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Hird K, Campeciño JO, Lehnert N, Hegg EL. Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway. J Inorg Biochem 2024; 256:112542. [PMID: 38631103 DOI: 10.1016/j.jinorgbio.2024.112542] [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: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/19/2024]
Abstract
Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.
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Affiliation(s)
- Krystina Hird
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Julius O Campeciño
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Eric L Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.
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2
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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3
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Lehnert N, Kim E, Dong HT, Harland JB, Hunt AP, Manickas EC, Oakley KM, Pham J, Reed GC, Alfaro VS. The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity. Chem Rev 2021; 121:14682-14905. [PMID: 34902255 DOI: 10.1021/acs.chemrev.1c00253] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.
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Affiliation(s)
- Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Hai T Dong
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jill B Harland
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Andrew P Hunt
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Elizabeth C Manickas
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Kady M Oakley
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - John Pham
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Garrett C Reed
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Victor Sosa Alfaro
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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4
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Shahid S, Ali M, Legaspi-Humiston D, Wilcoxen J, Pacheco AA. A Kinetic Investigation of the Early Steps in Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite. Biochemistry 2021; 60:2098-2115. [PMID: 34143605 DOI: 10.1021/acs.biochem.1c00172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The decaheme enzyme cytochrome c nitrite reductase (ccNiR) catalyzes reduction of nitrite to ammonium in a six-electron, eight-proton process. With a strong reductant as the electron source, ammonium is the sole product. However, intermediates accumulate when weaker reductants are employed, facilitating study of the ccNiR mechanism. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated by using the weak reductants N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) and ferrocyanide. In stopped-flow experiments, reduction of nitrite-loaded ccNiR by TMPD generated a transient intermediate, identified as FeH1II(NO2-), where FeH1 represents the ccNiR active site. FeH1II(NO2-) accumulated rapidly and was then more slowly converted to the two-electron-reduced moiety {FeH1NO}7; ccNiR was not reduced beyond the {FeH1NO}7 state. The midpoint potentials for sequential reduction of FeH1III(NO2-) to FeH1II(NO2-) and then to {FeH1NO}7 were estimated to be 130 and 370 mV versus the standard hydrogen electrode, respectively. FeH1II(NO2-) does not accumulate at equilibrium because its reduction to {FeH1NO}7 is so much easier than the reduction of FeH1III(NO2-) to FeH1II(NO2-). With weak reductants, free NO• was released from nitrite-loaded ccNiR. The release of NO• from {FeH1NO}7 is exceedingly slow (k ∼ 0.001 s-1), but it is somewhat faster (k ∼ 0.050 s-1) while FeH1III(NO2-) is being reduced to {FeH1NO}7; then, the release of NO• from the undetectable transient {FeH1NO}6 can compete with reduction of {FeH1NO}6 to {FeH1NO}7. CcNiR appears to be optimized to capture nitrite and minimize the release of free NO•. Nitrite capture is achieved by reducing bound nitrite with even weak electron donors, while NO• release is minimized by stabilizing the substitutionally inert {FeH1NO}7 over the more labile {FeH1NO}6.
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Affiliation(s)
- Shahid Shahid
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Mahbbat Ali
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Desiree Legaspi-Humiston
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Jarett Wilcoxen
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - A Andrew Pacheco
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
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5
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Yu YY, Ding XL, Quan WZ, Niu Q, Fang Z, Dapaah MF, You T, Xiao X, Cheng L. Dynamically controlling the electrode potential of a microbial fuel cell-powered biocathode for sensitive quantification of nitrate. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137661] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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6
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Amanullah S, Saha P, Nayek A, Ahmed ME, Dey A. Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis. Chem Soc Rev 2021; 50:3755-3823. [DOI: 10.1039/d0cs01405b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.
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Affiliation(s)
- Sk Amanullah
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Paramita Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhijit Nayek
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Md Estak Ahmed
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Abhishek Dey
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata
- India
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7
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Campeciño J, Lagishetty S, Wawrzak Z, Sosa Alfaro V, Lehnert N, Reguera G, Hu J, Hegg EL. Cytochrome c nitrite reductase from the bacterium Geobacter lovleyi represents a new NrfA subclass. J Biol Chem 2020; 295:11455-11465. [PMID: 32518164 PMCID: PMC7450111 DOI: 10.1074/jbc.ra120.013981] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/07/2020] [Indexed: 01/07/2023] Open
Abstract
Cytochrome c nitrite reductase (NrfA) catalyzes the reduction of nitrite to ammonium in the dissimilatory nitrate reduction to ammonium (DNRA) pathway, a process that competes with denitrification, conserves nitrogen, and minimizes nutrient loss in soils. The environmental bacterium Geobacter lovleyi has recently been recognized as a key driver of DNRA in nature, but its enzymatic pathway is still uncharacterized. To address this limitation, here we overexpressed, purified, and characterized G. lovleyi NrfA. We observed that the enzyme crystallizes as a dimer but remains monomeric in solution. Importantly, its crystal structure at 2.55-Å resolution revealed the presence of an arginine residue in the region otherwise occupied by calcium in canonical NrfA enzymes. The presence of EDTA did not affect the activity of G. lovleyi NrfA, and site-directed mutagenesis of this arginine reduced enzymatic activity to <3% of the WT levels. Phylogenetic analysis revealed four separate emergences of Arg-containing NrfA enzymes. Thus, the Ca2+-independent, Arg-containing NrfA from G. lovleyi represents a new subclass of cytochrome c nitrite reductase. Most genera from the exclusive clades of Arg-containing NrfA proteins are also represented in clades containing Ca2+-dependent enzymes, suggesting convergent evolution.
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Affiliation(s)
- Julius Campeciño
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Satyanarayana Lagishetty
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - Victor Sosa Alfaro
- Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, Michigan, USA
| | - Nicolai Lehnert
- Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, Michigan, USA
| | - Gemma Reguera
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jian Hu
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA,Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Eric L. Hegg
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, USA,For correspondence: Eric L. Hegg,
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8
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Ali M, Stein N, Mao Y, Shahid S, Schmidt M, Bennett B, Pacheco AA. Trapping of a Putative Intermediate in the Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite: Implications for the ccNiR Reaction Mechanism. J Am Chem Soc 2019; 141:13358-13371. [DOI: 10.1021/jacs.9b03036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mahbbat Ali
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Natalia Stein
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Yingxi Mao
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Shahid Shahid
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Marius Schmidt
- Department of Physics, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Brian Bennett
- Department of Physics, Marquette University, Milwaukee, Wisconsin 53233, United States
| | - A. Andrew Pacheco
- Department of Chemistry and Biochemistry, University of Wisconsin−Milwaukee, Milwaukee, Wisconsin 53211, United States
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9
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Protein Electrochemistry: Questions and Answers. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 158:1-41. [DOI: 10.1007/10_2015_5016] [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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10
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Breuer M, Rosso KM, Blumberger J, Butt JN. Multi-haem cytochromes in Shewanella oneidensis MR-1: structures, functions and opportunities. J R Soc Interface 2015; 12:20141117. [PMID: 25411412 DOI: 10.1098/rsif.2014.1117] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multi-haem cytochromes are employed by a range of microorganisms to transport electrons over distances of up to tens of nanometres. Perhaps the most spectacular utilization of these proteins is in the reduction of extracellular solid substrates, including electrodes and insoluble mineral oxides of Fe(III) and Mn(III/IV), by species of Shewanella and Geobacter. However, multi-haem cytochromes are found in numerous and phylogenetically diverse prokaryotes where they participate in electron transfer and redox catalysis that contributes to biogeochemical cycling of N, S and Fe on the global scale. These properties of multi-haem cytochromes have attracted much interest and contributed to advances in bioenergy applications and bioremediation of contaminated soils. Looking forward, there are opportunities to engage multi-haem cytochromes for biological photovoltaic cells, microbial electrosynthesis and developing bespoke molecular devices. As a consequence, it is timely to review our present understanding of these proteins and we do this here with a focus on the multitude of functionally diverse multi-haem cytochromes in Shewanella oneidensis MR-1. We draw on findings from experimental and computational approaches which ideally complement each other in the study of these systems: computational methods can interpret experimentally determined properties in terms of molecular structure to cast light on the relation between structure and function. We show how this synergy has contributed to our understanding of multi-haem cytochromes and can be expected to continue to do so for greater insight into natural processes and their informed exploitation in biotechnologies.
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Affiliation(s)
- Marian Breuer
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jochen Blumberger
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Julea N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK
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11
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Alves MN, Neto SE, Alves AS, Fonseca BM, Carrêlo A, Pacheco I, Paquete CM, Soares CM, Louro RO. Characterization of the periplasmic redox network that sustains the versatile anaerobic metabolism of Shewanella oneidensis MR-1. Front Microbiol 2015; 6:665. [PMID: 26175726 PMCID: PMC4484225 DOI: 10.3389/fmicb.2015.00665] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/17/2015] [Indexed: 01/14/2023] Open
Abstract
The versatile anaerobic metabolism of the Gram-negative bacterium Shewanella oneidensis MR-1 (SOMR-1) relies on a multitude of redox proteins found in its periplasm. Most are multiheme cytochromes that carry electrons to terminal reductases of insoluble electron acceptors located at the cell surface, or bona fide terminal reductases of soluble electron acceptors. In this study, the interaction network of several multiheme cytochromes was explored by a combination of NMR spectroscopy, activity assays followed by UV-visible spectroscopy and comparison of surface electrostatic potentials. From these data the small tetraheme cytochrome (STC) emerges as the main periplasmic redox shuttle in SOMR-1. It accepts electrons from CymA and distributes them to a number of terminal oxidoreductases involved in the respiration of various compounds. STC is also involved in the electron transfer pathway to reduce nitrite by interaction with the octaheme tetrathionate reductase (OTR), but not with cytochrome c nitrite reductase (ccNiR). In the main pathway leading the metal respiration STC pairs with flavocytochrome c (FccA), the other major periplasmic cytochrome, which provides redundancy in this important pathway. The data reveals that the two proteins compete for the binding site at the surface of MtrA, the decaheme cytochrome inserted on the periplasmic side of the MtrCAB-OmcA outer-membrane complex. However, this is not observed for the MtrA homologues. Indeed, neither STC nor FccA interact with MtrD, the best replacement for MtrA, and only STC is able to interact with the decaheme cytochrome DmsE of the outer-membrane complex DmsEFABGH. Overall, these results shown that STC plays a central role in the anaerobic respiratory metabolism of SOMR-1. Nonetheless, the trans-periplasmic electron transfer chain is functionally resilient as a consequence of redundancies that arise from the presence of alternative pathways that bypass/compete with STC.
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Affiliation(s)
- Mónica N Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Sónia E Neto
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Alexandra S Alves
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Bruno M Fonseca
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Afonso Carrêlo
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Isabel Pacheco
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Catarina M Paquete
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Cláudio M Soares
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
| | - Ricardo O Louro
- Inorganic Biochemistry and NMR Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras, Portugal
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12
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Bauß A, Koslowski T. Storage, transport, release: heme versatility in nitrite reductase electron transfer studied by molecular dynamics simulations. Phys Chem Chem Phys 2015; 17:4483-91. [DOI: 10.1039/c4cp04383a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Using molecular dynamics simulations of the thermodynamic integration type, we study the energetics and kinetics of electron transfer through the nitrite reductase enzyme of Sulfurospirillum deleyianum, Wolinella succinogenes and Campylobacter jejuni.
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Affiliation(s)
- Anna Bauß
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
| | - Thorsten Koslowski
- Institut für Physikalische Chemie
- Universität Freiburg
- D-79104 Freiburg im Breisgau
- Germany
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13
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Judd ET, Stein N, Pacheco AA, Elliott SJ. Hydrogen bonding networks tune proton-coupled redox steps during the enzymatic six-electron conversion of nitrite to ammonia. Biochemistry 2014; 53:5638-46. [PMID: 25137350 PMCID: PMC4159211 DOI: 10.1021/bi500854p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Multielectron
multiproton reactions play an important role in both
biological systems and chemical reactions involved in energy storage
and manipulation. A key strategy employed by nature in achieving such
complex chemistry is the use of proton-coupled redox steps. Cytochrome c nitrite reductase (ccNiR) catalyzes the six-electron seven-proton
reduction of nitrite to ammonia. While a catalytic mechanism for ccNiR
has been proposed on the basis of studies combining computation and
crystallography, there have been few studies directly addressing the
nature of the proton-coupled events that are predicted to occur along
the nitrite reduction pathway. Here we use protein film voltammetry
to directly interrogate the proton-coupled steps that occur during
nitrite reduction by ccNiR. We find that conversion of nitrite to
ammonia by ccNiR adsorbed to graphite electrodes is defined by two
distinct phases; one is proton-coupled, and the other is not. Mutation
of key active site residues (H257, R103, and Y206) modulates these
phases and specifically alters the properties of the detected proton-dependent
step but does not inhibit the ability of ccNiR to conduct the full
reduction of nitrite to ammonia. We conclude that the active site
residues examined are responsible for tuning the protonation steps
that occur during catalysis, likely through an extensive hydrogen
bonding network, but are not necessarily required for the reaction
to proceed. These results provide important insight into how enzymes
can specifically tune proton- and electron transfer steps to achieve
high turnover numbers in a physiological pH range.
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Affiliation(s)
- Evan T Judd
- Department of Chemistry, Boston University , 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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14
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Paquete CM, Saraiva IH, Louro RO. Redox tuning of the catalytic activity of soluble fumarate reductases from Shewanella. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:717-25. [DOI: 10.1016/j.bbabio.2014.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/04/2014] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
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15
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Youngblut M, Pauly DJ, Stein N, Walters D, Conrad JA, Moran GR, Bennett B, Pacheco AA. Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) does not disproportionate hydroxylamine to ammonia and nitrite, despite a strongly favorable driving force. Biochemistry 2014; 53:2136-44. [PMID: 24645742 DOI: 10.1021/bi401705d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c nitrite reductase (ccNiR) from Shewanella oneidensis, which catalyzes the six-electron reduction of nitrite to ammonia in vivo, was shown to oxidize hydroxylamine in the presence of large quantities of this substrate, yielding nitrite as the sole free nitrogenous product. UV-visible stopped-flow and rapid-freeze-quench electron paramagnetic resonance data, along with product analysis, showed that the equilibrium between hydroxylamine and nitrite is fairly rapidly established in the presence of high initial concentrations of hydroxylamine, despite said equilibrium lying far to the left. By contrast, reduction of hydroxylamine to ammonia did not occur, even though disproportionation of hydroxylamine to yield both nitrite and ammonia is strongly thermodynamically favored. This suggests a kinetic barrier to the ccNiR-catalyzed reduction of hydroxylamine to ammonia. A mechanism for hydroxylamine reduction is proposed in which the hydroxide group is first protonated and released as water, leaving what is formally an NH2(+) moiety bound at the heme active site. This species could be a metastable intermediate or a transition state but in either case would exist only if it were stabilized by the donation of electrons from the ccNiR heme pool into the empty nitrogen p orbital. In this scenario, ccNiR does not catalyze disproportionation because the electron-donating hydroxylamine does not poise the enzyme at a sufficiently low potential to stabilize the putative dehydrated hydroxylamine; presumably, a stronger reductant is required for this.
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Affiliation(s)
- Matthew Youngblut
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53211, United States
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16
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Contrasting catalytic profiles of multiheme nitrite reductases containing CxxCK heme-binding motifs. J Biol Inorg Chem 2013; 18:655-67. [DOI: 10.1007/s00775-013-1011-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
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17
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Bewley KD, Ellis KE, Firer-Sherwood MA, Elliott SJ. Multi-heme proteins: nature's electronic multi-purpose tool. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:938-48. [PMID: 23558243 DOI: 10.1016/j.bbabio.2013.03.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 02/06/2023]
Abstract
While iron is often a limiting nutrient to Biology, when the element is found in the form of heme cofactors (iron protoporphyrin IX), living systems have excelled at modifying and tailoring the chemistry of the metal. In the context of proteins and enzymes, heme cofactors are increasingly found in stoichiometries greater than one, where a single protein macromolecule contains more than one heme unit. When paired or coupled together, these protein associated heme groups perform a wide variety of tasks, such as redox communication, long range electron transfer and storage of reducing/oxidizing equivalents. Here, we review recent advances in the field of multi-heme proteins, focusing on emergent properties of these complex redox proteins, and strategies found in Nature where such proteins appear to be modular and essential components of larger biochemical pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Affiliation(s)
- Kathryn D Bewley
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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