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Kirk ML, Hille R. Spectroscopic Studies of Mononuclear Molybdenum Enzyme Centers. Molecules 2022; 27:4802. [PMID: 35956757 PMCID: PMC9370002 DOI: 10.3390/molecules27154802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 02/06/2023] Open
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
| | - Russ Hille
- Department of Biochemistry, Boyce Hall 1463, University of California, Riverside, CA 82521, USA
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2
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Hille R, Niks D. Application of EPR and related methods to molybdenum-containing enzymes. Methods Enzymol 2022; 666:373-412. [PMID: 35465925 DOI: 10.1016/bs.mie.2022.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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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3
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Kirk ML, Kc K. Molybdenum and Tungsten Cofactors and the Reactions They Catalyze. Met Ions Life Sci 2020; 20:/books/9783110589757/9783110589757-015/9783110589757-015.xml. [PMID: 32851830 PMCID: PMC8176780 DOI: 10.1515/9783110589757-015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The last 20 years have seen a dramatic increase in our mechanistic understanding of the reactions catalyzed by pyranopterin Mo and W enzymes. These enzymes possess a unique cofactor (Moco) that contains a novel ligand in bioinorganic chemistry, the pyranopterin ene-1,2-dithiolate. A synopsis of Moco biosynthesis and structure is presented, along with our current understanding of the role Moco plays in enzymatic catalysis. Oxygen atom transfer (OAT) reactivity is discussed in terms of breaking strong metal-oxo bonds and the mechanism of OAT catalyzed by enzymes of the sulfite oxidase (SO) family that possess dioxo Mo(VI) active sites. OAT reactivity is also discussed in members of the dimethyl sulfoxide (DMSO) reductase family, which possess des-oxo Mo(IV) sites. Finally, we reveal what is known about hydride transfer reactivity in xanthine oxidase (XO) family enzymes and the formate dehydrogenases. The formal hydride transfer reactivity catalyzed by xanthine oxidase family enzymes is complex and cleaves substrate C-H bonds using a mechanism that is distinct from monooxygenases. The chapter primarily highlights developments in the field that have occurred since ~2000, which have contributed to our collective structural and mechanistic understanding of the three canonical pyranopterin Mo enzymes families: XO, SO, and DMSO reductase.
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4
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Djeghader A, Rossotti M, Abdulkarim S, Biaso F, Gerbaud G, Nitschke W, Schoepp-Cothenet B, Soulimane T, Grimaldi S. Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase. Chem Commun (Camb) 2020; 56:9850-9853. [DOI: 10.1039/d0cc03634j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We provide structural and spectroscopic evidence for a molybdenum–phosphate adduct mimicking a proposed reaction intermediate in the active site of a prokaryotic sulfite oxidizing enzyme.
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Affiliation(s)
- Ahmed Djeghader
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
| | | | - Saleh Abdulkarim
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
| | | | | | | | | | - Tewfik Soulimane
- Department of Chemical Sciences and Bernal Institute
- University of Limerick
- Ireland
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5
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Zaripov R, Avdoshenko S, Khairuzhdinov I, Salikhov K, Voronkova V, Weheabby S, Rüffer T, Popov A, Büchner B, Kataev V. Effect of the Diamagnetic Single-Crystalline Host on the Angular-Resolved Electron Nuclear Double Resonance Experiments: Case of Paramagnetic [ nBu 4N] 2[Cu(opba)] Embedded in Diamagnetic [ nBu 4N] 2[Ni(opba)]. J Phys Chem Lett 2019; 10:6565-6571. [PMID: 31593633 DOI: 10.1021/acs.jpclett.9b02523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The electron spin resonance (ESR) and electron nuclear double resonance (ENDOR) spectroscopies are frequently used to determine hyperfine (A) and quadrupole (Q) tensors for the paramagnetic transition-metal complexes, which knowledge enables estimation of the spin density distribution in the complex and the assessment of magnetic exchange pathways in polynuclear molecular networks. The most accurate results can be obtained if paramagnetic complexes are isolated in a single-crystalline diamagnetic host. In this work we were able to detect angle-resolved ESR/ENDOR spectra of the paramagnetic [nBu4N]2[Cu(opba)] (opba = o-phenylenebis(oxamato) complex hosted by the single crystal of diamagnetic [nBu4N]2[Ni(opba)], which allow recovery of A, Q, and g-tensors, all at once. Remarkably, with the aid of theoretical modeling, our data have unveiled the effect of multipositional hosting of the paramagnetic complex in the diamagnetic matrix. This effect can have a profound influence on the data handling and must be carefully considered while interpreting similar experiments.
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Affiliation(s)
- Ruslan Zaripov
- Zavoisky Physical-Technical Institute , FRC Kazan Scientific Center of RAS , 420029 Kazan , Russia
| | - Stanislav Avdoshenko
- Leibniz Institute for Solid State and Materials Research IFW Dresden , D-01171 Dresden , Germany
| | - Iskander Khairuzhdinov
- Zavoisky Physical-Technical Institute , FRC Kazan Scientific Center of RAS , 420029 Kazan , Russia
| | - Kev Salikhov
- Zavoisky Physical-Technical Institute , FRC Kazan Scientific Center of RAS , 420029 Kazan , Russia
| | - Violeta Voronkova
- Zavoisky Physical-Technical Institute , FRC Kazan Scientific Center of RAS , 420029 Kazan , Russia
| | - Saddam Weheabby
- Technische Universität Chemnitz , Fakultät für Naturwissenschaften, Institut für Chemie , Straße der Nationen 62 , D-09111 Chemnitz , Germany
| | - Tobias Rüffer
- Technische Universität Chemnitz , Fakultät für Naturwissenschaften, Institut für Chemie , Straße der Nationen 62 , D-09111 Chemnitz , Germany
| | - Alexey Popov
- Leibniz Institute for Solid State and Materials Research IFW Dresden , D-01171 Dresden , Germany
| | - Bernd Büchner
- Leibniz Institute for Solid State and Materials Research IFW Dresden , D-01171 Dresden , Germany
- Institut für Festkörper- und Materialphysik , Technische Universität Dresden , D-01062 Dresden , Germany
| | - Vladislav Kataev
- Institut für Festkörper- und Materialphysik , Technische Universität Dresden , D-01062 Dresden , Germany
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6
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Enemark JH. Consensus structures of the Mo(v) sites of sulfite-oxidizing enzymes derived from variable frequency pulsed EPR spectroscopy, isotopic labelling and DFT calculations. Dalton Trans 2017. [PMID: 28640289 DOI: 10.1039/c7dt01731f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sulfite-oxidizing enzymes from eukaryotes and prokaryotes have five-coordinate distorted square-pyramidal coordination about the molybdenum atom. The paramagnetic Mo(v) state is easily generated, and over the years four distinct CW EPR spectra have been identified, depending upon enzyme source and the reaction conditions, namely high and low pH (hpH and lpH), phosphate inhibited (Pi) and sulfite (or blocked). Extensive studies of these paramagnetic forms of sulfite-oxidizing enzymes using variable frequency pulsed electron spin echo (ESE) spectroscopy, isotopic labeling and density functional theory (DFT) calculations have led to the consensus structures that are described here. Errors in some of the previously proposed structures are corrected.
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Affiliation(s)
- John H Enemark
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85711, USA.
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7
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Ramirez Cohen M, Mendelman N, Radoul M, Wilson TD, Savelieff MG, Zimmermann H, Kaminker I, Feintuch A, Lu Y, Goldfarb D. Thiolate Spin Population of Type I Copper in Azurin Derived from 33S Hyperfine Coupling. Inorg Chem 2017; 56:6163-6174. [DOI: 10.1021/acs.inorgchem.7b00167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Marie Ramirez Cohen
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Netanel Mendelman
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marina Radoul
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tiffany D. Wilson
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Masha G. Savelieff
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Herbert Zimmermann
- Abteilung Biophysik, Max Planck-Institut für Medizinische Forschung, Heidelberg 69120, Germany
| | - Ilia Kaminker
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akiva Feintuch
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Daniella Goldfarb
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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8
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Eaton SS, Huber K, Elajaili H, McPeak J, Eaton GR, Longobardi LE, Stephan DW. Electron spin relaxation of a boron-containing heterocyclic radical. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 276:7-13. [PMID: 28081476 DOI: 10.1016/j.jmr.2016.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
Preparation of the stable boron-containing heterocyclic phenanthrenedione radical, (C6F5)2B(O2C14H8), by frustrated Lewis pair chemistry has been reported recently. Electron paramagnetic resonance measurements of this radical were made at X-band in toluene:dichloromethane (9:1) from 10 to 293K, in toluene from 180 to 293K and at Q-band at 80K. In well-deoxygenated 0.1mM toluene solution at room temperature hyperfine splittings from 11B, four pairs of 1H, and 5 pairs of 19F contribute to an EPR spectrum with many resolved lines. Observed hyperfine couplings were assigned based on DFT calculations and account for all of the fluorines and protons in the molecule. Rigid lattice g values are gx=2.0053, gy=2.0044, and gz=2.0028. Near the melting point of the solvent 1/Tm is enhanced due to motional averaging of g and A anisotropy. Increasing motion above the melting point enhances 1/T1 due to contributions from tumbling-dependent processes. The overall temperature dependence of 1/T1 from 10 to 293K was modeled with the sum of contributions of a process that is linear in T, a Raman process, spin rotation, and modulation of g anisotropy by molecular tumbling. The EPR measurements are consistent with the description of this compound as a substituted aromatic radical, with relatively small spin density on the boron.
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Affiliation(s)
- Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Kirby Huber
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Hanan Elajaili
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Joseph McPeak
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA.
| | | | - Douglas W Stephan
- University of Toronto, 80 St. George St, Toronto, ON M5S 3H6, Canada
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9
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Maia LB, Moura I, Moura JJ. EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Astashkin AV, Chen L, Elmore BO, Kunwar D, Miao Y, Li H, Poulos TL, Roman LJ, Feng C. Probing the Hydrogen Bonding of the Ferrous-NO Heme Center of nNOS by Pulsed Electron Paramagnetic Resonance. J Phys Chem A 2015; 119:6641-9. [PMID: 26035438 DOI: 10.1021/acs.jpca.5b01804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxidation of L-arginine (L-Arg) to nitric oxide (NO) by NO synthase (NOS) takes place at the heme active site. It is of current interest to study structures of the heme species that activates O2 and transforms the substrate. The NOS ferrous-NO complex is a close mimic of the obligatory ferric (hydro)peroxo intermediate in NOS catalysis. In this work, pulsed electron-nuclear double resonance (ENDOR) spectroscopy was used to probe the hydrogen bonding of the NO ligand in the ferrous-NO heme center of neuronal NOS (nNOS) without a substrate and with L-Arg or N-hydroxy-L-arginine (NOHA) substrates. Unexpectedly, no H-bonding interaction connecting the NO ligand to the active site water molecule or the Arg substrate was detected, in contrast to the results obtained by X-ray crystallography for the Arg-bound nNOS heme domain [Li et al. J. Biol. Inorg. Chem. 2006, 11, 753-768]. The nearby exchangeable proton in both the no-substrate and Arg-containing nNOS samples is located outside the H-bonding range and, on the basis of the obtained structural constraints, can belong to the active site water (or OH). On the contrary, in the NOHA-bound sample, the nearby exchangeable hydrogen forms an H-bond with the NO ligand (on the basis of its distance from the NO ligand and a nonzero isotropic hfi constant), but it does not belong to the active site water molecule because the water oxygen atom (detected by (17)O ENDOR) is too far. This hydrogen should therefore come from the NOHA substrate, which is in agreement with the X-ray crystallography work [Li et al. Biochemistry 2009, 48, 10246-10254]. The nearby nonexchangeable hydrogen atom assigned as H(ε) of Phe584 was detected in all three samples. This hydrogen atom may have a stabilizing effect on the NO ligand and probably determines its position.
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Affiliation(s)
- Andrei V Astashkin
- †Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Li Chen
- ‡College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Bradley O Elmore
- ‡College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Deepak Kunwar
- ‡College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yubin Miao
- ‡College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Huiying Li
- §Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Thomas L Poulos
- §Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Linda J Roman
- ∥Department of Biochemistry, University of Texas Health Science Center in San Antonio, San Antonio, Texas 78229, United States
| | - Changjian Feng
- ‡College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131, United States
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11
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Kappler U, Enemark JH. Sulfite-oxidizing enzymes. J Biol Inorg Chem 2014; 20:253-64. [DOI: 10.1007/s00775-014-1197-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/15/2014] [Indexed: 11/24/2022]
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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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13
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Klein EL, Belaidi AA, Raitsimring AM, Davis AC, Krämer T, Astashkin AV, Neese F, Schwarz G, Enemark JH. Pulsed electron paramagnetic resonance spectroscopy of (33)S-labeled molybdenum cofactor in catalytically active bioengineered sulfite oxidase. Inorg Chem 2014; 53:961-71. [PMID: 24387640 PMCID: PMC3927148 DOI: 10.1021/ic4023954] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molybdenum enzymes contain at least one pyranopterin dithiolate (molybdopterin, MPT) moiety that coordinates Mo through two dithiolate (dithiolene) sulfur atoms. For sulfite oxidase (SO), hyperfine interactions (hfi) and nuclear quadrupole interactions (nqi) of magnetic nuclei (I ≠ 0) near the Mo(V) (d(1)) center have been measured using high-resolution pulsed electron paramagnetic resonance (EPR) methods and interpreted with the help of density functional theory (DFT) calculations. These have provided important insights about the active site structure and the reaction mechanism of the enzyme. However, it has not been possible to use EPR to probe the dithiolene sulfurs directly since naturally abundant (32)S has no nuclear spin (I = 0). Here we describe direct incorporation of (33)S (I = 3/2), the only stable magnetic sulfur isotope, into MPT using controlled in vitro synthesis with purified proteins. The electron spin echo envelope modulation (ESEEM) spectra from (33)S-labeled MPT in this catalytically active SO variant are dominated by the "interdoublet" transition arising from the strong nuclear quadrupole interaction, as also occurs for the (33)S-labeled exchangeable equatorial sulfite ligand [ Klein, E. L., et al. Inorg. Chem. 2012 , 51 , 1408 - 1418 ]. The estimated experimental hfi and nqi parameters for (33)S (aiso = 3 MHz and e(2)Qq/h = 25 MHz) are in good agreement with those predicted by DFT. In addition, the DFT calculations show that the two (33)S atoms are indistinguishable by EPR and reveal a strong intermixing between their out-of-plane pz orbitals and the dxy orbital of Mo(V).
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Affiliation(s)
- Eric L. Klein
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Blvd., Tucson, AZ 85721-0041, USA
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Abdel Ali Belaidi
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674 Cologne, Germany
| | - Arnold M. Raitsimring
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Blvd., Tucson, AZ 85721-0041, USA
| | - Amanda C. Davis
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Blvd., Tucson, AZ 85721-0041, USA
| | - Tobias Krämer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Andrei V. Astashkin
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Blvd., Tucson, AZ 85721-0041, USA
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Günter Schwarz
- Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674 Cologne, Germany
| | - John H. Enemark
- Department of Chemistry and Biochemistry, The University of Arizona, 1306 E. University Blvd., Tucson, AZ 85721-0041, USA
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Klein EL, Astashkin AV, Raitsimring AM, Enemark JH. Applications of pulsed EPR spectroscopy to structural studies of sulfite oxidizing enzymes(). Coord Chem Rev 2013; 257:110-118. [PMID: 23440026 DOI: 10.1016/j.ccr.2012.05.038] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Sulfite oxidizing enzymes (SOEs), including sulfite oxidase (SO) and bacterial sulfite dehydrogenase (SDH), catalyze the oxidation of sulfite (SO(3) (2-)) to sulfate (SO(4) (2-)). The active sites of SO and SDH are nearly identical, each having a 5-coordinate, pseudo-square-pyramidal Mo with an axial oxo ligand and three equatorial sulfur donor atoms. One sulfur is from a conserved Cys residue and two are from a pyranopterindithiolene (molybdopterin, MPT) cofactor. The identity of the remaining equatorial ligand, which is solvent-exposed, varies during the catalytic cycle. Numerous in vitro studies, particularly those involving electron paramagnetic resonance (EPR) spectroscopy of the Mo(V) states of SOEs, have shown that the identity and orientation of this exchangeable equatorial ligand depends on the buffer pH, the presence and concentration of certain anions in the buffer, as well as specific point mutations in the protein. Until very recently, however, EPR has not been a practical technique for directly probing specific structures in which the solvent-exposed, exchangeable ligand is an O, OH(-), H(2)O, SO(3) (2-), or SO(4) (2-) group, because the primary O and S isotopes ((16)O and (32)S) are magnetically silent (I = 0). This review focuses on the recent advances in the use of isotopic labeling, variable-frequency high resolution pulsed EPR spectroscopy, synthetic model compounds, and DFT calculations to elucidate the roles of various anions, point mutations, and steric factors in the formation, stabilization, and transformation of SOE active site structures.
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Affiliation(s)
- Eric L Klein
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721-0041, USA
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15
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Astashkin AV, Elmore BO, Chen L, Fan W, Guillemette JG, Feng C. Pulsed ENDOR determination of the arginine location in the ferrous-NO form of neuronal NOS. J Phys Chem A 2012; 116:6731-9. [PMID: 22667467 DOI: 10.1021/jp302319c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mammalian nitric oxide synthases (NOSs) are enzymes responsible for oxidation of L-arginine (L-Arg) to nitric oxide (NO). Mechanisms of reactions at the catalytic heme site are not well understood, and it is of current interest to study structures of the heme species that activates O(2) and transforms the substrate. The NOS ferrous-NO complex is a close mimic of the obligatory ferric (hydro)peroxo intermediate in NOS catalysis. In this work, pulsed electron-nuclear double resonance (ENDOR) was used to probe the position of the l-Arg substrate at the NO(•)-coordinated ferrous heme center(s) in the oxygenase domain of rat neuronal NOS (nNOS). The analysis of (2)H and (15)N ENDOR spectra of samples containing d(7)- or guanidino-(15)N(2) labeled L-Arg has resulted in distance estimates for the nearby guanidino nitrogen and the nearby proton (deuteron) at C(δ). The L-Arg position was found to be noticeably different from that in the X-ray crystal structure of nNOS ferrous-NO complex [Li et al. J. Biol. Inorg. Chem.2006, 11, 753-768], with the nearby guanidino nitrogen being ~0.5 Å closer to, and the nearby H(δ) about 1 Å further from, the NO ligand than in the X-ray structure. The difference might be related to the structural constraints imposed on the protein by the crystal. Importantly, in spite of its closer position, the guanidino nitrogen does not form a hydrogen bond with the NO ligand, as evidenced by the absence of significant isotropic hfi constant for N(g1). This is consistent with the previous reports that it is not the L-Arg substrate itself that would most likely serve as a direct proton donor to the diatomic ligands (NO and O(2)) bound to the heme.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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16
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Klein EL, Raitsimring AM, Astashkin AV, Rajapakshe A, Johnson-Winters K, Arnold AR, Potapov A, Goldfarb D, Enemark JH. Identity of the exchangeable sulfur-containing ligand at the Mo(V) center of R160Q human sulfite oxidase. Inorg Chem 2012; 51:1408-18. [PMID: 22225516 DOI: 10.1021/ic201643t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In our previous study of the fatal R160Q mutant of human sulfite oxidase (hSO) at low pH (Astashkin et al. J. Am. Chem. Soc.2008, 130, 8471-8480), a new Mo(V) species, denoted "species 1", was observed at low pH values. Species 1 was ascribed to a six-coordinate Mo(V) center with an exchangeable terminal oxo ligand and an equatorial sulfate group on the basis of pulsed EPR spectroscopy and (33)S and (17)O labeling. Here we report new results for species 1 of R160Q, based on substitution of the sulfur-containing ligand by a phosphate group, pulsed EPR spectroscopy in K(a)- and W-bands, and extensive density functional theory (DFT) calculations applied to large, more realistic molecular models of the enzyme active site. The combined results unambiguously show that species 1 has an equatorial sulfite as the only exchangeable ligand. The two types of (17)O signals that are observed arise from the coordinated and remote oxygen atoms of the sulfite ligand. A typical five-coordinate Mo(V) site is compatible with the observed and calculated EPR parameters.
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Affiliation(s)
- Eric L Klein
- Department of Chemistry and Biochemistry, 1306 East University Boulevard, University of Arizona, Tucson, Arizona 85721-0041, United States
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Astashkin AV. Integrated refocused virtual ESEEM: detection of nuclear transition spectra without dead time and blind spots. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 209:69-74. [PMID: 21273102 DOI: 10.1016/j.jmr.2011.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 01/04/2011] [Accepted: 01/04/2011] [Indexed: 05/30/2023]
Abstract
General expressions describing the refocused stimulated (RS) and refocused virtual (RV) electron spin echo envelope modulations (ESEEM) generated with the same basic four-pulse sequence are derived. It is shown that integration of the 3D time domain trace over the two "low-resolution" time intervals (those between the first and second and between the third and fourth microwave pulses) results in a dead time-free 1D ESEEM trace in the "high-resolution" dimension (i.e., the time interval between the second and third microwave pulses) that only contains harmonics with the fundamental frequencies of nuclear transitions. The practical implementation of the integrated RS ESEEM requires pulse swapping, which leads to unrecoverable distortions in the ESEEM traces and the resulting spectra. The integrated RV ESEEM is free from such distortions and represents a robust practical technique for obtaining dead time- and blind spots-free spectra of nuclear transitions, without homonuclear combination lines. As an application example, the integrated RV ESEEM was used to obtain the spectrum of a strongly-coupled proton of the OH ligand of the Mo(V) active center of the low-pH form of the molybdoenzyme sulfite oxidase.
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Affiliation(s)
- Andrei V Astashkin
- University of Arizona, Department of Chemistry and Biochemistry, Tucson, AZ 85721, USA.
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Drew SC, Reijerse E, Quentmeier A, Rother D, Friedrich CG, Lubitz W. Spectroscopic Characterization of the Molybdenum Cofactor of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus. Inorg Chem 2011; 50:409-11. [DOI: 10.1021/ic102201f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon C. Drew
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany,
| | - Eduard Reijerse
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany,
| | - Armin Quentmeier
- Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Dagmar Rother
- Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Cornelius G. Friedrich
- Fakultät Bio- und Chemieingenieurwesen, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany,
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Enemark JH, Raitsimring AM, Astashkin AV, Klein EL. Implications for the mechanism of sulfite oxidizing enzymes from pulsed EPR spectroscopy and DFT calculations for "difficult" nuclei. Faraday Discuss 2011; 148:249-67; discussion 299-314. [PMID: 21322488 PMCID: PMC3079391 DOI: 10.1039/c004404k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalytic mechanisms of sulfite oxidizing enzymes (SOEs) have been investigated by multi-frequency pulsed EPR measurements of "difficult" magnetic nuclei (35.37Cl, 33S, 17O) associated with the Mo(v) center. Extensive DFT calculations have been used to relate the experimental magnetic resonance parameters of these nuclei to specific active site structures. This combined spectroscopic and computational approach has provided new insights concerning the structure/function relationships of the active sites of SOEs, including: (i) the exchange of oxo ligands; (ii) the nature of the blocked forms; and (iii) the role of Cl- in low pH forms.
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Affiliation(s)
- John H Enemark
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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Johnson-Winters K, Tollin G, Enemark JH. Elucidating the catalytic mechanism of sulfite oxidizing enzymes using structural, spectroscopic, and kinetic analyses. Biochemistry 2010; 49:7242-54. [PMID: 20666399 DOI: 10.1021/bi1008485] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sulfite oxidizing enzymes (SOEs) are molybdenum cofactor-dependent enzymes that are found in plants, animals, and bacteria. Sulfite oxidase (SO) is found in animals and plants, while sulfite dehydrogenase (SDH) is found in bacteria. In animals, SO catalyzes the oxidation of toxic sulfite to sulfate as the final step in the catabolism of the sulfur-containing amino acids, methionine and cysteine. In humans, sulfite oxidase deficiency is an inherited recessive disorder that produces severe neonatal neurological problems that lead to early death. Plant SO (PSO) also plays an important role in sulfite detoxification and in addition serves as an intermediate enzyme in the assimilatory reduction of sulfate. In vertebrates, the proposed catalytic mechanism of SO involves two intramolecular one-electron transfer (IET) steps from the molybdenum cofactor to the iron of the integral b-type heme. A similar mechanism is proposed for SDH, involving its molybdenum cofactor and c-type heme. However, PSO, which lacks an integral heme cofactor, uses molecular oxygen as its electron acceptor. Here we review recent results for SOEs from kinetic measurements, computational studies, electron paramagnetic resonance (EPR) spectroscopy, electrochemical measurements, and site-directed mutagenesis on active site residues of SOEs and of the flexible polypepetide tether that connects the heme and molybdenum domains of human SO. Rapid kinetic studies of PSO are also discussed.
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Affiliation(s)
- Kayunta Johnson-Winters
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
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Rajapakshe A, Johnson-Winters K, Nordstrom AR, Meyers KT, Emesh S, Astashkin AV, Enemark JH. Characterization of chloride-depleted human sulfite oxidase by electron paramagnetic resonance spectroscopy: experimental evidence for the role of anions in product release. Biochemistry 2010; 49:5154-9. [PMID: 20491442 DOI: 10.1021/bi902172n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Mo(V) state of the molybdoenzyme sulfite oxidase (SO) is paramagnetic and can be studied by electron paramagnetic resonance (EPR) spectroscopy. Vertebrate SO at pH <7 and >9 exhibits characteristic EPR spectra that correspond to two structurally different forms of the Mo(V) active center termed the low-pH (lpH) and high-pH (hpH) forms, respectively. Both EPR forms have an exchangeable equatorial OH ligand, but its orientation in the two forms is different. It has been hypothesized that the formation of the lpH species is dependent on the presence of chloride. In this work, we have prepared and purified samples of the wild type and various mutants of human SO that are depleted of chloride. These samples do not exhibit the typical lpH EPR spectrum at low pH but rather exhibit spectra that are characteristic of the blocked species that contains an exchangeable equatorial sulfate ligand. Addition of chloride to these samples results in the disappearance of the blocked species and the formation of the lpH species. Similarly, if chloride is added before sulfite, the lpH species is formed instead of the blocked one. Qualitatively similar results were observed for samples of sulfite-oxidizing enzymes from other organisms that were previously reported to form a blocked species at low pH. However, the depletion of chloride has no effect upon the formation of the hpH species.
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Affiliation(s)
- Asha Rajapakshe
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
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Johnson-Winters K, Nordstrom AR, Emesh S, Astashkin AV, Rajapakshe A, Berry RE, Tollin G, Enemark JH. Effects of interdomain tether length and flexibility on the kinetics of intramolecular electron transfer in human sulfite oxidase. Biochemistry 2010; 49:1290-6. [PMID: 20063894 DOI: 10.1021/bi9020296] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfite oxidase (SO) is a vitally important molybdenum enzyme that catalyzes the oxidation of toxic sulfite to sulfate. The proposed catalytic mechanism of vertebrate SO involves two intramolecular one-electron transfer (IET) steps from the molybdenum cofactor to the iron of the integral b-type heme and two intermolecular one-electron steps to exogenous cytochrome c. In the crystal structure of chicken SO [Kisker, C., et al. (1997) Cell 91, 973-983], which is highly homologous to human SO (HSO), the heme iron and molybdenum centers are separated by 32 A and the domains containing these centers are linked by a flexible polypeptide tether. Conformational changes that bring these two centers into greater proximity have been proposed [Feng, C., et al. (2003) Biochemistry 42, 5816-5821] to explain the relatively rapid IET kinetics, which are much faster than those theoretically predicted from the crystal structure. To explore the proposed role(s) of the tether in facilitating this conformational change, we altered both its length and flexibility in HSO by site-specific mutagenesis, and the reactivities of the resulting variants have been studied using laser flash photolysis and steady-state kinetics assays. Increasing the flexibility of the tether by mutating several conserved proline residues to alanines did not produce a discernible systematic trend in the kinetic parameters, although mutation of one residue (P105) to alanine produced a 3-fold decrease in the IET rate constant. Deletions of nonconserved amino acids in the 14-residue tether, thereby shortening its length, resulted in more drastically reduced IET rate constants. Thus, the deletion of five amino acid residues decreased IET by 70-fold, so that it was rate-limiting in the overall reaction. The steady-state kinetic parameters were also significantly affected by these mutations, with the P111A mutation causing a 5-fold increase in the sulfite K(m) value, perhaps reflecting a decrease in the ability to bind sulfite. The electron paramagnetic resonance spectra of these proline to alanine and deletion mutants are identical to those of wild-type HSO, indicating no significant change in the Mo active site geometry.
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Affiliation(s)
- Kayunta Johnson-Winters
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, USA
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Rapson TD, Astashkin AV, Johnson-Winters K, Bernhardt PV, Kappler U, Raitsimring AM, Enemark JH. Pulsed EPR investigations of the Mo(V) centers of the R55Q and R55M variants of sulfite dehydrogenase from Starkeya novella. J Biol Inorg Chem 2010; 15:505-14. [PMID: 20084533 DOI: 10.1007/s00775-009-0619-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 12/13/2009] [Indexed: 10/20/2022]
Abstract
Continuous-wave and pulsed electron paramagnetic resonance (EPR) spectroscopy have been used to characterize two variants of bacterial sulfite dehydrogenase (SDH) from Starkeya novella in which the conserved active-site arginine residue (R55) is replaced by a neutral amino acid residue. Substitution by the hydrophobic methionine residue (SDH(R55M)) has essentially no effect on the pH dependence of the EPR properties of the Mo(V) center, even though the X-ray structure of this variant shows that the methionine residue is rotated away from the Mo center and a sulfate anion is present in the active-site pocket (Bailey et al. in J Biol Chem 284:2053-2063, 2009). For SDH(R55M) only the high-pH form is observed, and samples prepared in H(2)(17)O-enriched buffer show essentially the same (17)O hyperfine interaction and nuclear quadrupole interaction parameters as SDH(WT) enzyme. However, the pH dependence of the EPR spectra of SDH(R55Q), in which the positively charged arginine is replaced by the neutral hydrophilic glutamine, differs significantly from that of SDH(WT). For SDH(R55Q) the blocked form with bound sulfate is generated at low pH, as verified by (33)S couplings observed upon reduction with (33)S-labeled sulfite. This observation of bound sulfate for SDH(R55Q) supports our previous hypothesis that sulfite-oxidizing enzymes can exhibit multiple pathways for electron transfer and product release (Emesh et al. in Biochemistry 48:2156-2163, 2009). At pH > or = 8 the high-pH form dominates for SDH(R55Q).
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Affiliation(s)
- Trevor D Rapson
- Centre for Metals in Biology, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
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HIGH-RESOLUTION EPR SPECTROSCOPY OF MO ENZYMES. SULFITE OXIDASES: STRUCTURAL AND FUNCTIONAL IMPLICATIONS. BIOLOGICAL MAGNETIC RESONANCE 2010; 29:121-168. [PMID: 21283528 PMCID: PMC3030814 DOI: 10.1007/978-1-4419-1139-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Sulfite oxidases (SOs) are physiologically vital Mo-containing enzymes that occur in animals, plants, and bacteria and which catalyze the oxidation of sulfite to sulfate, the terminal reaction in the oxidative degradation of sulfur-containing compounds. X-ray structure determinations of SOs from several species show nearly identical coordination structures of the molybdenum active center, and a common catalytic mechanism has been proposed that involves the generation of a transient paramagnetic Mo(V) state through a series of coupled electron-proton transfer steps. This chapter describes the use of pulsed electron-nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopic techniques to obtain information about the structure of this Mo(V) species from the hyperfine interactions (hfi) and nuclear quadrupole interactions (nqi) of nearby magnetic nuclei. Variable frequency instrumentation is essential to optimize the experimental conditions for measuring the couplings of different types of nuclei (e.g., (1)H, (2)H, (31)P, and (17)O). The theoretical background necessary for understanding the ESEEM and ENDOR spectra of the Mo(V) centers of SOs is outlined, and examples of the use of advanced pulsed EPR methods (RP-ESEEM, HYSCORE, integrated four-pulse ESEEM) for structure determination are presented. The analysis of variable-frequency pulsed EPR data from SOs is aided by parallel studies of model compounds that contain key functional groups or that are isotopically labeled and thus provide benchmark data for enzymes. Enormous progress has been made on the use of high-resolution variable-frequency pulsed EPR methods to investigate the structures and mechanisms of SOs during the past ~15 years, and the future is bright for the continued development and application of this technology to SOs, other molybdenum enzymes, and other problems in metallobiochemistry.
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Hanson GR, Lane I. Dimethylsulfoxide (DMSO) Reductase, a Member of the DMSO Reductase Family of Molybdenum Enzymes. METALS IN BIOLOGY 2010. [DOI: 10.1007/978-1-4419-1139-1_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Astashkin AV, Klein EL, Ganyushin D, Johnson-Winters K, Neese F, Kappler U, Enemark JH. Exchangeable oxygens in the vicinity of the molybdenum center of the high-pH form of sulfite oxidase and sulfite dehydrogenase. Phys Chem Chem Phys 2009; 11:6733-42. [PMID: 19639147 PMCID: PMC2789977 DOI: 10.1039/b907029j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electron spin echo envelope modulation (ESEEM) investigation of the high-pH (hpH) form of sulfite oxidase (SO) and sulfite dehydrogenase (SDH) prepared in buffer enriched with H(2)(17)O reveals the presence of three types of exchangeable oxygen atoms at the molybdenum center. Two of these oxygen atoms belong to the equatorial OH ligand and the axial oxo ligand, and are characterized by (17)O hyperfine interaction (hfi) constants of about 37 MHz and 6 MHz, respectively. The third oxygen has an isotropic hfi constant of 3-4 MHz and likely belongs to a hydroxyl moiety hydrogen-bonded to the equatorial OH ligand. This exchangeable oxygen atom is not observed in the ESEEM spectra of the Y236F mutant of SDH, where the active site tyrosine has been replaced by phenylalanine.
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Affiliation(s)
- Andrei V. Astashkin
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Fax: +1 (1)520 6218407; Tel: +1 (1)520 6219968
| | - Eric L. Klein
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Fax: +1 (1)520 6218407; Tel: +1 (1)520 6219968
| | - Dmitry Ganyushin
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, 53115 Bonn, Germany; Fax: +49 (0)228 739064; Tel: +49 28 732351
| | - Kayunta Johnson-Winters
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Fax: +1 (1)520 6218407; Tel: +1 (1)520 6219968
| | - Frank Neese
- Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, 53115 Bonn, Germany; Fax: +49 (0)228 739064; Tel: +49 28 732351
| | - Ulrike Kappler
- Centre for Metals in Biology, University of Queensland, St. Lucia, Queensland 4072, Australia; Fax: +61 (07)3365 4620; Tel: +61 (07)3365 2978
| | - John H. Enemark
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Fax: +1 (1)520 6218407; Tel: +1 (1)520 6219968
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Klein EL, Astashkin AV, Ganyushin D, Riplinger C, Johnson-Winters K, Neese F, Enemark JH. Direct detection and characterization of chloride in the active site of the low-pH form of sulfite oxidase using electron spin echo envelope modulation spectroscopy, isotopic labeling, and density functional theory calculations. Inorg Chem 2009; 48:4743-52. [PMID: 19402624 DOI: 10.1021/ic801787s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron spin echo envelope modulation (ESEEM) investigations were carried out on samples of the low-pH (lpH) form of vertebrate sulfite oxidase (SO) prepared with (35)Cl- and (37)Cl-enriched buffers, as well as with buffer containing the natural abundance of Cl isotopes. The isotope-related changes observed in the ESEEM spectra provide direct and unequivocal evidence that Cl(-) is located in close proximity to the Mo(V) center of lpH SO. The measured isotropic hyperfine interaction constant of about 4 MHz ((35)Cl) suggests that the Cl(-) ion is either weakly coordinated to Mo(V) at its otherwise vacant axial position, trans to the oxo ligand, or is hydrogen-bonded to the equatorial exchangeable OH ligand. Scalar relativistic all-electron density functional theory (DFT) calculations of the hyperfine and nuclear quadrupole interaction parameters, along with steric and energetic arguments, strongly support the possibility that Cl(-) is hydrogen-bonded to the equatorial OH ligand rather than being directly coordinated to the Mo(V).
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Affiliation(s)
- Eric L Klein
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Boulevard, Tucson, Arizona 85721, USA
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Structures and reaction pathways of the molybdenum centres of sulfite-oxidizing enzymes by pulsed EPR spectroscopy. Biochem Soc Trans 2009; 36:1129-33. [PMID: 19021510 DOI: 10.1042/bst0361129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
SOEs (sulfite-oxidizing enzymes) are physiologically vital and occur in all forms of life. During the catalytic cycle, the five-co-ordinate square pyramidal oxo-molybdenum active site passes through the Mo(V) state, and intimate details of the structure can be obtained from variable frequency pulsed EPR spectroscopy through the hyperfine and nuclear quadrupole interactions of nearby magnetic nuclei. By employing variable spectrometer operational frequencies, it is possible to optimize the measurement conditions for difficult quadrupolar nuclei of interest (e.g. (17)O, (33)S, (35)Cl and (37)Cl) and to simplify the interpretation of the spectra. Isotopically labelled model Mo(V) compounds provide further insight into the electronic and geometric structures and chemical reactions of the enzymes. Recently, blocked forms of SOEs having co-ordinated sulfate, the reaction product, were detected using (33)S (I=3/2) labelling. This blocking of product release is a possible contributor to fatal human sulfite oxidase deficiency in young children.
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Hernandez-Marin E, Ziegler T. Theoretical Study of the Oxidation Reaction and Electron Spin Resonance Parameters Involving Sulfite Oxidase. Inorg Chem 2009; 48:1323-33. [DOI: 10.1021/ic801158t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizabeth Hernandez-Marin
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Tom Ziegler
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
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Astashkin AV, Johnson-Winters K, Klein EL, Feng C, Wilson HL, Rajagopalan KV, Raitsimring AM, Enemark JH. Structural studies of the molybdenum center of the pathogenic R160Q mutant of human sulfite oxidase by pulsed EPR spectroscopy and 17O and 33S labeling. J Am Chem Soc 2008; 130:8471-80. [PMID: 18529001 PMCID: PMC2779766 DOI: 10.1021/ja801406f] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron paramagnetic resonance (EPR) investigation of the Mo(V) center of the pathogenic R160Q mutant of human sulfite oxidase (hSO) confirms the presence of three distinct species whose relative abundances depend upon pH. Species 1 is exclusively present at pH < or = 6, and remains in significant amounts even at pH 8. Variable-frequency electron spin echo envelope modulation (ESEEM) studies of this species prepared with (33)S-labeled sulfite clearly show the presence of coordinated sulfate, as has previously been found for the "blocked" form of Arabidopsis thaliana at low pH (Astashkin, A. V.; Johnson-Winters, K.; Klein, E. L.; Byrne, R. S.; Hille, R.; Raitsimring, A. M.; Enemark, J. H. J. Am. Chem. Soc. 2007, 129, 14800). The ESEEM spectra of Species 1 prepared in (17)O-enriched water show both strongly and weakly magnetically coupled (17)O atoms that can be assigned to an equatorial sulfate ligand and the axial oxo ligand, respectively. The nuclear quadrupole interaction (nqi) of the axial oxo ligand is substantially stronger than those found for other oxo-Mo(V) centers studied previously. Additionally, pulsed electron-nuclear double resonance (ENDOR) measurements reveal a nearby weakly coupled exchangeable proton. The structure for Species 1 proposed from the pulsed EPR results using isotopic labeling is a six-coordinate Mo(V) center with an equatorial sulfate ligand that is hydrogen bonded to an exchangeable proton. Six-coordination is supported by the (17)O nqi parameters for the axial oxo group of the model compound, (dttd)Mo(17)O((17)Otms), where H2dttd = 2,3:8,9-dibenzo-1,4,7,10-tetrathiadecane; tms = trimethylsilyl. Reduction of R160Q to Mo(V) with Ti(III) gives primarily Species 2, another low pH form, whereas reduction with sulfite at higher pH values gives a mixture of Species 1 and 2, as well as the "primary" high pH form of wild-type SO. The occurrence of significant amounts of the "sulfate-blocked" form of R160Q (Species 1) at physiological pH suggests that this species may be a contributing factor to the lethality of this mutation.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry, 1306 E University Blvd, University of Arizona, Tucson, Arizona 86721-0041, USA
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Feng C, Tollin G, Enemark JH. Sulfite oxidizing enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:527-39. [PMID: 17459792 PMCID: PMC1993547 DOI: 10.1016/j.bbapap.2007.03.006] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2007] [Revised: 03/02/2007] [Indexed: 11/19/2022]
Abstract
Sulfite oxidizing enzymes are essential mononuclear molybdenum (Mo) proteins involved in sulfur metabolism of animals, plants and bacteria. There are three such enzymes presently known: (1) sulfite oxidase (SO) in animals, (2) SO in plants, and (3) sulfite dehydrogenase (SDH) in bacteria. X-ray crystal structures of enzymes from all three sources (chicken SO, Arabidopsis thaliana SO, and Starkeya novella SDH) show nearly identical square pyramidal coordination around the Mo atom, even though the overall structures of the proteins and the presence of additional cofactors vary. This structural information provides a molecular basis for studying the role of specific amino acids in catalysis. Animal SO catalyzes the final step in the degradation of sulfur-containing amino acids and is critical in detoxifying excess sulfite. Human SO deficiency is a fatal genetic disorder that leads to early death, and impaired SO activity is implicated in sulfite neurotoxicity. Animal SO and bacterial SDH contain both Mo and heme domains, whereas plant SO only has the Mo domain. Intraprotein electron transfer (IET) between the Mo and Fe centers in animal SO and bacterial SDH is a key step in the catalysis, which can be studied by laser flash photolysis in the presence of deazariboflavin. IET studies on animal SO and bacterial SDH clearly demonstrate the similarities and differences between these two types of sulfite oxidizing enzymes. Conformational change is involved in the IET of animal SO, in which electrostatic interactions may play a major role in guiding the docking of the heme domain to the Mo domain prior to electron transfer. In contrast, IET measurements for SDH demonstrate that IET occurs directly through the protein medium, which is distinctly different from that in animal SO. Point mutations in human SO can result in significantly impaired IET or no IET, thus rationalizing their fatal effects. The recent developments in our understanding of sulfite oxidizing enzyme mechanisms that are driven by a combination of molecular biology, rapid kinetics, pulsed electron paramagnetic resonance (EPR), and computational techniques are the subject of this review.
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Affiliation(s)
- Changjian Feng
- College of Pharmacy, University of New Mexico, Albuquerque, NM 87131
| | - Gordon Tollin
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
| | - John H. Enemark
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
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