1
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Murray D, Ge X, Schut GJ, Rosenberg DJ, Hammel M, Bierma JC, Hille R, Adams MWW, Hura GL. Correlating Conformational Equilibria with Catalysis in the Electron Bifurcating EtfABCX of Thermotoga maritima. Biochemistry 2024; 63:128-140. [PMID: 38013433 PMCID: PMC10765413 DOI: 10.1021/acs.biochem.3c00472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
Electron bifurcation (BF) is an evolutionarily ancient energy coupling mechanism in anaerobes, whose associated enzymatic machinery remains enigmatic. In BF-flavoenzymes, a chemically high-potential electron forms in a thermodynamically favorable fashion by simultaneously dropping the potential of a second electron before its donation to physiological acceptors. The cryo-EM and spectroscopic analyses of the BF-enzyme Fix/EtfABCX from Thermotoga maritima suggest that the BF-site contains a special flavin-adenine dinucleotide and, upon its reduction with NADH, a low-potential electron transfers to ferredoxin and a high-potential electron reduces menaquinone. The transfer of energy from high-energy intermediates must be carefully orchestrated conformationally to avoid equilibration. Herein, anaerobic size exclusion-coupled small-angle X-ray scattering (SEC-SAXS) shows that the Fix/EtfAB heterodimer subcomplex, which houses BF- and electron transfer (ET)-flavins, exists in a conformational equilibrium of compacted and extended states between flavin-binding domains, the abundance of which is impacted by reduction and NAD(H) binding. The conformations identify dynamics associated with the T. maritima enzyme and also recapitulate states identified in static structures of homologous BF-flavoenzymes. Reduction of Fix/EtfABCX's flavins alone is insufficient to elicit domain movements conducive to ET but requires a structural "trigger" induced by NAD(H) binding. Models show that Fix/EtfABCX's superdimer exists in a combination of states with respect to its BF-subcomplexes, suggesting a cooperative mechanism between supermonomers for optimizing catalysis. The correlation of conformational states with pathway steps suggests a structural means with which Fix/EtfABCX may progress through its catalytic cycle. Collectively, these observations provide a structural framework for tracing Fix/EtfABCX's catalysis.
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Affiliation(s)
- Daniel
T. Murray
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xiaoxuan Ge
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Gerrit J. Schut
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Daniel J. Rosenberg
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Linac
Coherent Light Source, SLAC National Accelerator
Laboratory, Menlo
Park, California 94025, United States
| | - Michal Hammel
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jan C. Bierma
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Russ Hille
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Greg L. Hura
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Chemistry
and Biochemistry Department, University
of California, Santa Cruz, Santa
Cruz, California 95064, United States
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2
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Ge X, Schut GJ, Tran J, Poole II FL, Niks D, Menjivar K, Hille R, Adams MWW. Characterization of the Membrane-Associated Electron-Bifurcating Flavoenzyme EtfABCX from the Hyperthermophilic Bacterium Thermotoga maritima. Biochemistry 2023; 62:3554-3567. [PMID: 38061393 PMCID: PMC10734219 DOI: 10.1021/acs.biochem.3c00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023]
Abstract
Electron bifurcation is an energy-conservation mechanism in which a single enzyme couples an exergonic reaction with an endergonic one. Heterotetrameric EtfABCX drives the reduction of low-potential ferredoxin (E°' ∼ -450 mV) by oxidation of the midpotential NADH (E°' = -320 mV) by simultaneously coupling the reaction to reduction of the high-potential menaquinone (E°' = -74 mV). Electron bifurcation occurs at the NADH-oxidizing bifurcating-flavin adenine dinucleotide (BF-FAD) in EtfA, which has extremely crossed half-potentials and passes the first, high-potential electron to an electron-transferring FAD and via two iron-sulfur clusters eventually to menaquinone. The low-potential electron on the BF-FAD semiquinone simultaneously reduces ferredoxin. We have expressed the genes encodingThermotoga maritimaEtfABCX in E. coli and purified the EtfABCX holoenzyme and the EtfAB subcomplex. The bifurcation activity of EtfABCX was demonstrated by using electron paramagnetic resonance (EPR) to follow accumulation of reduced ferredoxin. To elucidate structural factors that impart the bifurcating ability, EPR and NADH titrations monitored by visible spectroscopy and dye-linked enzyme assays have been employed to characterize four conserved residues, R38, P239, and V242 in EtfA and R140 in EtfB, in the immediate vicinity of the BF-FAD. The R38, P239, and V242 variants showed diminished but still significant bifurcation activity. Despite still being partially reduced by NADH, the R140 variant had no bifurcation activity, and electron transfer to its two [4Fe-4S] clusters was prevented. The role of R140 is discussed in terms of the bifurcation mechanism in EtfABCX and in the other three families of bifurcating enzymes.
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Affiliation(s)
- Xiaoxuan Ge
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Gerrit J. Schut
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Jessica Tran
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Farris L. Poole II
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Dimitri Niks
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Kevin Menjivar
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Russ Hille
- Department
of Biochemistry, University of California,
Riverside, Riverside, California 92507, United States
| | - Michael W. W. Adams
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
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3
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Ortiz S, Niks D, Wiley S, Lubner CE, Hille R. Rapid-reaction kinetics of the bifurcating NAD +-dependent NADPH:ferredoxin oxidoreductase NfnI from Pyrococcus furiosus. J Biol Chem 2023; 299:105403. [PMID: 38229399 PMCID: PMC10724689 DOI: 10.1016/j.jbc.2023.105403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/02/2023] [Accepted: 10/22/2023] [Indexed: 01/18/2024] Open
Abstract
We have investigated the kinetics of NAD+-dependent NADPH:ferredoxin oxidoreductase (NfnI), a bifurcating transhydrogenase that takes two electron pairs from NADPH to reduce two ferredoxins and one NAD+ through successive bifurcation events. NADPH reduction takes place at the bifurcating FAD of NfnI's large subunit, with high-potential electrons transferred to the [2Fe-2S] cluster and S-FADH of the small subunit, ultimately on to NAD+; low-potential electrons are transferred to two [4Fe-4S] clusters of the large subunit and on to ferredoxin. Reduction of NfnI by NADPH goes to completion only at higher pH, with a limiting kred of 36 ± 1.6 s-1 and apparent KdNADPH of 5 ± 1.2 μM. Reduction of one of the [4Fe-4S] clusters of NfnI occurs within a second, indicating that in the absence of NAD+, the system can bifurcate and generate low-potential electrons without NAD+. When enzyme is reduced by NADPH in the absence of NAD+ but the presence of ferredoxin, up to three equivalents of ferredoxin become reduced, although the reaction is considerably slower than seen during steady-state turnover. Bifurcation appears to be limited by transfer of the first, high-potential electron into the high-potential pathway. Ferredoxin reduction without NAD+ demonstrates that electron bifurcation is an intrinsic property of the bifurcating FAD and is not dependent on the simultaneous presence of NAD+ and ferredoxin. The tight coupling between NAD+ and ferredoxin reduction observed under multiple-turnover conditions is instead simply due to the need to remove reducing equivalents from the high-potential electron pathway under multiple-turnover conditions.
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Affiliation(s)
- Steve Ortiz
- Department of Biochemistry and the Biophysics Graduate Program, University of California, Riverside, USA
| | - Dimitri Niks
- Department of Biochemistry and the Biophysics Graduate Program, University of California, Riverside, USA
| | - Seth Wiley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA.
| | - Russ Hille
- Department of Biochemistry and the Biophysics Graduate Program, University of California, Riverside, USA.
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4
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Harmer JR, Hakopian S, Niks D, Hille R, Bernhardt PV. Redox Characterization of the Complex Molybdenum Enzyme Formate Dehydrogenase from Cupriavidus necator. J Am Chem Soc 2023; 145:25850-25863. [PMID: 37967365 DOI: 10.1021/jacs.3c10199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The oxygen-tolerant and molybdenum-dependent formate dehydrogenase FdsDABG from Cupriavidus necator is capable of catalyzing both formate oxidation to CO2 and the reverse reaction (CO2 reduction to formate) at neutral pH, which are both reactions of great importance to energy production and carbon capture. FdsDABG is replete with redox cofactors comprising seven Fe/S clusters, flavin mononucleotide, and a molybdenum ion coordinated by two pyranopterin dithiolene ligands. The redox potentials of these centers are described herein and assigned to specific cofactors using combinations of potential-dependent continuous wave and pulse EPR spectroscopy and UV/visible spectroelectrochemistry on both the FdsDABG holoenzyme and the FdsBG subcomplex. These data represent the first redox characterization of a complex metal dependent formate dehydrogenase and provide an understanding of the highly efficient catalytic formate oxidation and CO2 reduction activity that are associated with the enzyme.
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Affiliation(s)
- Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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5
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Kalimuthu P, Hakopian S, Niks D, Hille R, Bernhardt PV. The Reversible Electrochemical Interconversion of Formate and CO 2 by Formate Dehydrogenase from Cupriavidus necator. J Phys Chem B 2023; 127:8382-8392. [PMID: 37728992 DOI: 10.1021/acs.jpcb.3c04652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The bacterial molybdenum (Mo)-containing formate dehydrogenase (FdsDABG) from Cupriavidus necator is a soluble NAD+-dependent enzyme belonging to the DMSO reductase family. The holoenzyme is complex and possesses nine redox-active cofactors including a bis(molybdopterin guanine dinucleotide) (bis-MGD) active site, seven iron-sulfur clusters, and 1 equiv of flavin mononucleotide (FMN). FdsDABG catalyzes the two-electron oxidation of HCOO- (formate) to CO2 and reversibly reduces CO2 to HCOO- under physiological conditions close to its thermodynamic redox potential. Here we develop an electrocatalytically active formate oxidation/CO2 reduction system by immobilizing FdsDABG on a glassy carbon electrode in the presence of coadsorbents such as chitosan and glutaraldehyde. The reversible enzymatic interconversion between HCOO- and CO2 by FdsDABG has been realized with cyclic voltammetry using a range of artificial electron transfer mediators, with methylene blue (MB) and phenazine methosulfate (PMS) being particularly effective as electron acceptors for FdsDABG in formate oxidation. Methyl viologen (MV) acts as both an electron acceptor (MV2+) in formate oxidation and an electron donor (MV+•) for CO2 reduction. The catalytic voltammetry was reproduced by electrochemical simulation across a range of sweep rates and concentrations of formate and mediators to provide new insights into the kinetics of the FdsDABG catalytic mechanism.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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6
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Sekine M, Okamoto K, Pai EF, Nagata K, Ichida K, Hille R, Nishino T. Allopurinol and oxypurinol differ in their strength and mechanisms of inhibition of xanthine oxidoreductase. J Biol Chem 2023; 299:105189. [PMID: 37625592 PMCID: PMC10511816 DOI: 10.1016/j.jbc.2023.105189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023] Open
Abstract
Xanthine oxidoreductase is a metalloenzyme that catalyzes the final steps in purine metabolism by converting hypoxanthine to xanthine and then uric acid. Allopurinol, an analog of hypoxanthine, is widely used as an antigout drug, as xanthine oxidoreductase-mediated metabolism of allopurinol to oxypurinol leads to oxypurinol rotation in the enzyme active site and reduction of the molybdenum Mo(VI) active center to Mo(IV), inhibiting subsequent urate production. However, when oxypurinol is administered directly to a mouse model of hyperuricemia, it yields a weaker urate-lowering effect than allopurinol. To better understand its mechanism of inhibition and inform patient dosing strategies, we performed kinetic and structural analyses of the inhibitory activity of oxypurinol. Our results demonstrated that oxypurinol was less effective than allopurinol both in vivo and in vitro. We show that upon reoxidation to Mo(VI), oxypurinol binding is greatly weakened, and reduction by xanthine, hypoxanthine, or allopurinol is required for reformation of the inhibitor-enzyme complex. In addition, we show oxypurinol only weakly inhibits the conversion of hypoxanthine to xanthine and is therefore unlikely to affect the feedback inhibition of de novo purine synthesis. Furthermore, we observed weak allosteric inhibition of purine nucleoside phosphorylase by oxypurinol which has potentially adverse effects for patients. Considering these results, we propose the single-dose method currently used to treat hyperuricemia can result in unnecessarily high levels of allopurinol. While the short half-life of allopurinol in blood suggests that oxypurinol is responsible for enzyme inhibition, we anticipate multiple, smaller doses of allopurinol would reduce the total allopurinol patient load.
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Affiliation(s)
- Mai Sekine
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan.
| | - Ken Okamoto
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Emil F Pai
- Departments of Biochemistry and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, Campbell Family Cancer Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kimiyoshi Ichida
- Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Takeshi Nishino
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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7
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Vigil W, Nguyen D, Niks D, Hille R. Rapid-reaction kinetics of the butyryl-CoA dehydrogenase component of the electron-bifurcating crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase from Megasphaera elsdenii. J Biol Chem 2023:104853. [PMID: 37220854 PMCID: PMC10320503 DOI: 10.1016/j.jbc.2023.104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/25/2023] Open
Abstract
We have investigated the equilibrium properties and rapid-reaction kinetics of the isolated butyryl-CoA dehydrogenase (bcd) component of the electron-bifurcating crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase (EtfAB:bcd) from Megasphaera elsdenii. We find that a neutral FADH• semiquinone accumulates transiently during both reduction with sodium dithionite and with NADH in the presence of catalytic concentrations of EtfAB. In both cases full reduction of bcd to the hydroquinone is eventually observed, but the accumulation of FADH• indicates that a substantial portion of reduction occurs in sequential one-electron processes rather than a single two-electron event. In rapid-reaction experiments following the reaction of reduced bcd with crotonyl-CoA and oxidized bcd with butyryl-CoA, long-wavelength-absorbing intermediates are observed that are assigned to bcdred:crotonyl-CoA and bcdox:butyryl-CoA charge-transfer complexes, demonstrating their kinetic competence in the course of the reaction. In the presence of crotonyl-CoA there is an accumulation of semiquinone that is unequivocally the anionic FAD•- rather than the neutral FADH• seen in the absence of substrate, indicating that binding of substrate/product results in ionization of the bcd semiquinone. In addition to fully characterizing the rapid-reaction kinetics of both the oxidative and reductive half-reactions, our results demonstrate that one-electron processes play an important role in the reduction of bcd in EtfAB:bcd.
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Affiliation(s)
- Wayne Vigil
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521.
| | - Derek Nguyen
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside CA 92521
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8
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Ortiz S, Niks D, Vigil W, Tran J, Lubner CE, Hille R. Spectral deconvolution of electron-bifurcating flavoproteins. Methods Enzymol 2023; 685:531-550. [PMID: 37245914 DOI: 10.1016/bs.mie.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Electron-bifurcating flavoproteins catalyze the tightly coupled reduction of high- and low-potential acceptors using a median-potential electron donor, and are invariably complex systems with multiple redox-active centers in two or more subunits. Methods are described that permit, in favorable cases, the deconvolution of spectral changes associated with reduction of specific centers, making it possible to dissect the overall process of electron bifurcation into individual, discrete steps.
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Affiliation(s)
- Steve Ortiz
- Department of Biochemistry, University of California, Riverside, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, United States
| | - Wayne Vigil
- Department of Biochemistry, University of California, Riverside, United States
| | - Jessica Tran
- Department of Biochemistry, University of California, Riverside, United States
| | - Carolyn E Lubner
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States.
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, United States.
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9
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Hille R. Xanthine Oxidase-A Personal History. Molecules 2023; 28:1921. [PMID: 36838909 PMCID: PMC9966888 DOI: 10.3390/molecules28041921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
A personal perspective is provided regarding the work in several laboratories, including the author's, that has established the reaction mechanism of xanthine oxidase and related enzymes.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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10
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Kusano T, Nishino T, Okamoto K, Hille R, Nishino T. The mechanism and significance of the conversion of xanthine dehydrogenase to xanthine oxidase in mammalian secretory gland cells. Redox Biol 2022; 59:102573. [PMID: 36525890 PMCID: PMC9760657 DOI: 10.1016/j.redox.2022.102573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The conversion of xanthine dehydrogenase (XDH) to xanthine oxidase (XO) occurs only in mammalian species. In fresh bovine milk, the enzyme exists predominantly as the oxidase form, in contrast to various normal organs where it is found primarily as the dehydrogenase: the mechanism of conversion to the oxidase in milk remains obscure. A systematic search for the essential factors for conversion from XDH to XO has been performed within fresh bovine milk using the highly purified dehydrogenase form after removal endogenous oxidase form by fractionation analysis. We find that conversion to the oxidase form requires four components under air: lactoperoxidase (LPO), XDH, SCN-, and substrate hypoxanthine or xanthine; the contribution of sulfhydryl oxidase appears to be minor. Disulfide bond formation between Cys-535 and Cys-995 is principally involved in the conversion, consistent with the result obtained from previous work with transgenic mice. In vitro reconstitution of LPO and SCN- results in synergistic conversion of the dehydrogenase to the oxidase the presence of xanthine, indicating the conversion is autocatalytic. Milk from an LPO knockout mouse contains a significantly greater proportion of the dehydrogenase form of the enzyme, although some oxidase form is also present, indicating that LPO contributes principally to the conversion, but that sulfhydryl oxidase (SO) may also be involved to a minor extent. All the components XDH/LPO/SCN- are necessary to inhibit bacterial growth in the presence of xanthine through disulfide bond formation in bacterial protein(s) required for replication, as part of an innate immunity system in mammals. Human GTEx Data suggest that mRNA of XDH and LPO are highly co-expressed in the salivary gland, mammary gland, mucosa of the airway and lung alveoli, and we have confirmed these human GTEx Data experimentally in mice. We discuss the possible roles of these components in the propagation of SARS-CoV-2 in these human cell types.
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Affiliation(s)
- Teruo Kusano
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan
| | - Tomoko Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan
| | - Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, USA
| | - Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-Ku, Tokyo, Japan.
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11
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Graham JE, Niks D, Zane GM, Gui Q, Hom K, Hille R, Wall JD, Raman CS. How a Formate Dehydrogenase Responds to Oxygen: Unexpected O 2 Insensitivity of an Enzyme Harboring Tungstopterin, Selenocysteine, and [4Fe–4S] Clusters. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel E. Graham
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Qin Gui
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - Kellie Hom
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California92521, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, Missouri65211, United States
| | - C. S. Raman
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland21201, United States
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12
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Abstract
A concise review is provided of the contributions that various spectroscopic methods have made to our understanding of the physical and electronic structures of mononuclear molybdenum enzymes. Contributions to our understanding of the structure and function of each of the major families of these enzymes is considered, providing a perspective on how spectroscopy has impacted the field.
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Affiliation(s)
- Martin L. Kirk
- Department of Chemistry and Chemical Biology, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, NM 87131-0001, USA
- Correspondence: (M.L.K.); (R.H.)
| | - Russ Hille
- Department of Biochemistry, Boyce Hall 1463, University of California, Riverside, CA 82521, USA
- Correspondence: (M.L.K.); (R.H.)
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13
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Abstract
A description is provided of the contributions made to our understanding of molybdenum-containing enzymes through the application of electron paramagnetic resonance spectroscopy and related methods, by way of illustrating how these can be applied to better understand enzyme structure and function. An emphasis is placed on the use of EPR to identify both the coordination environment of the molybdenum coordination sphere as well as the structures of paramagnetic intermediates observed transiently in the course of reaction that have led to the elucidation of reaction mechanism.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, CA, United States.
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA, United States
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14
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Vigil W, Tran J, Niks D, Schut GJ, Ge X, Adams MWW, Hille R. The reductive half-reaction of two bifurcating electron-transferring flavoproteins: Evidence for changes in flavin reduction potentials mediated by specific conformational changes. J Biol Chem 2022; 298:101927. [PMID: 35429498 PMCID: PMC9127580 DOI: 10.1016/j.jbc.2022.101927] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 10/25/2022] Open
Abstract
The EtfAB components of two bifurcating flavoprotein systems, the crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase from the bacterium Megasphaera elsdenii and the menaquinone-dependent NADH:ferredoxin oxidoreductase from the archaeon Pyrobaculum aerophilum, have been investigated. With both proteins, we find that removal of the electron-transferring flavin adenine dinucleotide (FAD) moiety from both proteins results in an uncrossing of the reduction potentials of the remaining bifurcating FAD; this significantly stabilizes the otherwise very unstable semiquinone state, which accumulates over the course of reductive titrations with sodium dithionite. Furthermore, reduction of both EtfABs depleted of their electron-transferring FAD by NADH was monophasic with a hyperbolic dependence of reaction rate on the concentration of NADH. On the other hand, NADH reduction of the replete proteins containing the electron-transferring FAD was multiphasic, consisting of a fast phase comparable to that seen with the depleted proteins followed by an intermediate phase that involves significant accumulation of FAD⋅-, again reflecting uncrossing of the half-potentials of the bifurcating FAD. This is then followed by a slow phase that represents the slow reduction of the electron-transferring FAD to FADH-, with reduction of the now fully reoxidized bifurcating FAD by a second equivalent of NADH. We suggest that the crossing and uncrossing of the reduction half-potentials of the bifurcating FAD is due to specific conformational changes that have been structurally characterized.
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Affiliation(s)
- Wayne Vigil
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Jessica Tran
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Xiaoxuan Ge
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California, USA.
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15
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Pillath J, Knaps A, Hille R. Area dose measurements by thermoluminescence dosemeters for environmental monitoring. KERNTECHNIK 2022. [DOI: 10.1515/kern-2003-0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
For more than 25 years, thermoluminescence dosemeters (TLDs) have been used at Research Centre Jülich for the dose determination of photon radiation in environmental monitoring. Dose measurements are performed in six-month exposure intervals at 78 measuring locations in total at the outer fence and some additional locations inside and outside the research centre. Long-term variations in natural background radiation are analysed in comparison with climate data and the local conditions near the measuring locations and discussed with a view to determining the area-specific parameters. Taking the special conditions of Research Centre Jülich into account, the problems relating to the detection limit of 0.1 mSv/a, stipulated in the guideline for the emission and immission monitoring of nuclear facilities, are considered in more detail compared to natural background radiation.
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Affiliation(s)
- J. Pillath
- Forschungszentrum Jülich GmbH, Geschäftsbereich Sicherheit und Strahlenschutz, Leo-Brandt-Straße , Jülich , Germany
| | - A. Knaps
- Forschungszentrum Jülich GmbH, Geschäftsbereich Sicherheit und Strahlenschutz, Leo-Brandt-Straße , Jülich , Germany
| | - R. Hille
- Forschungszentrum Jülich GmbH, Geschäftsbereich Sicherheit und Strahlenschutz, Leo-Brandt-Straße , Jülich , Germany
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16
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Hakopian S, Niks D, Hille R. The air-inactivation of formate dehydrogenase FdsDABG from Cupriavidus necator. J Inorg Biochem 2022; 231:111788. [DOI: 10.1016/j.jinorgbio.2022.111788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/15/2022]
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17
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Blaha G, Young T, Niks D, Hakopian S, Tam T, Yu X, Hille R. Crystallographic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsDABG from
Cupriavidus necator. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.02775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Heinemann K, Hille R. Determination of soil contamination by the CORAD system in comparison with other methods / Bestimmung der Bodenkontamination mit dem CORAD-System ım Vergleich mit anderen Methoden. KERNTECHNIK 2021. [DOI: 10.1515/kern-1996-622-316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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19
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Heinemann K, Hille R. Time-dependent specific 90Sr and 137Cs soil radioactivity in the area of the Research Centre Jülich / Zeitabhängigkeit der spezifischen 90Sr- und der 137Cs-Gehalte des Bodens im Bereich des Forschungszentrums Jülich. KERNTECHNIK 2021. [DOI: 10.1515/kern-2000-650409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Vigil W, Niks D, Franz-Badur S, Chowdhury N, Buckel W, Hille R. Spectral deconvolution of redox species in the crotonyl-CoA-dependent NADH:ferredoxin oxidoreductase from Megasphaera elsdenii. A flavin-dependent bifurcating enzyme. Arch Biochem Biophys 2021; 701:108793. [PMID: 33587905 PMCID: PMC8040930 DOI: 10.1016/j.abb.2021.108793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022]
Abstract
We have undertaken a spectral deconvolution of the three FADs of EtfAB/bcd to the spectral changes seen in the course of reduction, including the spectrally distinct anionic and neutral semiquinone states of electron-transferring and bcd flavins. We also demonstrate that, unlike similar systems, no charge-transfer complex is observed on titration of the reduced M. elsdenii EtfAB with NAD+. Finally, and significantly, we find that removal of the et FAD from EtfAB results in an uncrossing of the half-potentials of the bifurcating FAD that remains in the protein, as reflected in the accumulation of substantial FAD•− in the course of reductive titrations of the depleted EtfAB with sodium dithionite.
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Affiliation(s)
- Wayne Vigil
- Department of Biochemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | - Sophie Franz-Badur
- Department of Biochemistry, University of California, Riverside, Riverside, CA, 92521, USA
| | | | - Wolfgang Buckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Fachbereich Biologie and Synmikro, Philipps-Universität, Marburg, Germany
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, CA, 92521, USA.
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21
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Young T, Niks D, Hakopian S, Tam TK, Yu X, Hille R, Blaha GM. Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator. J Biol Chem 2020; 295:6570-6585. [PMID: 32249211 PMCID: PMC7212643 DOI: 10.1074/jbc.ra120.013264] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/30/2020] [Indexed: 01/07/2023] Open
Abstract
Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD+-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH-, initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD+ binding in proper NADH dehydrogenases.
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Affiliation(s)
- Tynan Young
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Sheron Hakopian
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Timothy K. Tam
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Xuejun Yu
- Department of Biochemistry, University of California, Riverside, California 92521
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521, To whom correspondence may be addressed:
Dept. of Biochemistry, University of California, Riverside, 900 University Ave., Boyce Hall 2404, Riverside, CA 92521. Tel.:
951-827-6354; E-mail:
| | - Gregor M. Blaha
- Department of Biochemistry, University of California, Riverside, California 92521, To whom correspondence may be addressed:
Dept. of Biochemistry, University of California, Riverside, 900 University Ave., Boyce Hall 5489, Riverside, CA 92521. Tel.:
951-827-3832; Fax:
951-827-4294; E-mail:
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22
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Blaha G, Young T, Niks D, Hakopian S, Tam TK, Yu X, Hille R. The cytosolic formate dehydrogenase FdsABG from
Cupriavidus necator
. Crystal structure of the FdsBG fragment which is responsible for the oxidative half‐reaction. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.09333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Kalimuthu P, Petitgenet M, Niks D, Dingwall S, Harmer JR, Hille R, Bernhardt PV. The oxidation-reduction and electrocatalytic properties of CO dehydrogenase from Oligotropha carboxidovorans. Biochim Biophys Acta Bioenerg 2019; 1861:148118. [PMID: 31734195 DOI: 10.1016/j.bbabio.2019.148118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/19/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023]
Abstract
CO dehydrogenase (CODH) from the Gram-negative bacterium Oligotropha carboxidovorans is a complex metalloenzyme from the xanthine oxidase family of molybdenum-containing enzymes, bearing a unique binuclear Mo-S-Cu active site in addition to two [2Fe-2S] clusters (FeSI and FeSII) and one equivalent of FAD. CODH catalyzes the oxidation of CO to CO2 with the concomitant introduction of reducing equivalents into the quinone pool, thus enabling the organism to utilize CO as sole source of both carbon and energy. Using a variety of EPR monitored redox titrations and spectroelectrochemistry, we report the redox potentials of CO dehydrogenase at pH 7.2 namely MoVI/V, MoV/IV, FeSI2+/+, FeSII2+/+, FAD/FADH and FADH/FADH-. These potentials are systematically higher than the corresponding potentials seen for other members of the xanthine oxidase family of Mo enzymes, and are in line with CODH utilising the higher potential quinone pool as an electron acceptor instead of pyridine nucleotides. CODH is also active when immobilised on a modified Au working electrode as demonstrated by cyclic voltammetry in the presence of CO.
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Affiliation(s)
- Palraj Kalimuthu
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Mélanie Petitgenet
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
| | - Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Stephanie Dingwall
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
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24
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Walker LM, Li B, Niks D, Hille R, Elliott SJ. Deconvolution of reduction potentials of formate dehydrogenase from Cupriavidus necator. J Biol Inorg Chem 2019; 24:889-898. [PMID: 31463592 DOI: 10.1007/s00775-019-01701-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022]
Abstract
The formate dehydrogenase enzyme from Cupriavidus necator (FdsABG) carries out the two-electron oxidation of formate to CO2, but is also capable of reducing CO2 back to formate, a potential biofuel. FdsABG is a heterotrimeric enzyme that performs this transformation using nine redox-active cofactors: a bis(molybdopterin guanine dinucleotide) (bis-MGD) at the active site coupled to seven iron-sulfur clusters, and one equivalent of flavin mononucleotide (FMN). To better understand the pathway of electron flow in FdsABG, the reduction potentials of the various cofactors were examined through direct electrochemistry. Given the redundancy of cofactors, a truncated form of the FdsA subunit was developed that possesses only the bis-MGD active site and a singular [4Fe-4S] cluster. Electrochemical characterization of FdsABG compared to truncated FdsA shows that the measured reduction potentials are remarkably similar despite the truncation with two observable features at - 265 mV and - 455 mV vs SHE, indicating that the voltammetry of the truncated enzyme is representative of the reduction potentials of the intact heterotrimer. By producing truncated FdsA without the necessary maturation factors required for bis-MGD insertion, a form of the truncated FdsA that possesses only the [4Fe-4S] was produced, which gives a single voltammetric feature at - 525 mV, allowing the contributions of the molybdenum cofactor to be associated with the observed feature at - 265 mV. This method allowed for the deconvolution of reduction potentials for an enzyme with highly complex cofactor content to know more about the thermodynamic landscape of catalysis.
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Affiliation(s)
- Lindsey M Walker
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Bin Li
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA.
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25
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Yu X, Niks D, Ge X, Liu H, Hille R, Mulchandani A. Synthesis of Formate from CO 2 Gas Catalyzed by an O 2-Tolerant NAD-Dependent Formate Dehydrogenase and Glucose Dehydrogenase. Biochemistry 2019; 58:1861-1868. [PMID: 30839197 DOI: 10.1021/acs.biochem.8b01301] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct biocatalytic conversion of CO2 to formic acid is an attractive means of reversibly storing energy in chemical bonds. Formate dehydrogenases (FDHs) are a heterogeneous group of enzymes that catalyze the oxidation of formic acid to carbon dioxide, generating two protons and two electrons. Several FDHs have recently been reported to catalyze the reverse reaction, i.e., the reduction of carbon dioxide to formic acid, under appropriate conditions. The main challenges with these enzymes are relatively low rates of CO2 reduction and high oxygen sensitivity. Our earlier studies (Yu et al. (2017) J. Biol. Chem. 292, 16872-16879) have shown that the FdsABG formate dehydrogenase from Cupriavidus necator is able to effectively catalyze the reduction of CO2, using NADH as a source of reducing equivalents, with a good oxygen tolerance. On the basis of this result, we have developed a highly thermodynamically efficient and cost-effective biocatalytic process for the transformation of CO2 to formic acid using FdsABG. We have cloned the full-length soluble formate dehydrogenase (FdsABG) from C. necator and expressed it in Escherichia coli with a His-tag fused to the N terminus of the FdsG subunit; this overexpression system has greatly simplified the FdsABG purification process. Importantly, we have also combined this recombinant C. necator FdsABG with another enzyme, glucose dehydrogenase, for continuous regeneration of NADH for CO2 reduction and demonstrated that the combined system is highly effective in reducing CO2 to formate. The results indicate that this system shows significant promise for the future development of an enzyme-based system for the industrial reduction of CO2.
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26
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Niks D, Hille R. Molybdenum- and tungsten-containing formate dehydrogenases and formylmethanofuran dehydrogenases: Structure, mechanism, and cofactor insertion. Protein Sci 2019; 28:111-122. [PMID: 30120799 PMCID: PMC6295890 DOI: 10.1002/pro.3498] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022]
Abstract
An overview is provided of the molybdenum- and tungsten-containing enzymes that catalyze the interconversion of formate and CO2 , focusing on common structural and mechanistic themes, as well as a consideration of the manner in which the mature Mo- or W-containing cofactor is inserted into apoprotein.
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Affiliation(s)
- Dimitri Niks
- Department of BiochemistryUniversity of CaliforniaRiverside
| | - Russ Hille
- Department of BiochemistryUniversity of CaliforniaRiverside
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27
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Abstract
Two factors, climate change brought on by rising atmospheric CO2 levels and the accelerating shift toward renewable energy sources, have together worked to heighten interest in understanding how biological catalysts so effectively bring about the reduction of CO2 to formate, with potential applications for both bioremediation and energy storage. Most metal-dependent formate dehydrogenases, containing either molybdenum or tungsten in their active sites, function physiologically in the direction of formate oxidation to CO2, but it has become clear that many, if not all, are also effective in catalyzing the reverse reaction. In this chapter, we describe methods for isolating and characterizing these enzymes.
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Affiliation(s)
- Dimitri Niks
- Department of Biochemistry, University of California, Riverside, CA, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, CA, United States.
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28
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Peters JW, Beratan DN, Bothner B, Dyer RB, Harwood CS, Heiden ZM, Hille R, Jones AK, King PW, Lu Y, Lubner CE, Minteer SD, Mulder DW, Raugei S, Schut GJ, Seefeldt LC, Tokmina-Lukaszewska M, Zadvornyy OA, Zhang P, Adams MW. A new era for electron bifurcation. Curr Opin Chem Biol 2018; 47:32-38. [PMID: 30077080 DOI: 10.1016/j.cbpa.2018.07.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/16/2018] [Accepted: 07/18/2018] [Indexed: 11/17/2022]
Abstract
Electron bifurcation, or the coupling of exergonic and endergonic oxidation-reduction reactions, was discovered by Peter Mitchell and provides an elegant mechanism to rationalize and understand the logic that underpins the Q cycle of the respiratory chain. Thought to be a unique reaction of respiratory complex III for nearly 40 years, about a decade ago Wolfgang Buckel and Rudolf Thauer discovered that flavin-based electron bifurcation is also an important component of anaerobic microbial metabolism. Their discovery spawned a surge of research activity, providing a basis to understand flavin-based bifurcation, forging fundamental parallels with Mitchell's Q cycle and leading to the proposal of metal-based bifurcating enzymes. New insights into the mechanism of electron bifurcation provide a foundation to establish the unifying principles and essential elements of this fascinating biochemical phenomenon.
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Affiliation(s)
- John W Peters
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States; Pacific Northwest National Laboratory, Richland, WA 99352, United States.
| | - David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, NC 27708, United States; Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Zachariah M Heiden
- Department of Chemistry, Washington State University, Pullman WA 99163, United States
| | - Russ Hille
- Biochemistry Department, University of California at Riverside, Riverside, CA 92521, United States
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Paul W King
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Yi Lu
- Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Carolyn E Lubner
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - David W Mulder
- National Renewable Energy Laboratory, Golden, CO 8040, United States
| | - Simone Raugei
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States; Pacific Northwest National Laboratory, Richland, WA 99352, United States
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Lance C Seefeldt
- Pacific Northwest National Laboratory, Richland, WA 99352, United States; Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, United States
| | | | - Oleg A Zadvornyy
- Institute of Biological Chemistry, Washington State University, Pullman WA 99163, United States
| | - Peng Zhang
- Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Michael Ww Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, United States
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29
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Watson C, Niks D, Hille R, Vieira M, Schoepp-Cothenet B, Marques AT, Romão MJ, Santos-Silva T, Santini JM. Electron transfer through arsenite oxidase: Insights into Rieske interaction with cytochrome c. Biochim Biophys Acta Bioenerg 2017; 1858:865-872. [PMID: 28801050 PMCID: PMC5574378 DOI: 10.1016/j.bbabio.2017.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/05/2017] [Accepted: 08/05/2017] [Indexed: 11/25/2022]
Abstract
Arsenic is a widely distributed environmental toxin whose presence in drinking water poses a threat to >140 million people worldwide. The respiratory enzyme arsenite oxidase from various bacteria catalyses the oxidation of arsenite to arsenate and is being developed as a biosensor for arsenite. The arsenite oxidase from Rhizobium sp. str. NT-26 (a member of the Alphaproteobacteria) is a heterotetramer consisting of a large catalytic subunit (AioA), which contains a molybdenum centre and a 3Fe-4S cluster, and a small subunit (AioB) containing a Rieske 2Fe-2S cluster. Stopped-flow spectroscopy and isothermal titration calorimetry (ITC) have been used to better understand electron transfer through the redox-active centres of the enzyme, which is essential for biosensor development. Results show that oxidation of arsenite at the active site is extremely fast with a rate of >4000s-1 and reduction of the electron acceptor is rate-limiting. An AioB-F108A mutation results in increased activity with the artificial electron acceptor DCPIP and decreased activity with cytochrome c, which in the latter as demonstrated by ITC is not due to an effect on the protein-protein interaction but instead to an effect on electron transfer. These results provide further support that the AioB F108 is important in electron transfer between the Rieske subunit and cytochrome c and its absence in the arsenite oxidases from the Betaproteobacteria may explain the inability of these enzymes to use this electron acceptor.
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Affiliation(s)
- Cameron Watson
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, United Kingdom
| | - Dimitri Niks
- Department of Biochemistry, University of California; Riverside, Riverside, CA 92521, USA
| | - Russ Hille
- Department of Biochemistry, University of California; Riverside, Riverside, CA 92521, USA
| | - Marta Vieira
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | | | - Alexandra T Marques
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | - Maria João Romão
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | - Teresa Santos-Silva
- UCIBIO-Requimte, Department of Chemistry, Faculty of Sciences and Technology, Universidade Nova de Lisboa, Portugal
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, WC1E 6BT, United Kingdom.
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30
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Yu X, Niks D, Mulchandani A, Hille R. Efficient reduction of CO 2 by the molybdenum-containing formate dehydrogenase from Cupriavidus necator ( Ralstonia eutropha). J Biol Chem 2017; 292:16872-16879. [PMID: 28784661 DOI: 10.1074/jbc.m117.785576] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 08/03/2017] [Indexed: 11/06/2022] Open
Abstract
The ability of the FdsABG formate dehydrogenase from Cupriavidus necator (formerly known as Ralstonia eutropha) to catalyze the reverse of the physiological reaction, the reduction of CO2 to formate utilizing NADH as electron donor, has been investigated. Contrary to previous studies of this enzyme, we demonstrate that it is in fact effective in catalyzing the reverse reaction with a kcat of 11 ± 0.4 s-1 We also quantify the stoichiometric accumulation of formic acid as the product of the reaction and demonstrate that the observed kinetic parameters for catalysis in the forward and reverse reactions are thermodynamically consistent, complying with the expected Haldane relationships. Finally, we demonstrate the reaction conditions necessary for gauging the ability of a given formate dehydrogenase or other CO2-utilizing enzyme to catalyze the reverse direction to avoid false negative results. In conjunction with our earlier studies on the reaction mechanism of this enzyme and on the basis of the present work, we conclude that all molybdenum- and tungsten-containing formate dehydrogenases and related enzymes likely operate via a simple hydride transfer mechanism and are effective in catalyzing the reversible interconversion of CO2 and formate under the appropriate experimental conditions.
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Affiliation(s)
- Xuejun Yu
- From the Departments of Chemical and Environmental Engineering.,Bioengineering Engineering and
| | | | - Ashok Mulchandani
- From the Departments of Chemical and Environmental Engineering, .,Materials Science and Engineering Program, University of California, Riverside, California 92521
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31
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32
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Niks D, Duvvuru J, Escalona M, Hille R. Spectroscopic and Kinetic Properties of the Molybdenum-containing, NAD+-dependent Formate Dehydrogenase from Ralstonia eutropha. J Biol Chem 2015; 291:1162-74. [PMID: 26553877 DOI: 10.1074/jbc.m115.688457] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 11/06/2022] Open
Abstract
We have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, NAD(+)-dependent FdsABG formate dehydrogenase from Ralstonia eutropha. We confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). We have also characterized the electron paramagnetic resonance signal of the molybdenum center in its Mo(V) state and demonstrated the direct transfer of the substrate Cα hydrogen to the molybdenum center in the course of the reaction. Varying temperature, microwave power, and level of enzyme reduction, we are able to clearly identify the electron paramagnetic resonance signals for four of the iron/sulfur clusters of the enzyme and find suggestive evidence for two others; we observe a magnetic interaction between the molybdenum center and one of the iron/sulfur centers, permitting assignment of this signal to a specific iron/sulfur cluster in the enzyme. In light of recent advances in our understanding of the structure of the molybdenum center, we propose a reaction mechanism involving direct hydride transfer from formate to a molybdenum-sulfur group of the molybdenum center.
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Affiliation(s)
- Dimitri Niks
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
| | - Jayant Duvvuru
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
| | - Miguel Escalona
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
| | - Russ Hille
- From the Department of Biochemistry, University of California, Riverside, Riverside, California 92521
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33
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Wang J, Krizowski S, Fischer-Schrader K, Niks D, Tejero J, Sparacino-Watkins C, Wang L, Ragireddy V, Frizzell S, Kelley EE, Zhang Y, Basu P, Hille R, Schwarz G, Gladwin MT. Sulfite Oxidase Catalyzes Single-Electron Transfer at Molybdenum Domain to Reduce Nitrite to Nitric Oxide. Antioxid Redox Signal 2015; 23:283-94. [PMID: 25314640 PMCID: PMC4523048 DOI: 10.1089/ars.2013.5397] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
AIMS Recent studies suggest that the molybdenum enzymes xanthine oxidase, aldehyde oxidase, and mARC exhibit nitrite reductase activity at low oxygen pressures. However, inhibition studies of xanthine oxidase in humans have failed to block nitrite-dependent changes in blood flow, leading to continued exploration for other candidate nitrite reductases. Another physiologically important molybdenum enzyme—sulfite oxidase (SO)—has not been extensively studied. RESULTS Using gas-phase nitric oxide (NO) detection and physiological concentrations of nitrite, SO functions as nitrite reductase in the presence of a one-electron donor, exhibiting redox coupling of substrate oxidation and nitrite reduction to form NO. With sulfite, the physiological substrate, SO only facilitates one turnover of nitrite reduction. Studies with recombinant heme and molybdenum domains of SO indicate that nitrite reduction occurs at the molybdenum center via coupled oxidation of Mo(IV) to Mo(V). Reaction rates of nitrite to NO decreased in the presence of a functional heme domain, mediated by steric and redox effects of this domain. Using knockdown of all molybdopterin enzymes and SO in fibroblasts isolated from patients with genetic deficiencies of molybdenum cofactor and SO, respectively, SO was found to significantly contribute to hypoxic nitrite signaling as demonstrated by activation of the canonical NO-sGC-cGMP pathway. INNOVATION Nitrite binds to and is reduced at the molybdenum site of mammalian SO, which may be allosterically regulated by heme and molybdenum domain interactions, and contributes to the mammalian nitrate-nitrite-NO signaling pathway in human fibroblasts. CONCLUSION SO is a putative mammalian nitrite reductase, catalyzing nitrite reduction at the Mo(IV) center.
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Affiliation(s)
- Jun Wang
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Sabina Krizowski
- 3 Department of Biochemistry, Center for Molecular Medicine, Institute of Biochemistry, Cologne University , Cologne, Germany
| | - Katrin Fischer-Schrader
- 3 Department of Biochemistry, Center for Molecular Medicine, Institute of Biochemistry, Cologne University , Cologne, Germany
| | - Dimitri Niks
- 4 Department of Biochemistry, University of California at Riverside , Riverside, California
| | - Jesús Tejero
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Courtney Sparacino-Watkins
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Ling Wang
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Venkata Ragireddy
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Sheila Frizzell
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Eric E Kelley
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,5 Department of Anesthesiology, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Yingze Zhang
- 2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Partha Basu
- 6 Department of Chemistry and Biochemistry, Duquesne University , Pittsburgh, Pennsylvania
| | - Russ Hille
- 4 Department of Biochemistry, University of California at Riverside , Riverside, California
| | - Guenter Schwarz
- 3 Department of Biochemistry, Center for Molecular Medicine, Institute of Biochemistry, Cologne University , Cologne, Germany
| | - Mark T Gladwin
- 1 Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh , Pittsburgh, Pennsylvania.,2 Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania
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34
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Hall J, Reschke S, Cao H, Leimkühler S, Hille R. The reductive half-reaction of xanthine dehydrogenase from Rhodobacter capsulatus: the role of Glu232 in catalysis. J Biol Chem 2014; 289:32121-32130. [PMID: 25258317 DOI: 10.1074/jbc.m114.603456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The kinetic properties of an E232Q variant of the xanthine dehydrogenase from Rhodobacter capsulatus have been examined to ascertain whether Glu(232) in wild-type enzyme is protonated or unprotonated in the course of catalysis at neutral pH. We find that kred, the limiting rate constant for reduction at high [xanthine], is significantly compromised in the variant, a result that is inconsistent with Glu(232) being neutral in the active site of the wild-type enzyme. A comparison of the pH dependence of both kred and kred/Kd from reductive half-reaction experiments between wild-type and enzyme and the E232Q variant suggests that the ionized Glu(232) of wild-type enzyme plays an important role in catalysis by discriminating against the monoanionic form of substrate, effectively increasing the pKa of substrate by two pH units and ensuring that at physiological pH the neutral form of substrate predominates in the Michaelis complex. A kinetic isotope study of the wild-type R. capsulatus enzyme indicates that, as previously determined for the bovine and chicken enzymes, product release is principally rate-limiting in catalysis. The disparity in rate constants for the chemical step of the reaction and product release, however, is not as great in the bacterial enzyme as compared with the vertebrate forms. The results indicate that the bacterial and bovine enzymes catalyze the chemical step of the reaction to the same degree and that the faster turnover observed with the bacterial enzyme is due to a faster rate constant for product release than is seen with the vertebrate enzyme.
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Affiliation(s)
- James Hall
- Department of Biochemistry, University of California, Riverside, California 92521 and
| | - Stefan Reschke
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University Potsdam, 14476 Potsdam, Germany
| | - Hongnan Cao
- Department of Biochemistry, University of California, Riverside, California 92521 and
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University Potsdam, 14476 Potsdam, Germany
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521 and.
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35
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Schwarz G, Krizowski S, Wang J, Niks D, Sparacino-Watkins C, Hille R, Gladwin M. Intramolecular electron transfer controls nitrite reduction in molybdenum-containing sulfite oxidase. Nitric Oxide 2014. [DOI: 10.1016/j.niox.2014.09.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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36
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Lee MCI, Velayutham M, Komatsu T, Hille R, Zweier JL. Measurement and characterization of superoxide generation from xanthine dehydrogenase: a redox-regulated pathway of radical generation in ischemic tissues. Biochemistry 2014; 53:6615-23. [PMID: 25243829 PMCID: PMC4204892 DOI: 10.1021/bi500582r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The enzyme xanthine oxidoreductase
(XOR) is an important source
of oxygen free radicals and related postischemic injury. Xanthine
dehydrogenase (XDH), the major form of XOR in tissues, can be converted
to xanthine oxidase (XO) by oxidation of sulfhydryl residues or by
proteolysis. The conversion of XDH to XO has been assumed to be required
for radical generation and tissue injury. It is also possible that
XDH could generate significant quantities of superoxide, •O2–, for cellular signaling or injury;
however, this possibility and its potential ramifications have not
been previously considered. To unambiguously determine if XDH can
be a significant source of •O2–, experiments were performed to measure and characterize •O2– generation using XDH from chicken
liver that is locked in the dehydrogenase conformation. Electron paramagnetic
resonance spin trapping experiments with 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline-N-oxide demonstrated that XDH in the presence of xanthine
produces significant amounts of •O2–. NAD+ and NADH inhibited the generation
of •O2– from XDH in
a dose-dependent manner, with NAD+ exhibiting stronger
inhibition than NADH at low physiological concentrations. Decreased
amounts of NAD+ and NADH, which occur during and following
tissue ischemia, enhanced the generation of •O2– from XDH in the presence of xanthine.
It was observed that XDH-mediated oxygen radical generation markedly
depressed Ca2+-ATPase activity of isolated sarcoplasmic
reticulum vesicles from cardiac muscle, and this was modulated by
NAD+ and NADH. Thus, XDH can be an important redox-regulated
source of •O2– generation
in ischemic tissue, and conversion to XO is not required to activate
radical formation and subsequent tissue injury.
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Affiliation(s)
- Masaichi-Chang-Il Lee
- Center for Biomedical EPR Spectroscopy and Imaging, The Davis Heart and Lung Research Institute, and Division of Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University Wexner Medical Center , Columbus, Ohio 43210, United States
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37
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Abstract
Xanthine oxidase catalyzes the sequential hydroxylation of hypoxanthine to uric acid via xanthine as intermediate. Deposition of crystals of the catalytic product uric acid or its monosodium salt in human joints with accompanying joint inflammation is the major cause of gout. Natural flavonoids are attractive leads for rational design of preventive and therapeutic xanthine oxidase inhibitors due to their beneficial antioxidant, anti-inflammatory, and antiproliferative activities in addition to their micromolar inhibitory activities toward xanthine oxidase. We determined the first complex X-ray structure of mammalian xanthine oxidase with the natural flavonoid inhibitor quercetin at 2.0 Å resolution. The inhibitor adopts a single orientation with its benzopyran moiety sandwiched between Phe 914 and Phe 1009 and ring B pointing toward the solvent channel leading to the molybdenum active center. The favorable steric complementarity of the conjugated three-ring structure of quercetin with the active site and specific hydrogen-bonding interactions of exocyclic hydroxy groups with catalytically relevant residues Arg 880 and Glu 802 correlate well with a previously reported structure-activity relationship of flavonoid inhibitors of xanthine oxidase. The current complex provides a structural basis for the rational design of flavonoid-type inhibitors against xanthine oxidase useful for the treatment of hyperuricemia, gout, and inflammatory disease states.
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Affiliation(s)
- Hongnan Cao
- Department of Biochemistry, University of California , Riverside, California 92521, United States
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38
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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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39
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Anderson RF, Shinde SS, Hille R, Rothery RA, Weiner JH, Rajagukguk S, Maklashina E, Cecchini G. Electron-transfer pathways in the heme and quinone-binding domain of complex II (succinate dehydrogenase). Biochemistry 2014; 53:1637-46. [PMID: 24559074 PMCID: PMC3985935 DOI: 10.1021/bi401630m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Single electron transfers have been
examined in complex II (succinate:ubiquinone
oxidoreductase) by the method of pulse radiolysis. Electrons are introduced
into the enzyme initially at the [3Fe–4S] and ubiquinone sites
followed by intramolecular equilibration with the b heme of the enzyme. To define thermodynamic and other controlling
parameters for the pathways of electron transfer in complex II, site-directed
variants were constructed and analyzed. Variants at SdhB-His207 and
SdhB-Ile209 exhibit significantly perturbed electron transfer between
the [3Fe–4S] cluster and ubiquinone. Analysis of the data using
Marcus theory shows that the electronic coupling constants for wild-type
and variant enzyme are all small, indicating that electron transfer
occurs by diabatic tunneling. The presence of the ubiquinone is necessary
for efficient electron transfer to the heme, which only slowly equilibrates
with the [3Fe–4S] cluster in the absence of the quinone.
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Affiliation(s)
- Robert F Anderson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland , Auckland 1142, New Zealand
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40
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Cao H, Hall J, Hille R. Substrate orientation and specificity in xanthine oxidase: crystal structures of the enzyme in complex with indole-3-acetaldehyde and guanine. Biochemistry 2014; 53:533-41. [PMID: 24397336 DOI: 10.1021/bi401465u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Xanthine oxidase is a molybdenum-containing hydroxylase that catalyzes the hydroxylation of sp(2)-hybridized carbon centers in a variety of aromatic heterocycles as well as aldehydes. Crystal structures of the oxidase form of the bovine enzyme in complex with a poor substrate indole-3-acetaldehyde and the nonsubstrate guanine have been determined, both at a resolution of 1.6 Å. In each structure, a specific and unambiguous orientation of the substrate in the active site is observed in which the hydroxylatable site is oriented away from the active site molybdenum center. The orientation seen with indole-3-acetaldehyde has the substrate positioned with the indole ring rather than the exocyclic aldehyde nearest the molybdenum center, indicating that the substrate must rotate some 30° in the enzyme active site to permit hydroxylation of the aldehyde group (as observed experimentally), accounting for the reduced reactivity of the enzyme toward this substrate. The principal product of hydroxylation of indole-3-acetaldehyde by the bovine enzyme is confirmed to be indole-3-carboxylic acid based on its characteristic UV-vis spectrum, and the kinetics of enzyme reduction are reported. With guanine, the dominant orientation seen crystallographically has the C-8 position that might be hydroxylated pointed away from the active site molybdenum center, in a configuration resembling that seen previously with hypoxanthine (a substrate that is effectively hydroxylated at position 2). The ∼180° reorientation required to permit reaction is sterically prohibited, indicating that substrate (mis)orientation in the active site is a major factor precluding formation of the highly mutagenic 8-hydroxyguanine.
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Affiliation(s)
- Hongnan Cao
- Department of Biochemistry, University of California , Riverside, California 92521, United States
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41
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Shanmugam M, Wilcoxen J, Habel-Rodriguez D, Cutsail GE, Kirk ML, Hoffman BM, Hille R. (13)C and (63,65)Cu ENDOR studies of CO dehydrogenase from Oligotropha carboxidovorans. Experimental evidence in support of a copper-carbonyl intermediate. J Am Chem Soc 2013; 135:17775-82. [PMID: 24147852 DOI: 10.1021/ja406136f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here an ENDOR study of an S = 1/2 intermediate state trapped during reduction of the binuclear Mo/Cu enzyme CO dehydrogenase by CO. ENDOR spectra of this state confirm that the (63,65)Cu nuclei exhibits strong and almost entirely isotropic coupling to the unpaired electron, show that this coupling atypically has a positive sign, aiso = +148 MHz, and indicate an apparently undetectably small quadrupolar coupling. When the intermediate is generated using (13)CO, coupling to the (13)C is observed, with aiso = +17.3 MHz. A comparison with the couplings seen in related, structurally assigned Mo(V) species from xanthine oxidase, in conjunction with complementary computational studies, leads us to conclude that the intermediate contains a partially reduced Mo(V)/Cu(I) center with CO bound at the copper. Our results provide strong experimental support for a reaction mechanism that proceeds from a comparable complex of CO with fully oxidized Mo(VI)/Cu(I) enzyme.
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Affiliation(s)
- Muralidharan Shanmugam
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208-3113, United States
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42
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Reschke S, Niks D, Wilson H, Sigfridsson KGV, Haumann M, Rajagopalan KV, Hille R, Leimkühler S. Effect of Exchange of the Cysteine Molybdenum Ligand with Selenocysteine on the Structure and Function of the Active Site in Human Sulfite Oxidase. Biochemistry 2013; 52:8295-303. [DOI: 10.1021/bi4008512] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Reschke
- Department
of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Dimitri Niks
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Heather Wilson
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | | | - Michael Haumann
- Institute
of Experimental Physics, Free University Berlin, 14195 Berlin, Germany
| | - K. V. Rajagopalan
- Department
of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Russ Hille
- Department
of Biochemistry, University of California, Riverside, California 92521, United States
| | - Silke Leimkühler
- Department
of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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43
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Wilcoxen J, Hille R. The hydrogenase activity of the molybdenum/copper-containing carbon monoxide dehydrogenase of Oligotropha carboxidovorans. J Biol Chem 2013; 288:36052-60. [PMID: 24165123 DOI: 10.1074/jbc.m113.522441] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The reaction of the air-tolerant CO dehydrogenase from Oligotropha carboxidovorans with H2 has been examined. Like the Ni-Fe CO dehydrogenase, the enzyme can be reduced by H2 with a limiting rate constant of 5.3 s(-1) and a dissociation constant Kd of 525 μM; both kred and kred/Kd, reflecting the breakdown of the Michaelis complex and the reaction of free enzyme with free substrate in the low [S] regime, respectively, are largely pH-independent. During the reaction with H2, a new EPR signal arising from the Mo/Cu-containing active site of the enzyme is observed which is distinct from the signal seen when the enzyme is reduced by CO, with greater g anisotropy and larger hyperfine coupling to the active site (63,65)Cu. The signal also exhibits hyperfine coupling to at least two solvent-exchangeable protons of bound substrate that are rapidly exchanged with solvent. Proton coupling is also evident in the EPR signal seen with the dithionite-reduced native enzyme, and this coupling is lost in the presence of bicarbonate. We attribute the coupled protons in the dithionite-reduced enzyme to coordinated water at the copper site in the native enzyme and conclude that bicarbonate is able to displace this water from the copper coordination sphere. On the basis of our results, a mechanism for H2 oxidation is proposed which involves initial binding of H2 to the copper of the binuclear center, displacing the bound water, followed by sequential deprotonation through a copper-hydride intermediate to reduce the binuclear center.
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Affiliation(s)
- Jarett Wilcoxen
- From the Department of Biochemistry, University of California, Riverside, California 92521
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44
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Appel AM, Bercaw JE, Bocarsly AB, Dobbek H, DuBois DL, Dupuis M, Ferry JG, Fujita E, Hille R, Kenis PJA, Kerfeld CA, Morris RH, Peden CHF, Portis AR, Ragsdale SW, Rauchfuss TB, Reek JNH, Seefeldt LC, Thauer RK, Waldrop GL. Frontiers, opportunities, and challenges in biochemical and chemical catalysis of CO2 fixation. Chem Rev 2013; 113:6621-58. [PMID: 23767781 PMCID: PMC3895110 DOI: 10.1021/cr300463y] [Citation(s) in RCA: 1262] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Aaron M. Appel
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - John E. Bercaw
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Andrew B. Bocarsly
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Daniel L. DuBois
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Michel Dupuis
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - James G. Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, United States
| | - Etsuko Fujita
- Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California 92521, United States
| | - Paul J. A. Kenis
- Department of Chemical and Biochemical Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Cheryl A. Kerfeld
- DOE Joint Genome Institute, 2800 Mitchell Drive Walnut Creek, California 94598, United States, and Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall Berkeley, California 94720, United States
| | - Robert H. Morris
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Charles H. F. Peden
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Archie R. Portis
- Departments of Crop Sciences and Plant Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Stephen W. Ragsdale
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas B. Rauchfuss
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Joost N. H. Reek
- van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lance C. Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Rudolf K. Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl von Frisch Strasse 10, D-35043 Marburg, Germany
| | - Grover L. Waldrop
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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45
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Brugger N, Krause R, Carlen F, Rimensberger C, Hille R, Steck H, Wilhelm M, Seiler C. Effect of lifetime endurance training on left atrial mechanical function and on the risk of atrial fibrillation. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht308.1907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Kümmerle E, Möllmann-Coers M, Pomplun E, Hille R. Fast online system for forecasting environmental impact during an incident. KERNTECHNIK 2013. [DOI: 10.3139/124.100344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
In an incident, the operational control staff needs a rapid general view of the radiological situation in the vicinity of the emission source which is suitable for decision support. Because the measuring team cannot provide sufficient measurements immediately, model calculations based on the available information about the course of the accident are additionally required. Such calculations do not only serve to create an overview of the current situation but can also provide prognoses for several hours. For this purpose, a software system for environmental impact forecasting was developed at Research Centre Jülich, which calculates time-integrated doses as well as ambient gamma dose rates and activity values. The latter can be directly compared with values measured during the incident and consequently can be used to assess the model assumptions.
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Affiliation(s)
- E. Kümmerle
- Geschäftsbereich Sicherheit und Strahlenschutz, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - M. Möllmann-Coers
- Geschäftsbereich Sicherheit und Strahlenschutz, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - E. Pomplun
- Geschäftsbereich Sicherheit und Strahlenschutz, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - R. Hille
- Geschäftsbereich Sicherheit und Strahlenschutz, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
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47
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Dederichs H, Pillath J, Lennartz R, Hill P, Hille R. The time-dependent effect of the biological component of 137Cs soil contamination. KERNTECHNIK 2013. [DOI: 10.3139/124.100189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
In investigations of the long-term development of the population dose in the highly contaminated regions of the Commonwealth of Independence States it was found that the external dose has not decreased as strongly as expected since 1992. Further investigations have shown that, contrary to expectations, no linear correlation can be observed between soil contamination and measured area dose rate. As a contribution towards clarifying these issues, the area dose rate and the soil contamination including the plant fraction were investigated in the Korma district, Belarus. It was found that it is necessary to cover and average over larger areas in order to determine from ground contamination the long-term development of the external dose commitment. This means that for this purpose the introduction of an “effective” surface contamination (sum of mineral and organic contamination components) is necessary. The phenomena observed are described in a model, which permits an analytical calculation of the contamination profile in soil taking migration and transfer effects into account. The differences observed between the measured soil contamination and the resulting external doses or the directly measured dose rate can be explained by the proposed model. Moreover, their long-term development can be calculated. The results show that a time decade after the accident the biological part of the “effective” soil contamination becomes dominant and cannot be neglected.
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Affiliation(s)
- H. Dederichs
- (e-mail: )
- Forschungszentrum Jülich, 52425 Jülich, Germany
| | - J. Pillath
- (e-mail: )
- Forschungszentrum Jülich, 52425 Jülich, Germany
| | - R. Lennartz
- (e-mail: )
- Forschungszentrum Jülich, 52425 Jülich, Germany
| | - P. Hill
- (e-mail: )
- Forschungszentrum Jülich, 52425 Jülich, Germany
| | - R. Hille
- (e-mail: )
- Forschungszentrum Jülich, 52425 Jülich, Germany
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48
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Pushie MJ, Cotelesage JJH, Lyashenko G, Hille R, George GN. X-ray Absorption Spectroscopy of a Quantitatively Mo(V) Dimethyl Sulfoxide Reductase Species. Inorg Chem 2013; 52:2830-7. [DOI: 10.1021/ic301660e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- M. Jake Pushie
- Molecular and Environmental Sciences Research Group, Department of
Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
| | - Julien J. H. Cotelesage
- Molecular and Environmental Sciences Research Group, Department of
Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
- Canadian Light Source, 101 Perimeter Road,
Saskatoon, SK, S7N 0X4, Canada
| | - Ganna Lyashenko
- Department of Biochemistry, University of California-Riverside, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California-Riverside, Riverside, California 92521, United States
| | - Graham N. George
- Molecular and Environmental Sciences Research Group, Department of
Geological Sciences, University of Saskatchewan, SK, S7N 5E2, Canada
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Abstract
A perspective is provided of recent advances in our understanding of molybdenum-containing enzymes other than nitrogenase, a large and diverse group of enzymes that usually (but not always) catalyze oxygen atom transfer to or from a substrate, utilizing a Mo=O group as donor or acceptor. An emphasis is placed on the diversity of protein structure and reaction catalyzed by each of the three major families of these enzymes.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, 1643 Boyce Hall, Riverside, CA 92521, USA.
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50
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Lambeck IC, Fischer-Schrader K, Niks D, Roeper J, Chi JC, Hille R, Schwarz G. Molecular mechanism of 14-3-3 protein-mediated inhibition of plant nitrate reductase. J Biol Chem 2011; 287:4562-71. [PMID: 22170050 DOI: 10.1074/jbc.m111.323113] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
14-3-3 proteins regulate key processes in eukaryotic cells including nitrogen assimilation in plants by tuning the activity of nitrate reductase (NR), the first and rate-limiting enzyme in this pathway. The homodimeric NR harbors three cofactors, each of which is bound to separate domains, thus forming an electron transfer chain. 14-3-3 proteins inhibit NR by binding to a conserved phosphorylation site localized in the linker between the heme and molybdenum cofactor-containing domains. Here, we have investigated the molecular mechanism of 14-3-3-mediated NR inhibition using a fragment of the enzyme lacking the third domain, allowing us to analyze electron transfer from the heme cofactor via the molybdenum center to nitrate. The kinetic behavior of the inhibited Mo-heme fragment indicates that the principal point at which 14-3-3 acts is the electron transfer from the heme to the molybdenum cofactor. We demonstrate that this is not due to a perturbation of the reduction potentials of either the heme or the molybdenum center and conclude that 14-3-3 most likely inhibits nitrate reductase by inducing a conformational change that significantly increases the distance between the two redox-active sites.
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Affiliation(s)
- Iris C Lambeck
- Institute of Biochemistry, Department of Chemistry and Center for Molecular Medicine, University of Cologne, 50674 Cologne, Germany
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