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Lewis LC, Sanabria-Gracia JA, Lee Y, Jenkins AJ, Shafaat HS. Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase. Chem Sci 2024; 15:5916-5928. [PMID: 38665523 PMCID: PMC11040638 DOI: 10.1039/d4sc00023d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024] Open
Abstract
The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.
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Affiliation(s)
- Luke C Lewis
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - José A Sanabria-Gracia
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - Yuri Lee
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles CA 90095 USA
| | - Adam J Jenkins
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry, The Ohio State University Columbus OH 43210 USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles Los Angeles CA 90095 USA
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Cząstka K, Oughli AA, Rüdiger O, DeBeer S. Enzymatic X-ray absorption spectroelectrochemistry. Faraday Discuss 2022; 234:214-231. [PMID: 35142778 DOI: 10.1039/d1fd00079a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to observe the changes that occur at an enzyme active site during electrocatalysis can provide very valuable information for understanding the mechanism and ultimately aid in catalyst design. Herein, we discuss the development of X-ray absorption spectroscopy (XAS) in combination with electrochemistry for operando studies of enzymatic systems. XAS has had a long history of enabling geometric and electronic structural insights into the catalytic active sites of enzymes, however, XAS combined with electrochemistry (XA-SEC) has been exceedingly rare in bioinorganic applications. Herein, we discuss the challenges and opportunities of applying operando XAS to enzymatic electrocatalysts. The challenges due to the low concentration of the photoabsorber and the instability of the protein in the X-ray beam are discussed. Methods for immobilizing enzymes on the electrodes, while maintaining full redox control are highlighted. A case study of combined XAS and electrochemistry applied to a [NiFe] hydrogenase is presented. By entrapping the [NiFe] hydrogenase in a redox polymer, relatively high protein concentrations can be achieved on the electrode surface, while maintaining redox control. Overall, it is demonstrated that the experiments are feasible, but require precise redox control over the majority of the absorber atoms and careful controls to discriminate between electrochemically-driven changes and beam damage. Opportunities for future applications are discussed.
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Affiliation(s)
- Karolina Cząstka
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
| | - Alaa A Oughli
- Technical University Munich, Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315 Straubing, Germany
| | - Olaf Rüdiger
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, DE, Germany.
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Sarangi R. A biological perspective towards a standard for information exchange and reporting in XAS. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:944-952. [PMID: 29979154 PMCID: PMC6038602 DOI: 10.1107/s1600577518008779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/14/2018] [Indexed: 06/08/2023]
Abstract
The complex structural landscape of biological samples and their sensitivity to X-ray exposure leads to specific challenges in biological X-ray absorption spectroscopy (bio-XAS) research, which in turn has necessitated standardization of various aspects of bio-XAS data measurement, analysis and interpretation. The bio-XAS community is therefore well suited for the development of a data-reporting standard with the specific aim of creating a feedback loop for improving/standardizing data analysis protocols and optionally to make published data available to collaborators/researchers in a meaningful and quantitative format. The XIF (XAFS information file) reporting format presented here contains key experimental and analysis parameters, useful in developing a consistent platform for bio-XAS research worldwide. Such a reporting standard, enforced by the user community and publishing groups alike, can be an important step towards the standardization of data measurement and analysis techniques in bio-XAS.
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Affiliation(s)
- Ritimukta Sarangi
- Structural Molecular Biology, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94306, USA
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DeBeer S. Advanced X-ray Spectroscopic Methods for Studying Iron-Sulfur-Containing Proteins and Model Complexes. Methods Enzymol 2017; 599:427-450. [PMID: 29746249 DOI: 10.1016/bs.mie.2017.09.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this chapter, a brief overview of X-ray spectroscopic methods that may be utilized to obtain insight into the geometric and electronic structure of iron-sulfur proteins is provided. These methods include conventional methods, such as metal and ligand K-edge X-ray absorption, as well as more advanced methods including nonresonant and resonant X-ray emission. In each section, the basic information content of the spectra is highlighted and important experimental considerations are discussed. Throughout the chapter, recent applications to iron-sulfur-containing models and proteins are highlighted.
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Affiliation(s)
- Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany.
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Cramer SP, Hodgson KO. X-Ray Absorption Spectroscopy: A New Structural Method and Its Applications to Bioinorganic Chemistry. PROGRESS IN INORGANIC CHEMISTRY 2007. [DOI: 10.1002/9780470166260.ch1] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Sigfridsson E, Olsson MH, Ryde U. Inner-Sphere Reorganization Energy of Iron−Sulfur Clusters Studied with Theoretical Methods. Inorg Chem 2001; 40:2509-19. [PMID: 11350228 DOI: 10.1021/ic000752u] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Models of several types of iron-sulfur clusters (e.g., Fe(4)S(4)(SCH(3))(4)(2-/3-/4-)) have been studied with the density functional B3LYP method and medium-sized basis sets. In a vacuum, the inner-sphere reorganization energies are 40, 76, 40, 62, 43, and 42 kJ/mol for the rubredoxin, [2Fe-2S] ferredoxin, Rieske, [4Fe-4S] ferredoxin, high-potential iron protein, and desulfoferrodoxin models, respectively. The first two types of clusters were also studied in the protein, where the reorganization energy was approximately halved. This change is caused by the numerous NH.S(Cys) hydrogen bonds to the negatively charged iron-sulfur cluster, giving rise to a polar local environment. The reorganization energy of the iron-sulfur clusters is low because the iron ions retain the same geometry and coordination number in both oxidation states. Cysteine ligands give approximately the same reorganization energy as imidazole, but they have the advantage of stabilizing a lower coordination number and giving more covalent bonds and therefore more effective electron-transfer paths.
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Affiliation(s)
- E Sigfridsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, S-221 00 Lund, Sweden
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Phillips JC. Fluorescence EXAFS detection at the EMBL synchrotron radiation outstation, Hamburg: hardware, software and operational experience. ACTA ACUST UNITED AC 2000. [DOI: 10.1088/0022-3735/14/12/018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Knapp MJ, Krzystek J, Brunel LC, Hendrickson DN. High-frequency EPR study of the ferrous ion in the reduced rubredoxin model. Inorg Chem 2000; 39:281-8. [PMID: 11272536 DOI: 10.1021/ic9910054] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-frequency (94-371 GHz) EPR data are reported for powdered samples of [PPh4]2[Fe(SPh)4], an accurate model for the reduced site of rubredoxins. This is the first HFEPR investigation of an S = 2 ferrous complex, illustrating the utility of this technique for the investigation of integer-spin systems. A full-matrix diagonalization approach is used to simulate spectra over the 94-371 GHz frequency range, providing the spin-Hamiltonian parameters g, D, and E. It is observed that g is anisotropic, characterized by gx = gy = 2.08 and gz = 2.00, and that D = +5.84 cm(-1) and E = +1.42 cm(-1), where the uncertainty in each parameter is estimated as +/- 2%. The spin-Hamiltonian for [PPh4]2[Fe(SPh)4] is related to fundamental properties, such as the crystal-field splitting and the spin-orbit coupling of Fe2+. It is shown that the conventional spin-Hamiltonian accurately represents the electronic structure of the Fe2+ ion in this molecule. Through a comparison with Fe(SPh)4(PPh4)2, the zero-field splitting of the Fe2+ site in reduced rubredoxin is estimated to be D = +5.3 cm(-1) and E = +1.5 cm(-1). This is one of the few HFEPR investigations of a rhombic, high-spin system; as such, it is a step toward the eventual investigation of similar Fe2+ sites in proteins.
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Affiliation(s)
- M J Knapp
- Department of Chemistry and Biochemistry-0358, University of California at San Diego, La Jolla 92093, USA
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StÅlhandske CM, Dong J, Tavares P, Liu MY, LeGall J, Moura JJ, Moura I, Park JB, Adams MW, Scott RA. Probing the iron environment in desulforedoxin. EXAFS of oxidized and reduced states. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)06028-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Xiao Z, Lavery MJ, Ayhan M, Scrofani SDB, Wilce MCJ, Guss JM, Tregloan PA, George GN, Wedd AG. The Rubredoxin from Clostridium pasteurianum: Mutation of the Iron Cysteinyl Ligands to Serine. Crystal and Molecular Structures of Oxidized and Dithionite-Treated Forms of the Cys42Ser Mutant. J Am Chem Soc 1998. [DOI: 10.1021/ja973162c] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhiguang Xiao
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Megan J. Lavery
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Mustafa Ayhan
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Sergio D. B. Scrofani
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Matthew C. J. Wilce
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - J. Mitchell Guss
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Peter A. Tregloan
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Graham N. George
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
| | - Anthony G. Wedd
- Contribution from the School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia, Department of Biochemistry, University of Sydney, Sydney, New South Wales 2006, Australia, and Stanford Synchrotron Radiation Laboratory, SLAC, Stanford University, P.O. Box 4349, MS 69, Stanford, California 94309
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Morante S, Furenlid L, Schiavo G, Tonello F, Zwilling R, Montecucco C. X-ray absorption spectroscopy study of zinc coordination in tetanus neurotoxin, astacin, alkaline protease and thermolysin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 235:606-12. [PMID: 8654408 DOI: 10.1111/j.1432-1033.1996.00606.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tetanus and botulinum neurotoxins constitute a new group of Zn-endopeptidases which has been recently actively investigated with the purpose of correlating their biochemical properties to their neurobiocytosis inhibitory capacity. Crystallographic data show that Zn-endopeptidases are characterized by an active site with a Zn atom coordinated to two histidines and glutamate-bound water molecule. The two histidines and glutamate resides belong to the HEXXH motif which is characteristic of most Zn-endopeptidases. A forth metal ligand is a glutamate in thermolysin-like proteinases, but it is an histidine in the astacin family of proteinases and in alkaline protease. Astacin and alkaline protease possess a tyrosine as fifth Zn ligand, whose position in the case of alkaline protease could not be determined by X-ray crystallography. Not much is known about the atom arrangement around the active site in tetanus neurotoxin. In this work X-ray absorption spectroscopy has been used to obtain information on the Zn coordination mode in tetanus neurotoxin. The near-edge and extended fine-structure absorption spectra of this toxin are compared with those of astacin, alkaline protease and thermolysin. The present data and sequence information suggest a new pattern of Zn coordination in tetanus neurotoxin with one water molecule and three aromatic residues as metal ligands. These residues are the two histidines of the characteristic motif and a tyrosine which is tentatively identified with Tyr242, on the basis of sequence comparison and mutagenesis experiments. The mean distances of the Zn from the nearest coordinated atoms is reported. Our results indicate that alkaline protease, like astacin, also possesses a tyrosine as a fifth ligand.
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Affiliation(s)
- S Morante
- Dipartimento di Fisica, Universita' degli Studi di Roma 'Tor Vergata', Roma, Italy
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Millar M, Lee JF, O'Sullivan T, Koch SA, Fikar R. Models for the iron-sulfur protein rubredoxin: the use of sterically hindered thiolate ligands to stabilize [Fe(SR)4]1− complexes; some considerations of the structure of the [Fe(S-Cys)4] centers in oxidized rubredoxins. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(96)04924-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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X-Ray Absorption Spectroscopy and the Structures of Transition Metal Centers in Proteins. ADVANCES IN INORGANIC CHEMISTRY 1991. [DOI: 10.1016/s0898-8838(08)60042-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Moura I, Tavares P, Moura JJ, Ravi N, Huynh BH, Liu MY, LeGall J. Purification and characterization of desulfoferrodoxin. A novel protein from Desulfovibrio desulfuricans (ATCC 27774) and from Desulfovibrio vulgaris (strain Hildenborough) that contains a distorted rubredoxin center and a mononuclear ferrous center. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)45782-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Bertrand P, Gayda JP. A ligand field analysis of the spectroscopic differences between rubredoxin and desulforedoxin in the reduced state. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 954:347-50. [PMID: 3370220 DOI: 10.1016/0167-4838(88)90090-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We propose a ligand field model to interpret the differences between the spectroscopic properties of reduced rubredoxin and desulforedoxin. The experimental data are well reproduced by using a common set of ligand field parameters and slightly different values of the mixing parameter theta for the two proteins. In this class of iron-sulfur clusters, the rhombic distortion could be modulated by variations of the S-Fe-S angles.
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Affiliation(s)
- P Bertrand
- Laboratoire d'Electronique des Milieux Condensés, UA CNRS 784, Université de Provence, Marseille, France
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Frey M, Sieker L, Payan F, Haser R, Bruschi M, Pepe G, LeGall J. Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4 A resolution. J Mol Biol 1987; 197:525-41. [PMID: 3441010 DOI: 10.1016/0022-2836(87)90562-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The crystal structure of rubredoxin from the sulfate-reducing bacterium Desulfovibrio gigas has been determined at 1.4 A resolution (1 A = 0.1 nm) by X-ray diffraction methods; starting with a model of the isostructural rubredoxin from Desulfovibrio vulgaris. Refinement of the molecular model has been carried out by restrained least-squares techniques and Fourier series calculations. The present model includes a formyl at the N-terminal end and 121 possible sites for solvent molecules with full or partial occupancy, which corresponds to the modeling of nearly all the solvent medium. The crystallographic R factor against the data with 10 A greater than d greater than 1.4 A with F greater than 2 sig(F), is 0.136; and R = 0.140 when all the data are considered. The estimated average root-mean-square (r.m.s.) error on the positional parameters is about 0.12 A. The overall structural features of this molecule are close to those of the two highly refined rubredoxins from Clostridium pasteurianum and D. vulgaris. Superposition of these two molecules on the rubredoxin from D. gigas shows in both cases an overall r.m.s. deviation of 0.5 A for the atoms in the main-chain and of 0.4 A for the atoms in the side-chains that make up the hydrophobic core. The iron atom is co-ordinated to four cysteine sulfur atoms forming an almost regular tetrahedron, with Fe-SG distances ranging from 2.27 A to 2.31 A and angles varying from 103 degrees to 115 degrees. The intramolecular hydrogen-bonding pattern is quite comparable to those found in other proteins refined at high resolution. All the polar groups are involved in hydrogen bonds: intramolecular, intermolecular or with solvent molecules. The main structural differences from the other rubredoxins are in the nature and the distribution of some of the charged residues over the molecular surface. The possible influence of several structural factors on the intramolecular and intermolecular electron transfer properties such as the NH...SG bonds, the solvent exposure of the redox center, and the aromatic core is discussed. The conservation, during evolution, of a ring of acidic residues in the proximity of the FeSG4 center suggests that this ring may be implicated in the recognition processes between rubredoxins and their functional partners.
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Affiliation(s)
- M Frey
- CRMC2-CNRS Campus, Marseille, France
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Bennett DE, Johnson MK. The electronic and magnetic properties of rubredoxin: a low-temperature magnetic circular dichroism study. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 911:71-80. [PMID: 3024732 DOI: 10.1016/0167-4838(87)90272-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oxidized rubredoxin from Clostridium pasteurianum has been investigated by magnetic circular dichroism (MCD) spectroscopy over the temperature range 1.5 to 150 K and at magnetic fields between 0 and 4.5 tesla. The results show that studies of the temperature and field dependence of MCD transitions afford insight into the polarization of electronic transitions for ground states with large g-value anisotropy, in addition to estimates of ground-state g values and zero-field splitting parameters. In agreement with the assignment made by Eaton and Lovenberg (Eaton, W.A. and Lovenberg, W. (1973) in Iron-Sulfur Proteins, Vol. II (Lovenberg, W., ed.), pp. 131-162, Academic Press, New York), the ultraviolet-visible spectrum of oxidized rubredoxin is assigned to two S----Fe(III) charge transfer transitions (both 6A1----6T2 under tetrahedral symmetry), each spanning a range of 650-430 nm and 430-330 nm, respectively. The observed splitting in each of these transitions is attributed to a predominant axial distortion in the excited state resulting in effective D2d symmetry.
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Hasnain SS, Garner CD. Characterization of metal centres in biological systems by X-ray absorption spectroscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1987; 50:47-65. [PMID: 3329745 DOI: 10.1016/0079-6107(87)90003-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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CHANCE B, POWERS L. Structure Of Cytochrome Oxidase Redox Centers in Native and Modified Forms: An EXAFS Study. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/b978-0-12-152514-9.50008-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Abstract
Contents. 1. Introduction and history. 2. Characteristic spectroscopic features of 3Fe clusters. 1. General considerations. 2. Mössbauer spectroscopy. 3. Magnetic circular dichroism (MCD) spectroscopy. 4. Electron paramagnetic resonance (EPR) spectroscopy. 5. Resonance Raman (RR) spectroscopy. 6. Extended X-ray fine-structure (EXAFS) spectroscopy. 3. Results of X-Ray diffraction studies. 4. Proteins containing or showing features characteristic of 3Fe clusters 1. Overview. 2. Ferredoxin I of Azotobacter vinelandii. 3. Ferredoxin II of Desulfovibrio gigas. 4. Aconitase from beef heart. 5. Other observations and considerations relevant to 3Fe clusters or cluster interconversions 1. Oxidative degradation of [4Fe-4S] clusters to 3Fe clusters. 2. Extrusion studies on 3Fe clusters. 3. Reconstitution of 3Fe clusters. 4. Disposition of iron ligands in cluster interconversions. 6. Do all 3Fe clusters have the same structure? Evidence for [3Fe-4S] clusters. 7. Are 3Fe clusters artifacts or biologically significant structures?
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Hahn JE, Hodgson KO, Andersson LA, Dawson JH. Endogenous cysteine ligation in ferric and ferrous cytochrome P-450. Direct evidence from x-ray absorption spectroscopy. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33913-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Powers L. X-ray absorption spectroscopy. Application to biological molecules. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 683:1-38. [PMID: 6291603 DOI: 10.1016/0304-4173(82)90011-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Chance B, Pennie W, Carman M, Legallais V, Powers L. Synchrotron X-ray studies of biological preparations at low temperatures with optical monitoring of sample integrity. Anal Biochem 1982; 124:248-57. [PMID: 7149223 DOI: 10.1016/0003-2697(82)90035-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Phillips JC, Bordas J, Foote AM, Koch MH, Moody MF. Zinc-sulfur bonds of aspartate transcarbamylase studied by x-ray absorption spectroscopy. Biochemistry 1982; 21:830-4. [PMID: 7041968 DOI: 10.1021/bi00534a003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
X-ray absorption spectra have been recorded for aspartate transcarbamylase [unligated and ligated with the transition-state analogue N-(phosphonoacetyl)-L-aspartate] and for the model compound zinc dimethyldithiocarbamate. The spectra confirm that, in the enzyme, the zinc atom is ligated to four sulfur atoms, with a mean distance of 2.34 +/- 0.03 A. A spread in bond lengths of 0.1 +/- 0.03 A is possible, due to thermal and/or static disorder. No significant difference was found between the spectra of the ligated and unligated enzymes.
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Eisenberger P, Okamura MY, Feher G. The electronic structure of Fe2+ in reaction centers from Rhodopseudomonas sphaeroides. II. Extended x-ray fine structure studies. Biophys J 1982; 37:523-38. [PMID: 6977381 PMCID: PMC1328834 DOI: 10.1016/s0006-3495(82)84698-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Extended x-ray absorption fine structure (EXAFS) studies were performed on reaction centers (RC) of the photosynthetic bacterium Rhodopseudomonas sphaeroides R-26. RC containing two, one, and no quinones (2Q, 1Q, 0Q) samples were studied. The average ligand distance of the first coordination shell was determined to be 2.10 +/- 0.02 A with a more distant shell at 4.14 +/- 0.05 A. The Fe2+ site in RC was found to have a very large structural disorder parameter, from which a spread in ligand distance per iron site of approximately +/- 0.1 A was deduced. The most likely coordination number of the first shell is six, with a mixture of oxygens and nitrogens as ligands. The edge absorption results are consistent with the Fe2+ being in distorted octahedral environment. The EXAFS spectra of the 2Q and 1Q samples with and without O-phenanthroline were found to be the same. This indicates that either the secondary quinone and o-phenanthroline do not bind to Fe2+ or that they replace an equivalent ligand. The 0Q sample showed a 12% decrease in the EXAFS amplitude, which was restored upon addition of o-phenanthroline. These results can be explained by either a loss of a ligand or a severe conformational change when the primary quinone was removed.
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Chance B. Structure and function of the redox site of cytochrome oxidase. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1982; 148:95-109. [PMID: 6289641 DOI: 10.1007/978-1-4615-9281-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Il'in VE, Chermashentsev VM. Algorithms and a set of programs for the analysis of exafs spectra. J STRUCT CHEM+ 1982. [DOI: 10.1007/bf00750896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Torensma R, Phillips JC. A comparison of the copper sites in arthropod and mollusc oxyhemocyanins. FEBS Lett 1981; 130:314-6. [PMID: 7286232 DOI: 10.1016/0014-5793(81)81147-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
Synthetic metal complexes can closely approach the properties of metal ions in proteins and yield useful information concerning biological structure and function.
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Abstract
Although the phenomena of extended x=ray absorption fine structure (EXAFS) were observed as early as the 1930's, EXAFS has only recently, with the utilization of synchrotron radiation, been transformed into a powerful structural technique. The theory and experimental practice of the technique are described and illustrated with data on germanium. Applications to systems as diverse as hemoglobin, polymer-bound catalysts, ions in solution, amorphous solids, and adsorbate atoms on surfaces are reviewed. With the recent approval of funding for new, more powerful dedicated synchrotron sources, the future holds the possibility of a virtual revolution in structure determinations.
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