1
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Maghsoud Y, Dong C, Cisneros GA. Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat. ACS Catal 2023; 13:6023-6043. [PMID: 37547543 PMCID: PMC10399974 DOI: 10.1021/acscatal.3c01245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Xanthine oxidase (XO) is a member of the molybdopterin-containing enzyme family. It interconverts xanthine to uric acid as the last step of purine catabolism in the human body. The high uric acid concentration in the blood directly leads to human diseases like gout and hyperuricemia. Therefore, drugs that inhibit the biosynthesis of uric acid by human XO have been clinically used for many years to decrease the concentration of uric acid in the blood. In this study, the inhibition mechanism of XO and a new promising drug, topiroxostat (code: FYX-051), is investigated by employing molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. This drug has been reported to act as both a noncovalent and covalent inhibitor and undergoes a stepwise inhibition by all its hydroxylated metabolites, which include 2-hydroxy-FYX-051, dihydroxy-FYX-051, and trihydroxy-FYX-051. However, the detailed mechanism of inhibition of each metabolite remains elusive and can be useful for designing more effective drugs with similar inhibition functions. Hence, herein we present the computational investigation of the structural and dynamical effects of FYX-051 and the calculated reaction mechanism for all of the oxidation steps catalyzed by the molybdopterin center in the active site. Calculated results for the proposed reaction mechanisms for each metabolite's inhibition reaction in the enzyme's active site, binding affinities, and the noncovalent interactions with the surrounding amino acid residues are consistent with previously reported experimental findings. Analysis of the noncovalent interactions via energy decomposition analysis (EDA) and noncovalent interaction (NCI) techniques suggests that residues L648, K771, E802, R839, L873, R880, R912, F914, F1009, L1014, and A1079 can be used as key interacting residues for further hybrid-type inhibitor development.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Chao Dong
- Department of Chemistry and Physics, The University of Texas Permian Basin, Odessa, Texas 79762, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States; Department of Physics, The University of Texas at Dallas, Richardson, Texas 75080, United States
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2
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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] [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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3
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Kirk ML, Hille R. Spectroscopic Studies of Mononuclear Molybdenum Enzyme Centers. Molecules 2022; 27:molecules27154802. [PMID: 35956757 PMCID: PMC9370002 DOI: 10.3390/molecules27154802] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [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
- 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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4
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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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5
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Bailey GA, Buss JA, Oyala PH, Agapie T. Terminal, Open-Shell Mo Carbide and Carbyne Complexes: Spin Delocalization and Ligand Noninnocence. J Am Chem Soc 2021; 143:13091-13102. [PMID: 34379389 DOI: 10.1021/jacs.1c03806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Open-shell compounds bearing metal-carbon triple bonds, such as carbides and carbynes, are of significant interest as plausible intermediates in the reductive catenation of C1 oxygenates. Despite the abundance of closed-shell carbynes reported, open-shell variants are very limited, and an open-shell carbide has yet to be reported. Herein, we report the synthesis of the first terminal, open-shell carbide complexes, [K][1] and [1][BArF4] (1 = P2Mo(≡C:)(CO), P2 = a terphenyl diphosphine ligand), which differ by two redox states, as well as a series of related open-shell carbyne complexes. The complexes are characterized by single-crystal X-ray diffraction and NMR, EPR, and IR spectroscopies, while the electronic structures are probed by EPR studies and DFT calculations to assess spin delocalization. In the d1 complexes, the spin is primarily localized on the metal (∼55-77% Mo dxy) with delocalization on the triply bonded carbon of ∼0.05-0.09 e-. In the reduced carbide [K][1], a direct metal-arene interaction enables ancillary ligand reduction, resulting in reduced radical character on the terminal carbide (⩽0.02 e-). Reactivity studies with [K][1] reveal the formation of mixed-valent C-C coupled products at -40 °C, illustrating how productive reactivity manifolds can be engendered through the manipulation of redox states. Combined, the results inform on the electronic structure and reactivity of a new and underrepresented class of compounds with potential significance to a wide array of reactions involving open-shell species.
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Affiliation(s)
- Gwendolyn A Bailey
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Joshua A Buss
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Paul H Oyala
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Theodor Agapie
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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6
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Kisgeropoulos EC, Manesis AC, Shafaat HS. Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation. J Am Chem Soc 2021; 143:849-867. [PMID: 33415980 DOI: 10.1021/jacs.0c10135] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH3 states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH3 hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH3 species indicate a ligand-centered LUMO, with a d9 population on the metal center, rather than the d7 population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH3 Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH3 species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.
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Affiliation(s)
- Effie C Kisgeropoulos
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anastasia C Manesis
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry and Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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7
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Tao L, Stich TA, Fugate CJ, Jarrett JT, Britt RD. EPR-Derived Structure of a Paramagnetic Intermediate Generated by Biotin Synthase BioB. J Am Chem Soc 2018; 140:12947-12963. [PMID: 30222930 PMCID: PMC6363123 DOI: 10.1021/jacs.8b07613] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Biotin (vitamin B7) is an enzyme cofactor required by organisms from all branches of life but synthesized only in microbes and plants. In the final step of biotin biosynthesis, a radical S-adenosyl-l-methionine (SAM) enzyme, biotin synthase (BioB), converts the substrate dethiobiotin to biotin through the stepwise formation of two C-S bonds. Previous electron paramagnetic resonance (EPR) spectroscopic studies identified a semistable intermediate in the formation of the first C-S bond as 9-mercaptodethiobiotin linked to a paramagnetic [2Fe-2S] cluster through one of its bridging sulfides. Herein, we report orientation-selected pulse EPR spectroscopic results that reveal hyperfine interactions between the [2Fe-2S] cluster and a number of magnetic nuclei (e.g., 57Fe, 15N, 13C, and 2H) introduced in a site-specific manner via biosynthetic methods. Combining these results with quantum chemical modeling gives a structural model of the intermediate showing that C6, the target of the second hydrogen-atom abstraction, is now in close proximity to the nascent thioether sulfur and is ideally positioned for the second C-S bond forming event.
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Affiliation(s)
- Lizhi Tao
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Troy A. Stich
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Corey J. Fugate
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Joseph T. Jarrett
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - R. David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
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8
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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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9
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Stich TA, Gagnon DM, Anderson BL, Nocera DG, Britt RD. EPR Spectroscopic Characterization of a Jahn‐Teller Distorted (
C
3
v
→
C
s
) Four‐Coordinate Chromium(V) Oxo Species. Isr J Chem 2016. [DOI: 10.1002/ijch.201600036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Troy A. Stich
- Department of Chemistry University of California One Shields Avenue Davis CA 95616 USA
| | - Derek M. Gagnon
- Department of Chemistry University of California One Shields Avenue Davis CA 95616 USA
| | - Bryce L. Anderson
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - R. David Britt
- Department of Chemistry University of California One Shields Avenue Davis CA 95616 USA
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10
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Doonan CJ, Gourlay C, Nielsen DJ, Ng VWL, Smith PD, Evans DJ, George GN, White JM, Young CG. d(1) Oxosulfido-Mo(V) Compounds: First Isolation and Unambiguous Characterization of an Extended Series. Inorg Chem 2015; 54:6386-96. [PMID: 26046577 DOI: 10.1021/acs.inorgchem.5b00708] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reaction of Tp(iPr)Mo(VI)OS(OAr) with cobaltocene in toluene results in the precipitation of brown, microcrystalline oxosulfido-Mo(V) compounds, [CoCp2][Tp(iPr)Mo(V)OS(OAr)] (Cp(-) = η(5)-C5H5(-), Tp(iPr)(-) = hydrotris(3-isopropylpyrazol-1-yl)borate, OAr(-) = phenolate or 2-(s)Bu, 2-(t)Bu, 3-(t)Bu, 4-(s)Bu, 4-Ph, 3,5-(s)Bu2, 2-CO2Me, 2-CO2Et or 2-CO2Ph derivative thereof). The compounds are air- and water-sensitive and display ν(Mo═O) and ν(Mo[Formula: see text]S) IR absorption bands at ca. 890 and 435 cm(-1), respectively, 20-40 cm(-1) lower in energy than the corresponding bands in Tp(iPr)MoOS(OAr). They are electrochemically active and exhibit three reversible cyclovoltammetric waves (E(Mo(VI)/Mo(V)) = -0.40 to -0.66 V, E([CoCp2](+)/CoCp2) = -0.94 V and E(CoCp2/[CoCp2](-)) = -1.88 V vs SCE). Structural characterization of [CoCp2][Tp(iPr)MoOS(OC6H4CO2Et-2)]·2CH2Cl2 revealed a distorted octahedral Mo(V) anion with Mo═O and Mo[Formula: see text]S distances of 1.761(5) and 2.215(2) Å, respectively, longer than corresponding distances in related Tp(iPr)MoOS(OAr) compounds. The observation of strong S(1s) → (S(3p) + Mo(4d)) S K-preedge transitions indicative of a d(1) sulfido-Mo(V) moiety and the presence of short Mo═O (ca. 1.72 Å) and Mo[Formula: see text]S (ca. 2.25 Å) backscattering contributions in the Mo K-edge EXAFS further support the oxosulfido-Mo(V) formulation. The compounds are EPR-active, exhibiting highly anisotropic (Δg 0.124-0.150), rhombic, frozen-glass spectra with g1 close to the value observed for the free electron (ge = 2.0023). Spectroscopic studies are consistent with the presence of a highly covalent Mo[Formula: see text]S π* singly occupied molecular orbital. The compounds are highly reactive, with reactions localized at the terminal sulfido ligand. For example, the compounds react with cyanide and PPh3 to produce thiocyanate and SPPh3, respectively, and various (depending on solvent) oxo-Mo(V) species. Reactions with copper reagents also generally lead to desulfurization and the formation of oxo-Mo(V) or -Mo(IV) complexes.
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Affiliation(s)
| | | | | | | | | | | | - Graham N George
- §Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | | | - Charles G Young
- ¶Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
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11
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Stein BW, Kirk ML. Electronic structure contributions to reactivity in xanthine oxidase family enzymes. J Biol Inorg Chem 2015; 20:183-94. [PMID: 25425163 PMCID: PMC4867223 DOI: 10.1007/s00775-014-1212-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/30/2014] [Indexed: 11/25/2022]
Abstract
We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the two-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function.
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Affiliation(s)
- Benjamin W. Stein
- Department of Chemistry and Chemical Biology, University of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, NM 87131
| | - Martin L. Kirk
- Department of Chemistry and Chemical Biology, University of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, NM 87131
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12
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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13
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Cutsail III G, Stein BW, Subedi D, Smith JM, Kirk ML, Hoffman BM. EPR, ENDOR, and electronic structure studies of the Jahn-Teller distortion in an Fe(V) nitride. J Am Chem Soc 2014; 136:12323-36. [PMID: 25137531 PMCID: PMC4156863 DOI: 10.1021/ja505403j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Indexed: 01/26/2023]
Abstract
The recently synthesized and isolated low-coordinate Fe(V) nitride complex has numerous implications as a model for high-oxidation states in biological and industrial systems. The trigonal [PhB((t)BuIm)3Fe(V)≡N](+) (where (PhB((t)BuIm)3(-) = phenyltris(3-tert-butylimidazol-2-ylidene)), (1) low-spin d(3) (S = 1/2) coordination compound is subject to a Jahn-Teller (JT) distortion of its doubly degenerate (2)E ground state. The electronic structure of this complex is analyzed by a combination of extended versions of the formal two-orbital pseudo Jahn-Teller (PJT) treatment and of quantum chemical computations of the PJT effect. The formal treatment is extended to incorporate mixing of the two e orbital doublets (30%) that results from a lowering of the idealized molecular symmetry from D3h to C3v through strong "doming" of the Fe-C3 core. Correspondingly we introduce novel DFT/CASSCF computational methods in the computation of electronic structure, which reveal a quadratic JT distortion and significant e-e mixing, thus reaching a new level of synergism between computational and formal treatments. Hyperfine and quadrupole tensors are obtained by pulsed 35 GHz ENDOR measurements for the (14/15)N-nitride and the (11)B axial ligands, and spectra are obtained from the imidazole-2-ylidene (13)C atoms that are not bound to Fe. Analysis of the nitride ENDOR tensors surprisingly reveals an essentially spherical nitride trianion bound to Fe, with negative spin density and minimal charge density anisotropy. The four-coordinate (11)B, as expected, exhibits negligible bonding to Fe. A detailed analysis of the frontier orbitals provided by the electronic structure calculations provides insight into the reactivity of 1: JT-induced symmetry lowering provides an orbital selection mechanism for proton or H atom transfer reactivity.
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Affiliation(s)
- George
E. Cutsail III
- Department
of Chemistry Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Benjamin W. Stein
- Department
of Chemistry and Chemical Biology The University
of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, New Mexico 87131-0001, United States
| | - Deepak Subedi
- Department
of Chemistry and Biochemistry MSC 3C, New
Mexico State University, 1175 North Horseshoe Drive, Las Cruces, New Mexico 88003, United States
| | - Jeremy M. Smith
- Department
of Chemistry and Biochemistry MSC 3C, New
Mexico State University, 1175 North Horseshoe Drive, Las Cruces, New Mexico 88003, United States
| | - Martin L. Kirk
- Department
of Chemistry and Chemical Biology The University
of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, New Mexico 87131-0001, United States
| | - Brian M. Hoffman
- Department
of Chemistry and Biochemistry MSC 3C, New
Mexico State University, 1175 North Horseshoe Drive, Las Cruces, New Mexico 88003, United States
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14
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - James Hall
- Department of Biochemistry, University of California, Riverside, Riverside, California 92521, United States
| | - Partha Basu
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
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15
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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] [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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16
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Ng VWL, White JM, Young CG. Structural Characterization and Unusual Reactivity of Oxosulfido-Mo(V) Compounds: Implications for the Structure and Electronic Description of the Very Rapid Form of Xanthine Oxidase. J Am Chem Soc 2013; 135:7106-9. [DOI: 10.1021/ja4022057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Victor W. L. Ng
- School
of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010,
Australia
| | - Jonathan M. White
- School
of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010,
Australia
| | - Charles G. Young
- School
of Chemistry and ‡Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010,
Australia
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17
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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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18
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19
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Abstract
Recent progress in our understanding of the structural and catalytic properties of molybdenum-containing enzymes in eukaryotes is reviewed, along with aspects of the biosynthesis of the cofactor and its insertion into apoprotein.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Takeshi Nishino
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, Japan and Department of Biochemistry, University of California, Riverside, CA 92521
| | - Florian Bittner
- Department of Plant Biology, Technical University of Braunschweig, 38023 Braunschweig, Germany
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20
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21
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Shanmugam M, Zhang B, McNaughton RL, Kinney RA, Hille R, Hoffman BM. The structure of formaldehyde-inhibited xanthine oxidase determined by 35 GHz 2H ENDOR spectroscopy. J Am Chem Soc 2010; 132:14015-7. [PMID: 20860357 PMCID: PMC2958171 DOI: 10.1021/ja106432h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formaldehyde-inhibited Mo(V) state of xanthine oxidase (I) has been studied for four decades, yet it has not proven possible to distinguish unequivocally among the several structures proposed for this form. The uniquely large isotropic hyperfine coupling for (13)C from CH(2)O led to the intriguing suggestion of a direct Mo-C bond for the active site of I. This suggestion was supported by the recent crystal structures of glycol- and glycerol-inhibited forms of aldehyde oxidoreductase, a member of the xanthine oxidase family. (1)H and (2)H ENDOR spectra of I(C(1,2)H(2)O) in H(2)O/D(2)O buffer now have unambiguously revealed that the active-site structure of I contains a CH(2)O adduct of Mo(V) in the form of a four-membered ring with S and O linking the C to Mo and have ruled out a direct Mo-C bond. Density functional theory computations are consistent with this conclusion. We interpret the large (13)C coupling as resulting from a "transannular hyperfine interaction".
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Affiliation(s)
| | - Bo Zhang
- Department of Biochemistry, University of California, Riverside, California-95521
| | | | - R. Adam Kinney
- Chemistry Department, Northwestern University, Evanston, Illinois, 60208-3113
| | - Russ Hille
- Department of Biochemistry, University of California, Riverside, California-95521
| | - Brian M. Hoffman
- Chemistry Department, Northwestern University, Evanston, Illinois, 60208-3113
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22
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Doan PE, Lees NS, Shanmugam M, Hoffman BM. Simulating suppression effects in Pulsed ENDOR, and the 'hole in the middle' of Mims and Davies ENDOR Spectra. APPLIED MAGNETIC RESONANCE 2010; 37:763-779. [PMID: 20161480 PMCID: PMC2794149 DOI: 10.1007/s00723-009-0083-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
All pulsed ENDOR techniques, and in particular the Mims and Davies sequences, suffer from detectability biases ('blindspots') that are directly correlated to the size of the hyperfine interactions of coupled nuclei. Our efforts at ENDOR 'crystallography' and 'mechanism determination' with these techniques has led our group to refine our simulations of pulsed ENDOR spectra to take into account these biases, and we here describe the process and illustrate it with several examples. We first focus on an issue whose major significance is not widely appreciated, the 'hole in the middle' of pulsed ENDOR spectra caused by the n = 0 suppression hole in Mims ENDOR and by the analogous A→0 suppression in Davies ENDOR (Section I). This section discusses the issue for nuclei with I = ½ and also for (2)H (I = 1), using the treatment of Section II. In Section II we discuss the general treatment of suppression effects for I = 1, illustrating it with a treatment of Mims suppression for (14)N (I = 1) (Section II).
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Affiliation(s)
- Peter E Doan
- Department of Chemistry, Northwestern University, Evanston, IL, 60208-3113
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23
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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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24
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Hille R. EPR Studies of Xanthine Oxidoreductase and Other Molybdenum-Containing Hydroxylases. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4419-1139-1_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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25
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Metz S, Thiel W. A Combined QM/MM Study on the Reductive Half-Reaction of Xanthine Oxidase: Substrate Orientation and Mechanism. J Am Chem Soc 2009; 131:14885-902. [DOI: 10.1021/ja9045394] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sebastian Metz
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
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26
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Santos-Silva T, Ferroni F, Thapper A, Marangon J, González PJ, Rizzi AC, Moura I, Moura JJG, Romão MJ, Brondino CD. Kinetic, Structural, and EPR Studies Reveal That Aldehyde Oxidoreductase from Desulfovibrio gigas Does Not Need a Sulfido Ligand for Catalysis and Give Evidence for a Direct Mo−C Interaction in a Biological System. J Am Chem Soc 2009; 131:7990-8. [PMID: 19459677 DOI: 10.1021/ja809448r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teresa Santos-Silva
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Felix Ferroni
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Anders Thapper
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Jacopo Marangon
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Pablo J. González
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Alberto C. Rizzi
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Isabel Moura
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - José J. G. Moura
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Maria J. Romão
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
| | - Carlos D. Brondino
- REQUIMTE, Departamento de Química, Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal, and Departamento de Física, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000ZAA Santa Fe, Argentina
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27
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Metz S, Wang D, Thiel W. Reductive Half-Reaction of Aldehyde Oxidoreductase toward Acetaldehyde: A Combined QM/MM Study. J Am Chem Soc 2009; 131:4628-40. [DOI: 10.1021/ja805938w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sebastian Metz
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Dongqi Wang
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
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Hille R. The Reaction Mechanism of the Molybdenum Hydroxylase Xanthine Oxidoreductase: Evidence Against the Formation of Intermediates Having Metal-Carbon Bonds. METAL-CARBON BONDS IN ENZYMES AND COFACTORS 2009. [DOI: 10.1039/9781847559333-00395] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
ENDOR spectra of the catalytically relevant “very rapid” Mo(V) species generated in the course of the reaction of xanthine oxidoreductase with substrate have been examined by two different groups. While the data themselves are virtually identical, the analysis has been variously interpreted as supporting or refuting the existence of a molybdenum-carbon bond in the signal-giving species. While the basis for this difference in interpretation has now been generally agreed upon – the Mo-C distance in the signal-giving species is now understood to be too long to represent a direct Mo-C bond – independent information concerning the structure of the signal-giving species is highly desirable. Recently, several X-ray crystal structures of catalytically relevant complexes of the enzyme with several substrates and inhibitors have been reported. Taken together, these structures strongly and unambiguously support the interpretation that the intermediate giving rise to the “very rapid” EPR signal, as well as the Mo(IV) intermediate that precedes it in the reaction mechanism, has product coordinated to the active site molybdenum via the catalytically introduced hydroxyl group in a simple “end-on” fashion, with no metal-carbon bond character to the complex. The manner in which product is bound and its orientation within the active site provide important clues as to the specific catalytic roles of active sites in accelerating the reaction rate.
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Affiliation(s)
- Russ Hille
- Department of Biochemistry, The University of California Riverside CA 92521 USA
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29
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Doonan CJ, Rubie ND, Peariso K, Harris HH, Knottenbelt SZ, George GN, Young CG, Kirk ML. Electronic Structure Description of the cis-MoOS Unit in Models for Molybdenum Hydroxylases. J Am Chem Soc 2007; 130:55-65. [DOI: 10.1021/ja068512m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian J. Doonan
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Nick D. Rubie
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Katrina Peariso
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Hugh H. Harris
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Sushilla Z. Knottenbelt
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Graham N. George
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Charles G. Young
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
| | - Martin L. Kirk
- Contribution from The Department of Chemistry and Biological Chemistry, The University of New Mexico, MSC03 20601 University of New Mexico, Albuquerque, New Mexico 87131-0001, School of Chemistry, University of Melbourne, Victoria 3010, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC Stanford University, P.O. Box 4349, MS 69 Stanford, California 94309
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30
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Pauff JM, Zhang J, Bell CE, Hille R. Substrate orientation in xanthine oxidase: crystal structure of enzyme in reaction with 2-hydroxy-6-methylpurine. J Biol Chem 2007; 283:4818-24. [PMID: 18063585 DOI: 10.1074/jbc.m707918200] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Xanthine oxidoreductase catalyzes the final two steps of purine catabolism and is involved in a variety of pathological states ranging from hyperuricemia to ischemia-reperfusion injury. The human enzyme is expressed primarily in its dehydrogenase form utilizing NAD+ as the final electron acceptor from the enzyme's flavin site but can exist as an oxidase that utilizes O2 for this purpose. Central to an understanding of the enzyme's function is knowledge of purine substrate orientation in the enzyme's molybdenum-containing active site. We report here the crystal structure of xanthine oxidase, trapped at the stage of a critical intermediate in the course of reaction with the slow substrate 2-hydroxy-6-methylpurine at 2.3A. This is the first crystal structure of a reaction intermediate with a purine substrate that is hydroxylated at its C8 position as is xanthine and confirms the structure predicted to occur in the course of the presently favored reaction mechanism. The structure also corroborates recent work suggesting that 2-hydroxy-6-methylpurine orients in the active site with its C2 carbonyl group interacting with Arg-880 and extends our hypothesis that xanthine binds opposite this orientation, with its C6 carbonyl positioned to interact with Arg-880 in stabilizing the MoV transition state.
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Affiliation(s)
- James M Pauff
- Department of Biochemistry, University of California, Riverside, California 92521, USA
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31
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Dey M, Telser J, Kunz RC, Lees NS, Ragsdale SW, Hoffman BM. Biochemical and Spectroscopic Studies of the Electronic Structure and Reactivity of a Methyl−Ni Species Formed on Methyl-Coenzyme M Reductase. J Am Chem Soc 2007; 129:11030-2. [PMID: 17711283 DOI: 10.1021/ja074556z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mishtu Dey
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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32
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Hemann C, Ilich P, Stockert AL, Choi EY, Hille R. Resonance Raman studies of xanthine oxidase: The reduced enzyme-product complex with violapterin. J Phys Chem B 2007; 109:3023-31. [PMID: 16851316 DOI: 10.1021/jp046636k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A study of the molecular, electronic, and vibrational characteristics of the molybdenum-containing enzyme complex xanthine oxidase with violapterin has been carried out using density functional theory calculations and resonance Raman spectroscopy. The electronic structure calculations were carried out on a model consisting of the enzyme molybdopterin cofactor [in the four-valent, reduced state; Mo(IV)O(SH)] covalently linked to violapterin (1H,3H,8H-pteridine-2,4,7-trione in the neutral form) via an oxygen bridge, Mo-O-C7. Full geometry optimizations were performed for all models using the SDD basis set and the three-parameter exchange functional of Becke combined with the Lee, Yang, and Parr correlational functional. Harmonic vibrational frequencies were determined for a variety of isotopes in an attempt to correlate experimentally observed shifts upon 18O-labeling of the Mo-OR bridge to bound product as well as shifts seen upon substitution of solvent-exchangeable protons in samples prepared in D2O. The theoretical vibrational frequencies compared favorably with experimentally observed vibrational modes in the resonance Raman spectra of the reduced xanthine oxidase-violapterin complex prepared in H2O and D2O and with 18O-labeled product. Correlating the isotopic shifts from the calculations with those from the resonance Raman experiments resulted in complete normal mode assignments for all modes observed in the 350-1750 cm(-1) range. The present work demonstrates that a model in which the violapterin is coordinated to the molybdenum of the active site in a simple end-on manner via the hydroxyl group introduced by an enzyme accurately predicts the observed resonance Raman spectrum of the complex. Given the numerous modes involving the bridging oxygen, a side-on binding mode can be eliminated.
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Affiliation(s)
- Craig Hemann
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Affiliation(s)
- Russ Hille
- Department of Molecular and Cellular Biochemistry, The Ohio State University, 333 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210‐1218, USA
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34
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Clay MD, Yang TC, Jenney FE, Kung IY, Cosper CA, Krishnan R, Kurtz DM, Adams MW, Hoffman BM, Johnson MK. Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies. Biochemistry 2006; 45:427-38. [PMID: 16401073 PMCID: PMC2531258 DOI: 10.1021/bi052034v] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide and have used vibrational and ENDOR spectroscopies to study the properties of the active site paramagnetic iron center. Addition of cyanide changes the active site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe-CN stretching/Fe-C-N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe-C-N angle approximately 175 degrees) and two distinct bent conformations (Fe-C-N angles <140 degrees). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C-N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state, indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe-C-N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2), taking a reference value from vibrational studies of 175 degrees (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Brian M. Hoffman
- Corresponding authors: BMH: Department of Chemistry, Northwestern University, Evanston, IL 60208; Tel.: 847−491−3104, E-mail: . M.K.J.: Department of Chemistry, University of Georgia, Athens, GA 30602, USA; Tel.: 706−542−9378; Fax: 706−542−2353, E-mail:
| | - Michael K. Johnson
- Corresponding authors: BMH: Department of Chemistry, Northwestern University, Evanston, IL 60208; Tel.: 847−491−3104, E-mail: . M.K.J.: Department of Chemistry, University of Georgia, Athens, GA 30602, USA; Tel.: 706−542−9378; Fax: 706−542−2353, E-mail:
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35
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Bayse CA. Theoretical Characterization of the “Very Rapid” Mo(V) Species Generated in the Oxidation of Xanthine Oxidase. Inorg Chem 2006; 45:2199-202. [PMID: 16499383 DOI: 10.1021/ic0511930] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Density functional theory calculations of the "very rapid" Mo(V) intermediate of xanthine oxidase (XO) result in a square pyramidal geometry with end-on coordination of the model substrate. The Mo-C8 distance is 3.18 A, longer than previously reported from ENDOR experiments (<2.4 A Howes; et al. Biochemistry 1996, 35, 1432; 2.7-2.9 A Mandikandan; et al. J. Am. Chem. Soc. 2001, 123, 2658). Theoretical gas-phase isotropic hyperfine coupling constants A(iso)(C8) (B3LYP/BSII, 7.68 MHz; B3P86/BSII, 8.64 MHz) compare well with experimental values for the "very rapid" Mo(V) intermediate of XO with xanthine (8.8 MHz, Howes et al.) and 2-hydroxy-6-methylpurine (7.9 MHz, Mandikandan et al.). Absolute values of A(iso) of the metal-bound substrate oxygen are similar in magnitude to that of experiment.
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Affiliation(s)
- Craig A Bayse
- Department of Chemistry and Biochemistry, Old Dominion University, Hampton Boulevard, Norfolk, Virginia 23529, USA.
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36
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Walsby CJ, Telser J, Rigsby RE, Armstrong RN, Hoffman BM. Enzyme Control of Small-Molecule Coordination in FosA as Revealed by 31P Pulsed ENDOR and ESE-EPR. J Am Chem Soc 2005; 127:8310-9. [PMID: 15941264 DOI: 10.1021/ja044094e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FosA is a manganese metalloglutathione transferase that confers resistance to the broad-spectrum antibiotic fosfomycin, which contains a phosphonate group. The active site of this enzyme consists of a high-spin Mn(2+) ion coordinated by endogenous ligands (a glutamate and two histidine residues) and by exogenous ligands, such as substrate fosfomycin. To study the Mn(2+) coordination environment of FosA in the presence of substrate and the inhibitors phosphonoformate and phosphate, we have used (31)P pulsed electron-nuclear double resonance (ENDOR) at 35 GHz to obtain metrical information from (31)P-Mn(2+) interactions. We have found that continuous wave (CW) (31)P ENDOR is not successful in the study of phosphates and phosphonates coordinated to Mn(2+). Parallel studies of phosph(on)ate binding to the Mn(2+) of FosA and to aqueous Mn(2+) ion disclose how the enzyme modifies the coordination of these molecules to the active site Mn(2+). Through analysis of (31)P hyperfine parameters derived from simulations of the ENDOR spectra we have determined the binding modes of the phosph(on)ates in each sample and discerned details of the geometric and electronic structure of the metal center. The (31)P ENDOR studies of the protein samples agree with, or improve on, the Mn-P distances determined from crystal structures and provide Mn-phosph(on)ate bonding information not available from these studies. Electron spin echo electron paramagnetic resonance (ESE-EPR) spectra have also been recorded. Simulation of these spectra yield the axial and rhombic components of the Mn(2+) (S = (5)/(2)) zero-field splitting (zfs) tensor. Comparison of structural inferences based on these zfs parameters both with the known enzyme structures and the (31)P ENDOR results establishes that the time-honored procedure of analyzing Mn(2+) zfs parameters to describe the coordination environment of the metal ion is not valid or productive.
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Affiliation(s)
- Charles J Walsby
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA
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Abstract
Unlike monooxygenases, molybdenum-containing hydroxylases catalyze the hydroxylation of carbon centers using oxygen derived ultimately from water, rather than O(2), as the source of the oxygen atom incorporated into the product, and do not require an external source of reducing equivalents. The mechanism by which this interesting chemistry takes place has been the subject of investigation for some time, and in the last several years the chemical course of the reaction has become increasingly well understood. The present minireview summarizes recent mechanistic and structure/function studies of members of this large and growing family of enzymes.
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Affiliation(s)
- Russ Hille
- Department of Molecular and Cellular Biochemistry, The Ohio State University, 333 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA.
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38
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Kim SH, Yang TC, Perera R, Jin S, Bryson TA, Sono M, Davydov R, Dawson JH, Hoffman BM. Cryoreduction EPR and 13C, 19F ENDOR study of substrate-bound substates and solvent kinetic isotope effects in the catalytic cycle of cytochrome P450cam and its T252A mutant. Dalton Trans 2005:3464-9. [PMID: 16234926 DOI: 10.1039/b506764m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We recently used cryoreduction EPR/ENDOR techniques to show that a substrate can modulate the properties of both the monooxygenase active-oxygen intermediates and of the proton-delivery network which encompasses them. In the present report we use Q-band pulsed 19F ENDOR (Mims 3-pulse sequence) to examine the substrate binding geometries of camphor, through use of the 5,5'--difluorocamphor, and 13C ENDOR to examine the binding of 5-methylenyl camphor labeled with 13C at C11. These probes are examined in multiple states of the catalytic cycle of P450cam and its T252A mutant. As part of this investigation we further report a new cryoreduction reaction, the reduction of a ferroheme to the EPR-visible Fe(I) state, and use it to probe the substrate binding to the EPR-silent ferroheme state. Finally we report the solvent kinetic isotope effect on the decay of the camphor complex of the hydroperoxo-ferric intermediate, the first such measurement on an individual step within the P450cam reaction cycle. Following reduction of oxyferrous-P450cam, this step is the rate-limiting step in camphor hydroxylation, and its solv-KIE of 1.8 at 190 K establishes that it involves activation of the hydroperoxo moiety by transfer of the 'second' proton of catalysis. We suggest that the finding that the heme pocket can exist in multiple substates, including multiple substrate binding locations, even in P450cam, along with the established possibility that the hydroperoxo-ferriheme intermediate can react with substrate, may explain the formation of multiple products by P450s.
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Affiliation(s)
- Sun Hee Kim
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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Lee HI, Igarashi RY, Laryukhin M, Doan PE, Dos Santos PC, Dean DR, Seefeldt LC, Hoffman BM. An organometallic intermediate during alkyne reduction by nitrogenase. J Am Chem Soc 2004; 126:9563-9. [PMID: 15291559 DOI: 10.1021/ja048714n] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogenase is the metalloenzyme that catalyzes the nucleotide-dependent reduction of N(2), as well as reduction of a variety of other triply bonded substrates, including the alkyne, acetylene. Substitution of the alpha-70(Val) residue in the nitrogenase MoFe protein by alanine expands the range of substrates to include short-chain alkynes not reduced by the unaltered protein. Rapid freezing of the alpha-70(Ala) nitrogenase MoFe protein during reduction of the alkyne propargyl alcohol (HC triple bond CH(2)OH; PA) traps an S = (1)/(2) intermediate state of the active-site metal cluster, the FeMo-cofactor. We have combined CW and pulsed (13)C ENDOR (electron-nuclear double resonance) with two quantitative 35 GHz (1,2)H ENDOR techniques, Mims pulsed ENDOR and the newly devised "stochastic field-modulated" ENDOR, to study this intermediate prepared with isotopically substituted ((13)C, (1,2)H) propargyl alcohol in H(2)O and D(2)O buffers. These measurements allow the first description of a trapped nitrogenase reduction intermediate. The S = (1)/(2) turnover intermediate generated during the reduction of PA contains the 3-carbon chain of PA and exhibits resolved (1,2)H ENDOR signals from three protons, two strongly coupled (H(a)) and one weakly coupled (H(b)); H(a)(c) originates as the C3 proton of PA, while H(a)(s) and H(b) are solvent-derived. The two H(a) protons have identical hyperfine tensors, despite having different origins. The equality of the (H(a)(s), H(a)(c)) hyperfine tensors strongly constrains proposals for the structure of the cluster-bound reduced PA. Through consideration of model structures found in the Cambridge Structural Database, we propose that the intermediate contains a novel bio-organometallic complex in which a reduction product of propargyl alcohol binds as a metalla-cyclopropane ring to a single Fe atom of the Fe-S face of the FeMo-cofactor that is composed of Fe atoms 2, 3, 6, and 7. Of the two most attractive structures, one singly reduced at C3 (4), the other being the doubly reduced allyl alcohol product (6), we tentatively favor 6 because of the "natural" assignment it affords for H(b).
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Affiliation(s)
- Hong-In Lee
- Department of Chemistry Education, Kyungpook National University, Daegu 702-701, Korea.
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Boer DR, Thapper A, Brondino CD, Romão MJ, Moura JJG. X-ray Crystal Structure and EPR Spectra of “Arsenite-Inhibited” Desulfovibrio gigas Aldehyde Dehydrogenase: A Member of the Xanthine Oxidase Family. J Am Chem Soc 2004; 126:8614-5. [PMID: 15250689 DOI: 10.1021/ja0490222] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
X-ray crystallography has been used to determine the structure of arsenite-inhibited aldehyde dehydrogenase from Desulfovibrio gigas, a member of the xanthine oxidase family of mononuclear molybdenum enzymes. The structure shows an AsO3 moiety bound to the molybdenum atom of the active site through one of the oxygen atoms. A reduced sample of arsenite-inhibited aldehyde dehydrogenase has a Mo(V) signal that shows anisotropic hyperfine and quadrupole coupling to one arsenic atom. This signal has a strong resemblance with a previously reported signal for arsenite-inhibited xanthine oxidase.
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Affiliation(s)
- D Roeland Boer
- REQUIMTE-Departamento de Química, CQFB, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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Okamoto K, Matsumoto K, Hille R, Eger BT, Pai EF, Nishino T. The crystal structure of xanthine oxidoreductase during catalysis: implications for reaction mechanism and enzyme inhibition. Proc Natl Acad Sci U S A 2004; 101:7931-6. [PMID: 15148401 PMCID: PMC419534 DOI: 10.1073/pnas.0400973101] [Citation(s) in RCA: 210] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon-oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge-transfer band at approximately 640 nm. The crystal structure of the complex indicates that the catalytically labile Mo-OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the MoS group of the oxidized enzyme has become protonated to afford Mo-SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide.
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Affiliation(s)
- Ken Okamoto
- Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan
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McNaughton RL, Helton ME, Cosper MM, Enemark JH, Kirk ML. Nature of the Oxomolybdenum−Thiolate π-Bond: Implications for Mo−S Bonding in Sulfite Oxidase and Xanthine Oxidase. Inorg Chem 2004; 43:1625-37. [PMID: 14989655 DOI: 10.1021/ic034206n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electronic structure of cis,trans-(L-N(2)S(2))MoO(X) (where L-N(2)S(2) = N,N'-dimethyl-N,N'-bis(2-mercaptophenyl)ethylenediamine and X = Cl, SCH(2)C(6)H(5), SC(6)H(4)-OCH(3), or SC(6)H(4)CF(3)) has been probed by electronic absorption, magnetic circular dichroism, and resonance Raman spectroscopies to determine the nature of oxomolybdenum-thiolate bonding in complexes possessing three equatorial sulfur ligands. One of the phenyl mercaptide sulfur donors of the tetradentate L-N(2)S(2) chelating ligand, denoted S(180), coordinates to molybdenum in the equatorial plane such that the OMo-S(180)-C(phenyl) dihedral angle is approximately 180 degrees, resulting in a highly covalent pi-bonding interaction between an S(180) p orbital and the molybdenum d(xy) orbital. This highly covalent bonding scheme is the origin of an intense low-energy S --> Mo d(xy) bonding-to-antibonding LMCT transition (E(max) approximately 16000 cm(-)(1), epsilon approximately 4000 M(-)(1) cm(-)(1)). Spectroscopically calibrated bonding calculations performed at the DFT level of theory reveal that S(180) contributes approximately 22% to the HOMO, which is predominantly a pi antibonding molecular orbital between Mo d(xy) and the S(180) p orbital oriented in the same plane. The second sulfur donor of the L-N(2)S(2) ligand is essentially nonbonding with Mo d(xy) due to an OMo-S-C(phenyl) dihedral angle of approximately 90 degrees. Because the formal Mo d(xy) orbital is the electroactive or redox orbital, these Mo d(xy)-S 3p interactions are important with respect to defining key covalency contributions to the reduction potential in monooxomolybdenum thiolates, including the one- and two-electron reduced forms of sulfite oxidase. Interestingly, the highly covalent Mo-S(180) pi bonding interaction observed in these complexes is analogous to the well-known Cu-S(Cys) pi bond in type 1 blue copper proteins, which display electronic absorption and resonance Raman spectra that are remarkably similar to these monooxomolybdenum thiolate complexes. Finally, the presence of a covalent Mo-S pi interaction oriented orthogonal to the MOO bond is discussed with respect to electron-transfer regeneration in sulfite oxidase and Mo=S(sulfido) bonding in xanthine oxidase.
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Affiliation(s)
- Rebecca L McNaughton
- Departments of Chemistry, The University of New Mexico, MSC03 2060, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
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Abstract
This Account examines the role of electron-nuclear double resonance (endor) spectroscopy in furthering our understanding of how metal ions function in biological systems. It briefly describes endor and electron spin-echo envelope modulation (eseem) spectroscopies and then illustrates the uses of endor with several case studies from our own research: cytochrome c peroxidase compound ES; ribonucleotide reductase intermediate X; allylbenzene-inactivated chloroperoxidase; the role of the [4Fe-4S](+) cluster in enzymes of the "radical S-adenosylmethionine" superfamily; dioxygen activation by heme enzymes. Finally, it briefly considers future developments.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA.
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Stockert AL, Shinde SS, Anderson RF, Hille R. The reaction mechanism of xanthine oxidase: evidence for two-electron chemistry rather than sequential one-electron steps. J Am Chem Soc 2002; 124:14554-5. [PMID: 12465963 DOI: 10.1021/ja027388d] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Current research on xanthine oxidase has favored a mechanism involving base-catalyzed proton abstraction from a Mo-OH group, allowing nucleophilic attack on the substrate and hydride transfer from the substrate to Mo=S group in the active site. During the course of this reaction mechanism, the molybdenum redox cycles from MoVI to MoIV, with reoxidation of the MoIV speices to form the EPR active MoV intermediate. However, it has also been suggested that the reaction occurs in two subsequent one-electron steps. We have determined kinetic parameters kred and kred/Kd for a variety of plausible substrates as well as the one-electron reduction potentials for these substrates. Our data indicate no correlation between these kinetic parameters and their one-electron reduction potentials, as would be expected if the enzyme were using two subsequent one-electron reduction steps. Our results provide additional support to current evidence for the favored two-electron reduction mechanism.
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Affiliation(s)
- Amy L Stockert
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Abstract
Molybdenum is the only second-row transition metal that is required by most living organisms, and the few species that do not require molybdenum use tungsten, which lies immediately below molybdenum in the periodic table. Because of their unique chemical versatility and unusually high bioavailability these two transition metals have been incorporated into the active sites of enzymes over the course of evolution. Enzymes that contain molybdenum or tungsten continue to be discovered and several crystal structures have become available recently. This new structural information has been complemented by spectroscopic and kinetic methods, as well as computational approaches. Together, these studies provide an increasingly detailed view of the reaction mechanisms and the correlation between the electronic structure of the active site and catalytic function, one of the fundamental goals in metallobiochemistry.
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Affiliation(s)
- Russ Hille
- Dept of Molecular and Cellular Biochemistry and The Protein Research Group, The Ohio State University, Columbus, OH 43210-1218, USA.
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Astashkin AV, Raitsimring AM, Feng C, Johnson JL, Rajagopalan KV, Enemark JH. Pulsed EPR studies of nonexchangeable protons near the Mo(V) center of sulfite oxidase: direct detection of the alpha-proton of the coordinated cysteinyl residue and structural implications for the active site. J Am Chem Soc 2002; 124:6109-18. [PMID: 12022845 DOI: 10.1021/ja0115417] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pulsed electron nuclear double resonance (ENDOR) spectra of nonexchangeable protons in the vicinity of the Mo(V) center of the high pH (hpH) and low pH (lpH) forms of native chicken liver sulfite oxidase (SO) and recombinant human SO have been obtained and analyzed for the first time. The close similarity of the spectra for the chicken and human enzymes indicates that the structures of their molybdenum centers are essentially identical. For lpH SO, the closest nonexchangeable proton is found to be approximately 2.8 A from the Mo atom. To more accurately determine the distance to this proton and facilitate its assignment, the C-band electron spin-echo envelope modulation (ESEEM) spectra of lpH SO were also analyzed. From the obtained distance and comparison with the X-ray structure, this closest nonexchangeable proton is assigned to the alpha-proton of the coordinated conserved cysteinyl residue (Cys185 in chicken, Cys207 in human). The closest Mo...H distance for the nonexchangeable protons of hpH SO is found to be approximately 3.3 A. For the cysteinyl alpha-proton, such an increase in the Mo...H distance only requires a very small change in torsional angles. This study demonstrates that details of the enzyme structural rearrangements with pH can be monitored by ENDOR spectroscopy and suggests that a similar approach may be routinely used to probe the orientation of the coordinated cysteinyl residue in mutant forms of SO that are catalytically compromised.
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Affiliation(s)
- Andrei V Astashkin
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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Butler CS, Fairhurst SA, Ferguson SJ, Thomson AJ, Berks BC, Richardson DJ, Lowe DJ. Mo(V) co-ordination in the periplasmic nitrate reductase from Paracoccus pantotrophus probed by electron nuclear double resonance (ENDOR) spectroscopy. Biochem J 2002; 363:817-23. [PMID: 11964184 PMCID: PMC1222536 DOI: 10.1042/0264-6021:3630817] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The first electron nuclear double resonance (ENDOR) study of a member of the Mo-bis-molybdopterin guanine dinucleotide family of molybdoenzymes is presented, using the periplasmic nitrate reductase from Paracoccus pantotrophus. Rapid freeze-quenched time-resolved EPR revealed that during turnover the intensity of a Mo(V) EPR signal known as High-g [resting] increases. This signal is split by two interacting protons that are not solvent-exchangeable. X-band proton-ENDOR analysis resolved broad symmetrical resonance features that arose from four classes of protons weakly coupled to the Mo(V). Signals from two of these were lost upon exchange into deuterated buffer, suggesting that they may originate from OH(-) or H(2)O groups. One of these signals was also lost when the enzyme was redox-cycled in the presence of azide. Since these protons are very weakly coupled OH/H(2)O groups, they are not likely to be ligated directly to the Mo(V). This suggests that protonation of a Mo(VI)zO group does not occur on reduction to Mo(V), but most probably accompanies reduction of Mo(V) to Mo(IV). A resonance feature from a more strongly coupled proton, that was not lost following exchange into deuterated buffer, could also be resolved at 22-24 MHz. The anisotropy of this feature, determined from ENDOR spectra collected at a range of field positions, indicated a Mo-proton distance of approx. 3.2 A, consistent with this being one of the beta-methylene protons of a Mo-Cys ligand.
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Affiliation(s)
- Clive S Butler
- School of Biological Sciences, Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich NR4 7TJ, UK
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