- Tung-Hei Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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24
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Ferroni FM, Rivas MG, Rizzi AC, Lucca ME, Perotti NI, Brondino CD. Nitrate reduction associated with respiration in Sinorhizobium meliloti 2011 is performed by a membrane-bound molybdoenzyme. Biometals 2011; 24:891-902. [PMID: 21432624 DOI: 10.1007/s10534-011-9442-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
The purification and biochemical characterization of the respiratory membrane-bound nitrate reductase from Sinorhizobium meliloti 2011 (Sm NR) is reported together with the optimal conditions for cell growth and enzyme production. The best biomass yield was obtained under aerobic conditions in a fed-batch system using Luria-Bertani medium with glucose as carbon source. The highest level of Sm NR production was achieved using microaerobic conditions with the medium supplemented with both nitrate and nitrite. Sm NR is a mononuclear Mo-protein belonging to the DMSO reductase family isolated as a heterodimeric enzyme containing two subunits of 118 and 45 kDa. Protein characterization by mass spectrometry showed homology with respiratory nitrate reductases. UV-Vis spectra of as-isolated and dithionite reduced Sm NR showed characteristic absorption bands of iron-sulfur and heme centers. Kinetic studies indicate that Sm NR follows a Michaelis-Menten mechanism (K (m) = 97 ± 11 μM, V = 9.4 ± 0.5 μM min(-1), and k (cat) = 12.1 ± 0.6 s(-1)) and is inhibited by azide, chlorate, and cyanide with mixed inhibition patterns. Physiological and kinetic studies indicate that molybdenum is essential for NR activity and that replacement of this metal for tungsten inhibits the enzyme. Although no narGHI gene cluster has been annotated in the genome of rhizobia, the biochemical characterization indicates that Sm NR is a Mo-containing NR enzyme with molecular organization similar to NarGHI.
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Affiliation(s)
- Felix M Ferroni
- Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Ciudad Universitaria, S3000ZAA Santa Fe, Argentina
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25
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Fourmond V, Sabaty M, Arnoux P, Bertrand P, Pignol D, Léger C. Reassessing the Strategies for Trapping Catalytic Intermediates during Nitrate Reductase Turnover. J Phys Chem B 2010; 114:3341-7. [DOI: 10.1021/jp911443y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Vincent Fourmond
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Monique Sabaty
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Pascal Arnoux
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Patrick Bertrand
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - David Pignol
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
| | - Christophe Léger
- Unité de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, UPR 9036, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France, Laboratoire de Bioénergétique Cellulaire, Commissariat à l’Energie Atomique, DSV, IBEB, F-13108 Saint-Paul-lez-Durance, France, Centre National de la Recherche Scientifique, UMR 6191, Biologie Végétale et Microbiologie Environnementale, 13108 Saint-Paul-lez-Durance, France, and Aix-Marseille
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26
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Rothery RA, Bertero MG, Spreter T, Bouromand N, Strynadka NCJ, Weiner JH. Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation. J Biol Chem 2010; 285:8801-7. [PMID: 20053990 DOI: 10.1074/jbc.m109.066027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have used site-directed mutagenesis, EPR spectroscopy, redox potentiometry, and protein crystallography to monitor assembly of the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor (Mo-bisPGD) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). Cys and Ser mutants of NarG-His(49) both lack catalytic activity, with only the former assembling FS0 and Mo-bisPGD. Importantly, both prosthetic groups are absent in the NarG-H49S mutant. EPR spectroscopy of the Cys mutant reveals that the E(m) value of the FS0 cluster is decreased by at least 500 mV, preventing its participation in electron transfer to the Mo-bisPGD cofactor. To demonstrate that decreasing the FS0 cluster E(m) results in decreased enzyme activity, we mutated a critical Arg residue (NarG-Arg(94)) in the vicinity of FS0 to a Ser residue. In this case, the E(m) of FS0 is decreased by 115 mV, with a concomitant decrease in enzyme turnover to approximately 30% of the wild type. Analysis of the structure of the NarG-H49S mutant reveals two important aspects of NarGHI maturation: (i) apomolybdo-NarGHI is able to bind GDP moieties at their respective P and Q sites in the absence of the Mo-bisPGD cofactor, and (ii) a critical segment of residues in NarG, (49)HGVNCTG(55), must be correctly positioned to ensure holoenzyme maturation.
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Affiliation(s)
- Richard A Rothery
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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27
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The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase. J Comput Chem 2009; 30:2466-84. [DOI: 10.1002/jcc.21280] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Hofmann M. Density functional theory study of model complexes for the revised nitrate reductase active site in Desulfovibrio desulfuricans NapA. J Biol Inorg Chem 2009; 14:1023-35. [DOI: 10.1007/s00775-009-0545-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 04/20/2009] [Indexed: 11/30/2022]
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29
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Affiliation(s)
- Maria João Romão
- REQUIMTE-CQFB, Departamento de Química, FCT-Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
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30
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Fourmond V, Burlat B, Dementin S, Arnoux P, Sabaty M, Boiry S, Guigliarelli B, Bertrand P, Pignol D, Léger C. Major Mo(V) EPR Signature of Rhodobacter sphaeroides Periplasmic Nitrate Reductase Arising from a Dead-End Species That Activates upon Reduction. Relation to Other Molybdoenzymes from the DMSO Reductase Family. J Phys Chem B 2008; 112:15478-86. [DOI: 10.1021/jp807092y] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vincent Fourmond
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Bénédicte Burlat
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Sébastien Dementin
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Pascal Arnoux
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Monique Sabaty
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Séverine Boiry
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Patrick Bertrand
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - David Pignol
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
| | - Christophe Léger
- Unité de Bioénergétique et Ingénierie des Protéines, IBSM, UPR 9036, CNRS, 31 Chemin Joseph Aiguier, F-13402 Marseille Cedex 20, France, Aix-Marseille Université, 3 Place Victor Hugo, F-13333 Marseilles Cedex 3, France, Laboratoire de Bioénergétique Cellulaire, SBVME, IBEB, CEA, F-13108 Saint-Paul-lez-Durance, France, and Laboratoire de Biologie Végétale et Microbiologie Environnementales, UMR 6191, CNRS, F-13108 Saint-Paul-lez-Durance, France
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31
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Najmudin S, González PJ, Trincão J, Coelho C, Mukhopadhyay A, Cerqueira NMFSA, Romão CC, Moura I, Moura JJG, Brondino CD, Romão MJ. Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum. J Biol Inorg Chem 2008; 13:737-53. [PMID: 18327621 DOI: 10.1007/s00775-008-0359-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 02/21/2008] [Indexed: 11/30/2022]
Abstract
Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.
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Affiliation(s)
- Shabir Najmudin
- Departamento de Química, FCT-UNL, REQUIMTE/CQFB, Monte de Caparica, 2829-516, Almada, Portugal.
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32
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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33
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Dementin S, Arnoux P, Frangioni B, Grosse S, Léger C, Burlat B, Guigliarelli B, Sabaty M, Pignol D. Access to the Active Site of Periplasmic Nitrate Reductase: Insights from Site-Directed Mutagenesis and Zinc Inhibition Studies. Biochemistry 2007; 46:9713-21. [PMID: 17676770 DOI: 10.1021/bi700928m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The periplasmic nitrate reductase (NapAB), a member of the DMSO reductase superfamily, catalyzes the first step of the denitrification process in bacteria. In this heterodimer, a di-heme NapB subunit is associated to the catalytic NapA subunit that binds a [4Fe-4S] cluster and a bis(molybdopterin guanine dinucleotide) cofactor. Here, we report the kinetic characterization of purified mutated heterodimers from Rhodobacter sphaeroides. By combining site-directed mutagenesis, redox potentiometry, EPR spectroscopy, and enzymatic characterization, we investigate the catalytic role of two conserved residues (M153 and R392) located in the vicinity of the molybdenum active site. We demonstrate that M153 and R392 are involved in nitrate binding: the Vm measured on the M153A and R392A mutants are similar to that measured on the wild-type enzyme, whereas the Km for nitrate is increased 10-fold and 200-fold, respectively. The use of an alternative enzymatic assay led us to discover that NapAB is uncompetitively inhibited by Zn2+ ions (Ki' = 1 microM). We used this property to further probe the active site access in the mutant enzymes. It is proposed that R392 acts as a filter by preventing a direct reduction of the Mo atom by small reducing molecules and partially protecting the active site against zinc inhibition. In addition, we show that M153 is a key residue mediating this inhibition likely by coordinating Zn2+ ions via its sulfur atom. This residue is not conserved in the DMSO reductase superfamily while it is conserved in the periplasmic nitrate reductase family. Zinc inhibition is therefore likely to be specific and restricted to periplasmic nitrate reductases.
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Affiliation(s)
- Sébastien Dementin
- Laboratoire de Bioénergétique Cellulaire, CEA/Cadarache, DSV/IBEB/SBVME, 13108 St Paul lez Durance Cedex, France.
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34
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Coelho C, González PJ, Trincão J, Carvalho AL, Najmudin S, Hettman T, Dieckman S, Moura JJG, Moura I, Romão MJ. Heterodimeric nitrate reductase (NapAB) from Cupriavidus necator H16: purification, crystallization and preliminary X-ray analysis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:516-9. [PMID: 17554176 PMCID: PMC2335073 DOI: 10.1107/s1744309107022129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Accepted: 05/04/2007] [Indexed: 11/10/2022]
Abstract
The periplasmic nitrate reductase from Cupriavidus necator (also known as Ralstonia eutropha) is a heterodimer that is able to reduce nitrate to nitrite. It comprises a 91 kDa catalytic subunit (NapA) and a 17 kDa subunit (NapB) that is involved in electron transfer. The larger subunit contains a molybdenum active site with a bis-molybdopterin guanine dinucleotide cofactor as well as one [4Fe-4S] cluster, while the small subunit is a di-haem c-type cytochrome. Crystals of the oxidized form of this enzyme were obtained using polyethylene glycol 3350 as precipitant. A single crystal grown at the High Throughput Crystallization Laboratory of the EMBL in Grenoble diffracted to beyond 1.5 A at the ESRF (ID14-1), which is the highest resolution reported to date for a nitrate reductase. The unit-cell parameters are a = 142.2, b = 82.4, c = 96.8 A, beta = 100.7 degrees, space group C2, and one heterodimer is present per asymmetric unit.
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Affiliation(s)
- Catarina Coelho
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Pablo J. González
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José Trincão
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana L. Carvalho
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Shabir Najmudin
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Thomas Hettman
- Institute for Molecular Biotechnology, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Stephan Dieckman
- Institute for Molecular Biotechnology, Beutenbergstrasse 11, 07745 Jena, Germany
| | - José J. G. Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Isabel Moura
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Maria J. Romão
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Jepson BJN, Mohan S, Clarke TA, Gates AJ, Cole JA, Butler CS, Butt JN, Hemmings AM, Richardson DJ. Spectropotentiometric and structural analysis of the periplasmic nitrate reductase from Escherichia coli. J Biol Chem 2006; 282:6425-37. [PMID: 17130127 DOI: 10.1074/jbc.m607353200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli NapA (periplasmic nitrate reductase) contains a [4Fe-4S] cluster and a Mo-bis-molybdopterin guanine dinucleotide cofactor. The NapA holoenzyme associates with a di-heme c-type cytochrome redox partner (NapB). These proteins have been purified and studied by spectropotentiometry, and the structure of NapA has been determined. In contrast to the well characterized heterodimeric NapAB systems ofalpha-proteobacteria, such as Rhodobacter sphaeroides and Paracoccus pantotrophus, the gamma-proteobacterial E. coli NapA and NapB proteins purify independently and not as a tight heterodimeric complex. This relatively weak interaction is reflected in dissociation constants of 15 and 32 mum determined for oxidized and reduced NapAB complexes, respectively. The surface electrostatic potential of E. coli NapA in the apparent NapB binding region is markedly less polar and anionic than that of the alpha-proteobacterial NapA, which may underlie the weaker binding of NapB. The molybdenum ion coordination sphere of E. coli NapA includes two molybdopterin guanine dinucleotide dithiolenes, a protein-derived cysteinyl ligand and an oxygen atom. The Mo-O bond length is 2.6 A, which is indicative of a water ligand. The potential range over which the Mo(6+) state is reduced to the Mo(5+) state in either NapA (between +100 and -100 mV) or the NapAB complex (-150 to -350 mV) is much lower than that reported for R. sphaeroides NapA (midpoint potential Mo(6+/5+) > +350 mV), and the form of the Mo(5+) EPR signal is quite distinct. In E. coli NapA or NapAB, the Mo(5+) state could not be further reduced to Mo(4+). We then propose a catalytic cycle for E. coli NapA in which nitrate binds to the Mo(5+) ion and where a stable des-oxo Mo(6+) species may participate.
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Affiliation(s)
- Brian J N Jepson
- Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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