1
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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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2
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Asakura K, Abe H, Kimura M. The challenge of constructing an international XAFS database. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:967-971. [PMID: 29979157 PMCID: PMC6038598 DOI: 10.1107/s1600577518006963] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/07/2018] [Indexed: 05/27/2023]
Abstract
The present state of XAFS databases, particularly in Japan, and proposals for future directions are presented. International collaboration is important for enlarging the database for further development of XAFS spectroscopy.
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Affiliation(s)
- Kiyotaka Asakura
- Institute for Catalysis, Hokkaido University, 21-10 Kita, Sapporo, Hokkaido 001-0021, Japan
| | - Hitoshi Abe
- Photon Factory, Institute of Materials’ Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Department of Materials’ Structure Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Masao Kimura
- Photon Factory, Institute of Materials’ Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Department of Materials’ Structure Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
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3
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Küpper FC, Leblanc C, Meyer-Klaucke W, Potin P, Feiters MC. Different speciation for bromine in brown and red algae, revealed by in vivo X-ray absorption spectroscopic studies. JOURNAL OF PHYCOLOGY 2014; 50:652-664. [PMID: 26988449 DOI: 10.1111/jpy.12199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 03/22/2014] [Indexed: 06/05/2023]
Abstract
Members of various algal lineages are known to be strong producers of atmospherically relevant halogen emissions, that is a consequence of their capability to store and metabolize halogens. This study uses a noninvasive, synchrotron-based technique, X-ray absorption spectroscopy, for addressing in vivo bromine speciation in the brown algae Ectocarpus siliculosus, Ascophyllum nodosum, and Fucus serratus, the red algae Gracilaria dura, G. gracilis, Chondrus crispus, Osmundea pinnatifida, Asparagopsis armata, Polysiphonia elongata, and Corallina officinalis, the diatom Thalassiosira rotula, the dinoflagellate Lingulodinium polyedrum and a natural phytoplankton sample. The results highlight a diversity of fundamentally different bromine storage modes: while most of the stramenopile representatives and the dinoflagellate store mostly bromide, there is evidence for Br incorporated in nonaromatic hydrocarbons in Thalassiosira. Red algae operate various organic bromine stores - including a possible precursor (by the haloform reaction) for bromoform in Asparagopsis and aromatically bound Br in Polysiphonia and Corallina. Large fractions of the bromine in the red algae G. dura and C. crispus and the brown alga F. serratus are present as Br(-) defects in solid KCl, similar to what was reported earlier for Laminaria parts. These results are discussed according to different defensive strategies that are used within algal taxa to cope with biotic or abiotic stresses.
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Affiliation(s)
- Frithjof C Küpper
- Oceanlab, University of Aberdeen, Main Street, Newburgh, AB41 6 AA, UK
- Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Argyll, Oban, PA37 1QA, UK
| | - Catherine Leblanc
- Integrative Biology of Marine Models, Centre National de la Recherche Scientifique, Station Biologique, Roscoff, F-29680, France
- Marine Plants and Biomolecules Laboratory, Université Pierre et Marie Curie, Université Paris 6, Station Biologique, Roscoff, F-29680, France
| | - Wolfram Meyer-Klaucke
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, c/o DESY, Notkestrasse 85, Hamburg, D-22607, Germany
| | - Philippe Potin
- Integrative Biology of Marine Models, Centre National de la Recherche Scientifique, Station Biologique, Roscoff, F-29680, France
- Marine Plants and Biomolecules Laboratory, Université Pierre et Marie Curie, Université Paris 6, Station Biologique, Roscoff, F-29680, France
| | - Martin C Feiters
- Department of Organic Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, NL-6525 AJ, The Netherlands
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4
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Diaz-Moreno S. XAFS data collection: an integrated approach to delivering good data. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:863-868. [PMID: 23093743 DOI: 10.1107/s090904951203854x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/08/2012] [Indexed: 06/01/2023]
Abstract
Energy scale calibration and reliable intensity measurement are the main issues related to the collection of good spectroscopy data. The accurate determination of the energy scale is often established by using foils of optimum thickness to calibrate the monochromator. However, mechanical issues with the monochromator, movement of the source, or even the resolution of the spectrometer can have an effect on the measured energy scale. For the issue of accurate intensity measurements, calibrated detectors are necessary to ensure a reliable measurement of the spectroscopic signal, both in transmission and fluorescence detection modes. In this paper a review of the most common techniques used for energy calibration and for collecting X-ray absorption spectroscopy data is given, together with a brief description of the factors that have an impact on the intensity of the measured signal. A brief description of the versatile X-ray absorption spectroscopy beamline, I20, at Diamond Light Source is also presented, giving particular emphasis on how the beamline design has been undertaken to tackle these key issues. In particular, the use of a four-bounce monochromator will be discussed, highlighting the advantages of the device for the measurement of spectroscopy data.
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Affiliation(s)
- Sofia Diaz-Moreno
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK.
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5
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Zitolo A, Chillemi G, D’Angelo P. X-ray Absorption Study of the Solvation Structure of Cu2+ in Methanol and Dimethyl Sulfoxide. Inorg Chem 2012; 51:8827-33. [DOI: 10.1021/ic3006647] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Zitolo
- Dipartimento di
Chimica, Universit̀a di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Giovanni Chillemi
- CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii
6b, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento di
Chimica, Universit̀a di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
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6
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Hong X, Chen Z, Duffy TS. Absolute x-ray energy calibration over a wide energy range using a diffraction-based iterative method. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:063901. [PMID: 22755637 DOI: 10.1063/1.4722166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this paper, we report a method of precise and fast absolute x-ray energy calibration over a wide energy range using an iterative x-ray diffraction based method. Although accurate x-ray energy calibration is indispensable for x-ray energy-sensitive scattering and diffraction experiments, there is still a lack of effective methods to precisely calibrate energy over a wide range, especially when normal transmission monitoring is not an option and complicated micro-focusing optics are fixed in place. It is found that by using an iterative algorithm the x-ray energy is only tied to the relative offset of sample-to-detector distance, which can be readily varied with high precision of the order of 10(-5) -10(-6) spatial resolution using gauge blocks. Even starting with arbitrary initial values of 0.1 Å, 0.3 Å, and 0.4 Å, the iteration process converges to a value within 3.5 eV for 31.122 keV x-rays after three iterations. Different common diffraction standards CeO(2), Au, and Si show an energy deviation of 14 eV. As an application, the proposed method has been applied to determine the energy-sensitive first sharp diffraction peak of network forming GeO(2) glass at high pressure, exhibiting a distinct behavior in the pressure range of 2-4 GPa. Another application presented is pair distribution function measurement using calibrated high-energy x-rays at 82.273 keV. Unlike the traditional x-ray absorption-based calibration method, the proposed approach does not rely on any edges of specific elements, and is applicable to the hard x-ray region where no appropriate absorption edge is available.
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Affiliation(s)
- Xinguo Hong
- Mineral Physics Institute, Stony Brook University, Stony Brook, New York 11794, USA.
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7
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Migliorati V, Zitolo A, Chillemi G, D'Angelo P. Influence of the Second Coordination Shell on the XANES Spectra of the Zn2+ Ion in Water and Methanol. Chempluschem 2012. [DOI: 10.1002/cplu.201100070] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Migliorati V, Chillemi G, D’Angelo P. On the Solvation of the Zn2+ Ion in Methanol: A Combined Quantum Mechanics, Molecular Dynamics, and EXAFS Approach. Inorg Chem 2011; 50:8509-15. [DOI: 10.1021/ic201100q] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Giovanni Chillemi
- CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii 6b, 00185 Roma, Italy
| | - Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
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9
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Fritsch J, Löscher S, Sanganas O, Siebert E, Zebger I, Stein M, Ludwig M, De Lacey AL, Dau H, Friedrich B, Lenz O, Haumann M. [NiFe] and [FeS] Cofactors in the Membrane-Bound Hydrogenase of Ralstonia eutropha Investigated by X-ray Absorption Spectroscopy: Insights into O2-Tolerant H2 Cleavage. Biochemistry 2011; 50:5858-69. [DOI: 10.1021/bi200367u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Johannes Fritsch
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | - Simone Löscher
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Oliver Sanganas
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Elisabeth Siebert
- Technische Universität Berlin, Max-Volmer Institut, 10623 Berlin, Germany
| | - Ingo Zebger
- Technische Universität Berlin, Max-Volmer Institut, 10623 Berlin, Germany
| | - Matthias Stein
- Max-Planck-Institut für Dynamik komplexer technischer Systeme, 39106 Magdeburg, Germany
| | - Marcus Ludwig
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | | | - Holger Dau
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Bärbel Friedrich
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | - Oliver Lenz
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, 10115 Berlin, Germany
| | - Michael Haumann
- Freie Universität Berlin, Institut für Experimentalphysik, 14195 Berlin, Germany
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10
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Zitolo A, D’Angelo P. X-ray absorption spectroscopy study of the solvation structure of zinc(II) in dimethyl sulfoxide solution. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.09.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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X-Ray absorption spectroscopic studies on iron in soybean lipoxygenase: A model for mammalian lipoxygenases. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090302] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Löscher S, Gebler A, Stein M, Sanganas O, Buhrke T, Zebger I, Dau H, Friedrich B, Lenz O, Haumann M. Protein-protein complex formation affects the Ni-Fe and Fe-S centers in the H2-sensing regulatory hydrogenase from Ralstonia eutropha H16. Chemphyschem 2010; 11:1297-306. [PMID: 20340124 DOI: 10.1002/cphc.200901007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The regulatory Ni-Fe hydrogenase (RH) from the H(2)-oxidizing bacterium Ralstonia eutropha functions as an oxygen-resistant hydrogen sensor, which is composed of the large, active-site-containing HoxC subunit and the small subunit HoxB carrying Fe-S clusters. In vivo, the HoxBC subunits form a dimer designated as RH(wt). The RH(wt) protein transmits its signals to the histidine protein kinase HoxJ, which itself forms a homotetramer and a stable complex with RH(wt) (RH(wt)-HoxJ(wt)), located in the cytoplasm. In this study, we used X-ray absorption (XAS), electron paramagnetic resonance (EPR), and Fourier transform infrared (FTIR) spectroscopy to investigate the impact of various complexes between RH and HoxJ on the structural and electronic properties of the Ni-Fe active site and the Fe-S clusters. Aside from the RH(wt) protein and the RH(wt)-HoxJ(wt) complex, we investigated the RH(stop) protein, which consists of only one HoxB and HoxC unit due to the missing C-terminus of HoxB, as well as RH(wt)-HoxJ(Deltakinase), in which the histidine protein kinase lacks the transmitter domain. All constructs reacted with H(2), leading to the formation of the EPR-detectable Ni(III)-C state of the active site and to the reduction of Fe-S clusters detectable by XAS, thus corroborating that H(2) cleavage is independent of the presence of the HoxJ protein. In RH(stop), presumably one Fe-S cluster was lost during the preparation procedure. The coordination of the active site Ni in RH(stop) differed from that in RH(wt) and the RH(wt)-HoxJ complexes, in which additional Ni--O bonds were detected by XAS. The Ni--O bonds caused only very minor changes of the EPR g-values of the Ni-C and Ni-L states and of the IR vibrational frequencies of the diatomic CN(-) and CO ligands at the active-site Fe ion. Both one Fe-S cluster in HoxB and an oxygen-rich Ni coordination seem to be stabilized by RH dimerization involving the C-terminus of HoxB and by complex formation with HoxJ.
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Affiliation(s)
- Simone Löscher
- Experimental Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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13
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Liebisch P, Dau H. Linear Dichroism in the XANES of Partially Oriented Samples: Theory and Application to the Photosynthetic Manganese Complex. Chemphyschem 2010; 11:1236-47. [DOI: 10.1002/cphc.200900954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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14
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Trampczynska A, Küpper H, Meyer-Klaucke W, Schmidt H, Clemens S. Nicotianamine forms complexes with Zn(ii)in vivo. Metallomics 2010; 2:57-66. [DOI: 10.1039/b913299f] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Küpper H, Götz B, Mijovilovich A, Küpper FC, Meyer-Klaucke W. Complexation and toxicity of copper in higher plants. I. Characterization of copper accumulation, speciation, and toxicity in Crassula helmsii as a new copper accumulator. PLANT PHYSIOLOGY 2009; 151:702-14. [PMID: 19641032 PMCID: PMC2754650 DOI: 10.1104/pp.109.139717] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 07/20/2009] [Indexed: 05/19/2023]
Abstract
The amphibious water plant Crassula helmsii is an invasive copper (Cu)-tolerant neophyte in Europe. It now turned out to accumulate Cu up to more than 9,000 ppm in its shoots at 10 microm (=0.6 ppm) Cu(2+) in the nutrient solution, indicating that it is a Cu hyperaccumulator. We investigated uptake, binding environment, and toxicity of Cu in this plant under emerged and submerged conditions. Extended x-ray absorption fine structure measurements on frozen-hydrated samples revealed that Cu was bound almost exclusively by oxygen ligands, likely organic acids, and not any sulfur ligands. Despite significant differences in photosynthesis biochemistry and biophysics between emerged and submerged plants, no differences in Cu ligands were found. While measurements of tissue pH confirmed the diurnal acid cycle typical for Crassulacean acid metabolism, Delta(13)C measurements showed values typical for regular C3 photosynthesis. Cu-induced inhibition of photosynthesis mainly affected the photosystem II (PSII) reaction center, but with some unusual features. Most obviously, the degree of light saturation of electron transport increased during Cu stress, while maximal dark-adapted PSII quantum yield did not change and light-adapted quantum yield of PSII photochemistry decreased particularly in the first 50 s after onset of actinic irradiance. This combination of changes, which were strongest in submerged cultures, shows a decreasing number of functional reaction centers relative to the antenna in a system with high antenna connectivity. Nonphotochemical quenching, in contrast, was modified by Cu mainly in emerged cultures. Pigment concentrations in stressed plants strongly decreased, but no changes in their ratios occurred, indicating that cells either survived intact or died and bleached quickly.
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Affiliation(s)
- Hendrik Küpper
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, D-78457 Konstanz, Germany.
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Mijovilovich A, Leitenmaier B, Meyer-Klaucke W, Kroneck PMH, Götz B, Küpper H. Complexation and toxicity of copper in higher plants. II. Different mechanisms for copper versus cadmium detoxification in the copper-sensitive cadmium/zinc hyperaccumulator Thlaspi caerulescens (Ganges Ecotype). PLANT PHYSIOLOGY 2009; 151:715-31. [PMID: 19692532 PMCID: PMC2754615 DOI: 10.1104/pp.109.144675] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2009] [Accepted: 08/12/2009] [Indexed: 05/06/2023]
Abstract
The cadmium/zinc hyperaccumulator Thlaspi caerulescens is sensitive toward copper (Cu) toxicity, which is a problem for phytoremediation of soils with mixed contamination. Cu levels in T. caerulescens grown with 10 microm Cu(2+) remained in the nonaccumulator range (<50 ppm), and most individuals were as sensitive toward Cu as the related nonaccumulator Thlaspi fendleri. Obviously, hyperaccumulation and metal resistance are highly metal specific. Cu-induced inhibition of photosynthesis followed the "sun reaction" type of damage, with inhibition of the photosystem II reaction center charge separation and the water-splitting complex. A few individuals of T. caerulescens were more Cu resistant. Compared with Cu-sensitive individuals, they recovered faster from inhibition, at least partially by enhanced repair of chlorophyll-protein complexes but not by exclusion, since the content of Cu in their shoots was increased by about 25%. Extended x-ray absorption fine structure (EXAFS) measurements on frozen-hydrated leaf samples revealed that a large proportion of Cu in T. caerulescens is bound by sulfur ligands. This is in contrast to the known binding environment of cadmium and zinc in the same species, which is dominated by oxygen ligands. Clearly, hyperaccumulators detoxify hyperaccumulated metals differently compared with nonaccumulated metals. Furthermore, strong features in the Cu-EXAFS spectra ascribed to metal-metal contributions were found, in particular in the Cu-resistant specimens. Some of these features may be due to Cu binding to metallothioneins, but a larger proportion seems to result from biomineralization, most likely Cu(II) oxalate and Cu(II) oxides. Additional contributions in the EXAFS spectra indicate complexation of Cu(II) by the nonproteogenic amino acid nicotianamine, which has a very high affinity for Cu(II) as further characterized here.
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Affiliation(s)
- Ana Mijovilovich
- Department of Inorganic Chemistry and Catalysis, University of Utrecht, 3584 CA Utrecht, The Netherlands
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17
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Heinz U, Hemmingsen L, Kiefer M, Adolph HW. Structural Adaptability of Zinc Binding Sites: Different Structures in Partially, Fully, and Heavy-Metal Loaded States. Chemistry 2009; 15:7350-8. [DOI: 10.1002/chem.200900870] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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The two distinctive metal ion binding domains of the wheat metallothionein Ec-1. J Inorg Biochem 2009; 103:342-53. [DOI: 10.1016/j.jinorgbio.2008.11.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 11/12/2008] [Accepted: 11/18/2008] [Indexed: 11/23/2022]
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19
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Hollenstein K, Comellas-Bigler M, Bevers LE, Feiters MC, Meyer-Klaucke W, Hagedoorn PL, Locher KP. Distorted octahedral coordination of tungstate in a subfamily of specific binding proteins. J Biol Inorg Chem 2009; 14:663-72. [PMID: 19234723 DOI: 10.1007/s00775-009-0479-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 02/04/2009] [Indexed: 11/30/2022]
Abstract
Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). These substrates are captured by an external, high-affinity binding protein, and delivered to ATP binding cassette transporters, which move them across the cell membrane. We have recently reported a crystal structure of the molybdate/tungstate binding protein ModA/WtpA from Archaeoglobus fulgidus, which revealed an octahedrally coordinated central metal atom. By contrast, the previously determined structures of three bacterial homologs showed tetracoordinate molybdenum and tungsten atoms in their binding pockets. Until then, coordination numbers above four had only been found for molybdenum/tungsten in metalloenzymes where these metal atoms are part of the catalytic cofactors and coordinated by mostly non-oxygen ligands. We now report a high-resolution structure of A. fulgidus ModA/WtpA, as well as crystal structures of four additional homologs, all bound to tungstate. These crystal structures match X-ray absorption spectroscopy measurements from soluble, tungstate-bound protein, and reveal the details of the distorted octahedral coordination. Our results demonstrate that the distorted octahedral geometry is not an exclusive feature of the A. fulgidus protein, and suggest distinct binding modes of the binding proteins from archaea and bacteria.
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Affiliation(s)
- Kaspar Hollenstein
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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20
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D’Angelo P, Migliorati V, Mancini G, Chillemi G. A Coupled Molecular Dynamics and XANES Data Analysis Investigation of Aqueous Cadmium(II). J Phys Chem A 2008; 112:11833-41. [DOI: 10.1021/jp806098r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy, and CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii 6b, 00185 Roma, Italy
| | - Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy, and CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii 6b, 00185 Roma, Italy
| | - Giordano Mancini
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy, and CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii 6b, 00185 Roma, Italy
| | - Giovanni Chillemi
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Roma, Italy, and CASPUR, Inter-University Consortium for Supercomputing in Research, via dei Tizii 6b, 00185 Roma, Italy
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21
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D’Angelo P, Lapi A, Migliorati V, Arcovito A, Benfatto M, Roscioni OM, Meyer-Klaucke W, Della-Longa S. X-ray Absorption Spectroscopy of Hemes and Hemeproteins in Solution: Multiple Scattering Analysis. Inorg Chem 2008; 47:9905-18. [DOI: 10.1021/ic800982a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Paola D’Angelo
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Andrea Lapi
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Valentina Migliorati
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Alessandro Arcovito
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Maurizio Benfatto
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Otello Maria Roscioni
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Wolfram Meyer-Klaucke
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
| | - Stefano Della-Longa
- Dipartimento di Chimica, Università di Roma “La Sapienza”, P. le A. Moro 5, 00185 Rome, Italy, Istituto CNR di Metodologie Chimiche-IMC, Sezione Meccanismi di Reazione, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5, 00185 Rome, Italy, Laboratori Nazionali di Frascati, INFN CP13, 00044 Frascati, Italy, Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, L.go F. Vito 1, 00168 Rome, Italy, European Molecular Biology Laboratory, Hamburg Unit,
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22
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Comparative Fe and Zn K-edge X-ray absorption spectroscopic study of the ferroxidase centres of human H-chain ferritin and bacterioferritin from Desulfovibrio desulfuricans. J Biol Inorg Chem 2008; 14:35-49. [DOI: 10.1007/s00775-008-0422-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022]
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23
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Iron–sulfur repair YtfE protein from Escherichia coli: structural characterization of the di-iron center. J Biol Inorg Chem 2008; 13:765-70. [DOI: 10.1007/s00775-008-0362-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Accepted: 03/07/2008] [Indexed: 11/25/2022]
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24
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Voronova A, Meyer-Klaucke W, Meyer T, Rompel A, Krebs B, Kazantseva J, Sillard R, Palumaa P. Oxidative switches in functioning of mammalian copper chaperone Cox17. Biochem J 2007; 408:139-48. [PMID: 17672825 PMCID: PMC2049083 DOI: 10.1042/bj20070804] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cox17, a copper chaperone for cytochrome-c oxidase, is an essential and highly conserved protein in eukaryotic organisms. Yeast and mammalian Cox17 share six conserved cysteine residues, which are involved in complex redox reactions as well as in metal binding and transfer. Mammalian Cox17 exists in three oxidative states, each characterized by distinct metal-binding properties: fully reduced mammalian Cox17(0S-S) binds co-operatively to four Cu+; Cox17(2S-S), with two disulfide bridges, binds to one of either Cu+ or Zn2+; and Cox17(3S-S), with three disulfide bridges, does not bind to any metal ions. The E(m) (midpoint redox potential) values for two redox couples of Cox17, Cox17(3S-S)<-->Cox17(2S-S) (E(m1)) and Cox17(2S-S)<-->Cox17(0S-S) (E(m2)), were determined to be -197 mV and -340 mV respectively. The data indicate that an equilibrium exists in the cytosol between Cox17(0S-S) and Cox17(2S-S), which is slightly shifted towards Cox17(0S-S). In the IMS (mitochondrial intermembrane space), the equilibrium is shifted towards Cox17(2S-S), enabling retention of Cox17(2S-S) in the IMS and leading to the formation of a biologically competent form of the Cox17 protein, Cox17(2S-S), capable of copper transfer to the copper chaperone Sco1. XAS (X-ray absorption spectroscopy) determined that Cu4Cox17 contains a Cu4S6-type copper-thiolate cluster, which may provide safe storage of an excess of copper ions.
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Affiliation(s)
- Anastassia Voronova
- *Department of Gene Technology, Tallinn Technical University, Akadeemia tee 15, 12618 Tallinn, Estonia
| | | | - Thomas Meyer
- ‡Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Annette Rompel
- ‡Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Bernt Krebs
- ‡Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Jekaterina Kazantseva
- *Department of Gene Technology, Tallinn Technical University, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Rannar Sillard
- *Department of Gene Technology, Tallinn Technical University, Akadeemia tee 15, 12618 Tallinn, Estonia
| | - Peep Palumaa
- *Department of Gene Technology, Tallinn Technical University, Akadeemia tee 15, 12618 Tallinn, Estonia
- To whom correspondence should be addressed (email )
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25
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Lucarelli D, Russo S, Garman E, Milano A, Meyer-Klaucke W, Pohl E. Crystal Structure and Function of the Zinc Uptake Regulator FurB from Mycobacterium tuberculosis. J Biol Chem 2007; 282:9914-9922. [PMID: 17213192 DOI: 10.1074/jbc.m609974200] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Members of the ferric/zinc uptake regulator (Fur/Zur) family are the central metal-dependent regulator proteins in many Gram-negative and -positive bacteria. They are responsible for the control of a wide variety of basic physiological processes and the expression of important virulence factors in human pathogens. Therefore, Fur has gathered significant interest as a potential target for novel antibiotics. Here we report the crystal structure of FurB from Mycobacterium tuberculosis at a resolution of 2.7A, and we present biochemical and spectroscopic data that allow us to propose the functional role of this protein. Although the overall fold of FurB with an N-terminal DNA binding domain and a C-terminal dimerization domain is conserved among the Zur/Fur family, large differences in the spatial arrangement of the two domains with respect to each other can be observed. The biochemical and spectroscopic analysis presented here reveals that M. tuberculosis FurB is Zn(II)-dependent and is likely to control genes involved in the bacterial zinc uptake. The combination of the structural, spectroscopic, and biochemical results enables us to determine the structural basis for functional differences in this important family of bacterial regulators.
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Affiliation(s)
- Debora Lucarelli
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Santina Russo
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Elspeth Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anna Milano
- Department of Genetics and Microbiology, University of Pavia, 27100 Pavia, Italy
| | - Wolfram Meyer-Klaucke
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany.
| | - Ehmke Pohl
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen, Switzerland.
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26
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del Pino P, Weiss A, Bertsch U, Renner C, Mentler M, Grantner K, Fiorino F, Meyer-Klaucke W, Moroder L, Kretzschmar HA, Parak FG. The configuration of the Cu2+ binding region in full-length human prion protein. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:239-52. [PMID: 17225136 DOI: 10.1007/s00249-006-0124-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Revised: 12/11/2006] [Accepted: 12/18/2006] [Indexed: 11/28/2022]
Abstract
The cellular prion protein (PrP(C)) is a Cu(2+) binding protein connected to the outer cell membrane. The molecular features of the Cu(2+) binding sites have been investigated and characterized by spectroscopic experiments on PrP(C)-derived peptides and the recombinant human full-length PrP(C )(hPrP-[23-231]). The hPrP-[23-231] was loaded with (63)Cu under slightly acidic (pH 6.0) or neutral conditions. The PrP(C)/Cu(2+)-complexes were investigated by extended X-ray absorption fine structure (EXAFS), electron paramagnetic resonance (EPR), and electron nuclear double resonance (ENDOR). For comparison, peptides from the copper-binding octarepeat domain were investigated in different environments. Molecular mechanics computations were used to select sterically possible peptide/Cu(2+) structures. The simulated EPR, ENDOR, and EXAFS spectra of these structures were compared with our experimental data. For a stoichiometry of two octarepeats per copper the resulting model has a square planar four nitrogen Cu(2+) coordination. Two nitrogens belong to imidazole rings of histidine residues. Further ligands are two deprotonated backbone amide nitrogens of the adjacent glycine residues and an axial oxygen of a water molecule. Our complex model differs significantly from those previously obtained for shorter peptides. Sequence context, buffer conditions and stoichiometry of copper show marked influence on the configuration of copper binding to PrP(C).
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Affiliation(s)
- Pablo del Pino
- Physics Department E17, Technical University Munich, 85747 Garching, Germany
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27
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Mangani S, Benvenuti M, Moir AJG, Ranieri-Raggi M, Martini D, Sabbatini ARM, Raggi A. Characterization of the metallocenter of rabbit skeletal muscle AMP deaminase. Evidence for a dinuclear zinc site. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1774:312-22. [PMID: 17254852 DOI: 10.1016/j.bbapap.2006.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 12/06/2006] [Accepted: 12/18/2006] [Indexed: 11/29/2022]
Abstract
XAS of Zn-peptide binary and ternary complexes prepared using peptides mimicking the potential metal binding sites of rabbit skeletal muscle AMP deaminase (AMPD) strongly suggest that the region 48-61 of the enzyme contains a zinc binding site, whilst the region 360-372 of the enzyme is not able to form 1:1 complexes with zinc, in contrast with what has been suggested for the corresponding region of yeast AMPD. XAS performed on fresh preparations of rabbit skeletal muscle AMPD provides evidence for a dinuclear zinc site in the enzyme compatible with a (mu-aqua)(mu-carboxylato)dizinc(II) core with an average of two histidine residues at each metal site and a Zn-Zn distance of about 3.3 Angstrom. The data indicate that zinc is not required for HPRG/AMPD interaction, both zinc ions being bound to the catalytic subunit of the enzyme, one to the three conserved amino acid residues among those four assumed to be in contact with zinc in yeast AMPD, and the other at the N-terminal region, probably to His-52, Glu-53 and His-57. Tryptic digests of different enzyme preparations demonstrate the existence of two different protein conformations and of a zinc ion connecting the N-terminal and C-terminal regions of AMPD.
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Affiliation(s)
- Stefano Mangani
- Dipartimento di Chimica, Università di Siena, Via Aldo Moro, 53100-Siena, Italy; CERM, Università di Firenze, Via Luigi Sacconi 6, 50019 Firenze, Italy
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28
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Haumann M, Barra M, Loja P, Löscher S, Krivanek R, Grundmeier A, Andreasson LE, Dau H. Bromide does not bind to the Mn4Ca complex in its S1 state in Cl(-)-depleted and Br(-)-reconstituted oxygen-evolving photosystem II: evidence from X-ray absorption spectroscopy at the Br K-edge. Biochemistry 2006; 45:13101-7. [PMID: 17059227 DOI: 10.1021/bi061308r] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chloride is an important cofactor in photosynthetic water oxidation. It can be replaced by bromide with retention of the oxygen-evolving activity of photosystem II (PSII). Binding of bromide to the Mn(4)Ca complex of PSII in its dark-stable S(1) state was studied by X-ray absorption spectroscopy (XAS) at the Br K-edge in Cl(-)-depleted and Br(-)-substituted PSII membrane particles from spinach. The XAS spectra exclude the presence of metal ions in the first and second coordination spheres of Br(-). EXAFS analysis provided tentative evidence of at least one metal ion, which may be manganese or calcium, at a distance of approximately 5 A to Br(-). The native Cl(-) ion may bind at a similar distance. Accordingly, water oxidation may not require binding of a halide directly to the metal ions of the Mn complex in its S(1) state.
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Affiliation(s)
- Michael Haumann
- Freie Universität Berlin, FB Physik, Arnimallee 14, D-14195 Berlin, Germany
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29
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Spezia R, Duvail M, Vitorge P, Cartailler T, Tortajada J, Chillemi G, D'Angelo P, Gaigeot MP. A Coupled Car-Parrinello Molecular Dynamics and EXAFS Data Analysis Investigation of Aqueous Co2+. J Phys Chem A 2006; 110:13081-8. [PMID: 17134169 DOI: 10.1021/jp064688z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have studied the microscopic solvation structure of Co(2+) in liquid water by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations and extended X-ray absorption fine structure (EXAFS) data analysis. The effect of the number of explicit water molecules in the simulation box on the first and second hydration shell structures has been considered. Classical molecular dynamics simulations, using an effective two-body potential for Co(2+)-water interactions, were also performed to show box size effects in a larger range. We have found that the number of explicit solvent molecules has a marginal role on the first solvation shell structural parameters, whereas larger boxes may be necessary to provide a better description of the second solvation shell. Car-Parrinello simulations were determined to provide a reliable description of structural and dynamical properties of Co(2+) in liquid water. In particular, they seem to describe both the first and second hydration shells correctly. The EXAFS signal was reconstructed from Car-Parrinello simulations. Good agreement between the theoretical and experimental signals was observed, thus strengthening the microscopic picture of the Co(2+) solvation properties obtained using first-principle simulations.
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Affiliation(s)
- Riccardo Spezia
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR-CNRS 8587, Université d'Evry Val d'Essonne, Boulevard F. Mitterrand, 91025 Evry Cedex, France
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30
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Korbas M, Vogt S, Meyer-Klaucke W, Bill E, Lyon EJ, Thauer RK, Shima S. The iron-sulfur cluster-free hydrogenase (Hmd) is a metalloenzyme with a novel iron binding motif. J Biol Chem 2006; 281:30804-13. [PMID: 16887798 DOI: 10.1074/jbc.m605306200] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing cofactor of yet unknown structure. X-ray absorption spectroscopy of the active, as isolated enzyme from Methanothermobacter marburgensis (mHmd) and of the active, reconstituted enzyme from Methanocaldococcus jannaschii (jHmd) revealed the presence of mononuclear iron with two CO, one sulfur and one or two N/O in coordination distance. In jHmd, the single sulfur ligand is most probably provided by Cys176, as deduced from a comparison of the activity and of the x-ray absorption and Mössbauer spectra of the enzyme mutated in any of the three conserved cysteines. In the isolated Hmd cofactor, two CO, one sulfur, and two nitrogen/oxygen atoms coordinate the iron, the sulfur ligand being most probably provided by mercaptoethanol, which is absolutely required for the extraction of the iron-containing cofactor from the holoenzyme and for the stabilization of the extracted cofactor. In active mHmd holoenzyme, the number of iron ligands increased by one when one of the Hmd inhibitors (CO or KCN) were present, indicating that in active Hmd, the iron contains an open coordination site, which is proposed to be the site of H2 interaction.
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Affiliation(s)
- Malgorzata Korbas
- European Molecular Biology Laboratory (EMBL), Outstation Hamburg at Deutsches Electronen Synchroton (DESY), Notkestrasse 85, D-22603 Hamburg, Germany
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31
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Stola M, Musiani F, Mangani S, Turano P, Safarov N, Zambelli B, Ciurli S. The nickel site of Bacillus pasteurii UreE, a urease metallo-chaperone, as revealed by metal-binding studies and X-ray absorption spectroscopy. Biochemistry 2006; 45:6495-509. [PMID: 16700560 DOI: 10.1021/bi0601003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UreE is a homodimeric metallo-chaperone that assists the insertion of Ni(2+) ions in the active site of urease. The crystal structures of UreE from Bacillus pasteurii and Klebsiella aerogenes have been determined, but the details of the nickel-binding site were not elucidated due to solid-state effects that caused disorder in a key portion of the protein. A complementary approach to this problem is described here. Titrations of wild-type Bacillus pasteurii UreE (BpUreE) with Ni(2+), followed by metal ion quantitative analysis using inductively coupled plasma optical emission spectrometry (ICP-OES), established the binding of 2 Ni(2+) ions to the functional dimer, with an overall dissociation constant K(D) = 35 microM. To establish the nature, the number, and the geometry of the ligands around the Ni(2+) ions in BpUreE-Ni(2), X-ray absorption spectroscopy data were collected and analyzed using an approach that combines ab initio extended X-ray absorption fine structure (EXAFS) calculations with a systematic search of several possible coordination geometries, using the Simplex algorithm. This analysis indicated the presence of Ni(2+) ions in octahedral coordination geometry and an average of two histidine residues and four O/N ligands bound to each metal ion. The fit improved significantly with the incorporation, in the model, of a Ni-O-Ni moiety, suggesting the presence of a hydroxide-bridged dinuclear cluster in the Ni-loaded BpUreE. These results were interpreted using two possible models. One model involves the presence of two identical metal sites binding Ni(2+) with negative cooperativity, with each metal ion bound to the conserved His(100) as well as to either His(145) or His(147) from each monomer, residues found largely conserved at the C-terminal. The alternative model comprises the presence of two different binding sites featuring different affinity for Ni(2+). This latter model would involve the presence of a dinuclear metallic core, with one Ni(2+) ion bound to one His(100) from each monomer, and the second Ni(2+) ion bound to a pair of either His(145) or His(147). The arguments in favor of one model as compared to the other are discussed on the basis of the available biochemical data.
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Affiliation(s)
- Massimiliano Stola
- Laboratory of Bioinorganic Chemistry, Department of Agro-Environmental Science and Technology, University of Bologna, Viale Giuseppe Fanin 40, 40127 Bologna, Italy
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32
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D'Angelo P, Roscioni OM, Chillemi G, Della Longa S, Benfatto M. Detection of Second Hydration Shells in Ionic Solutions by XANES: Computed Spectra for Ni2+ in Water Based on Molecular Dynamics. J Am Chem Soc 2006; 128:1853-8. [PMID: 16464084 DOI: 10.1021/ja0562503] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general procedure to compute X-ray absorption near-edge structure (XANES) spectra within multiple-scattering theory starting from molecular dynamics (MD) structural data has been developed and applied to the study of a Ni(2+) aqueous solution. This method allows one to perform a quantitative analysis of the XANES spectra of disordered systems using a proper description of the thermal and structural fluctuations. The XANES spectrum of Ni(2+) in aqueous solution has been calculated using the structural information obtained from the MD simulations without carrying out any minimization in the structural parameter space. A very good reproduction of the experimental data was obtained including the second-shell water molecules in the calculation, thus showing that the second hydration shell provides a detectable contribution to the XANES spectra of ionic solutions. The analysis including the first-shell cluster only permitted us to quantitatively determine the effect of disorder on the amplitude of the XANES spectra for molecular complexes. These results simultaneously confirm the reliability of the procedure and the structural results obtained from MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.
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Affiliation(s)
- Paola D'Angelo
- Dipartimento di Chimica, Università di Roma La Sapienza, Piazzale A. Moro 5, 00185 Rome, Italy.
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33
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Küsel A, Zhang J, Alvariño Gil M, Stückl AC, Meyer-Klaucke W, Meyer F, Diederichsen U. Metal Binding Within a Peptide-Based Nucleobase Stack with Tuneable Double-Strand Topology. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500464] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Löscher S, Zebger I, Andersen LK, Hildebrandt P, Meyer-Klaucke W, Haumann M. The structure of the Ni-Fe site in the isolated HoxC subunit of the hydrogen-sensing hydrogenase from Ralstonia eutropha. FEBS Lett 2005; 579:4287-91. [PMID: 16051223 DOI: 10.1016/j.febslet.2005.06.063] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 06/16/2005] [Accepted: 06/28/2005] [Indexed: 10/25/2022]
Abstract
The regulatory Ni-Fe hydrogenase (RH) from Ralstonia eutropha which forms a [HoxBC]2 complex functions as a hydrogen sensor under aerobic conditions. We have studied a novel Strep-tag isolate of the RH large subunit, HoxC(ST), which lacks the Fe-S clusters of HoxB, allowing for structure determination of the catalytic site by X-ray absorption spectroscopy both at the Ni and, for the first time, also at the Fe K-edge. This technique, together with Fourier-transform infrared spectroscopy, revealed a Ni-Fe site with [O1(CysS)2Ni(II)(mu-SCys)2Fe(II)(CN)2(CO)] structure in about 50% of HoxC(ST) and a [(CysS)2Fe(II)(CN)2(CO)] site lacking Ni in the remainder protein. Possibly both sites may be intermediates in the maturation process of the RH.
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Affiliation(s)
- Simone Löscher
- Freie Universität Berlin, FB Physik, Arnimallee 14, D-14195 Berlin, Germany
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35
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Fenske D, Gnida M, Schneider K, Meyer-Klaucke W, Schemberg J, Henschel V, Meyer AK, Knöchel A, Müller A. A new type of metalloprotein: The Mo storage protein from azotobacter vinelandii contains a polynuclear molybdenum-oxide cluster. Chembiochem 2005; 6:405-13. [PMID: 15651045 DOI: 10.1002/cbic.200400263] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Azotobacter vinelandii is a diazotrophic bacterium characterized by the outstanding capability of storing Mo in a special storage protein, which guarantees Mo-dependent nitrogen fixation even under growth conditions of extreme Mo starvation. The Mo storage protein is constitutively synthesized with respect to the nitrogen source and is regulated by molybdenum at an extremely low concentration level (0-50 nM). This protein was isolated as an alpha4beta4 octamer with a total molecular mass of about 240 kg mol(-1) and its shape was determined by small-angle X-ray scattering. The genes of the alpha and beta subunits were unequivocally identified; the amino acid sequences thereby determined reveal that the Mo storage protein is not related to any other known molybdoprotein. Each protein molecule can store at least 90 Mo atoms. Extended X-ray absorption fine-structure spectroscopy identified a metal-oxygen cluster bound to the Mo storage protein. The binding of Mo (biosynthesis and incorporation of the cluster) is dependent on adenosine triphosphate (ATP); Mo release is ATP-independent but pH-regulated, occurring only above pH 7.1. This Mo storage protein is the only known noniron metal storage system in the biosphere containing a metal-oxygen cluster.
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Affiliation(s)
- Dirk Fenske
- Lehrstuhl für Anorganische Chemie I, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
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Jeżowska-Bojczuk M, Szczepanik W, Mangani S, Gaggelli E, Gaggelli N, Valensin G. Identification of Copper(II) Binding Sites in the Aminoglycosidic Antibiotic Neomycin B. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schilling O, Vogel A, Kostelecky B, Natal da Luz H, Spemann D, Späth B, Marchfelder A, Tröger W, Meyer-Klaucke W. Zinc- and iron-dependent cytosolic metallo-beta-lactamase domain proteins exhibit similar zinc-binding affinities, independent of an atypical glutamate at the metal-binding site. Biochem J 2005; 385:145-53. [PMID: 15324305 PMCID: PMC1134682 DOI: 10.1042/bj20040773] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ZiPD (zinc phosphodiesterase; synonyms are ElaC, ecoZ, RNaseZ and 3' tRNase) and the iron-dependent redox enzyme FlRd (flavorubredoxin) from Escherichia coli represent prototypical cases of proteins sharing the metallo-beta-lactamase fold that require strict metal selectivity for catalytic activity, yet their metal selectivity has only been partially understood. In contrast with hydrolytic metallo-beta-lactamase proteins, iron-dependent FlRd-like enzymes have an atypical glutamate ligand, which replaces one otherwise conserved histidine ligand. X-ray absorption spectroscopy revealed that the FlRd metallo-beta-lactamase domain is capable of incorporating two zinc ions into the binuclear metal-binding site. Zinc dissociation constants, determined by isothermal titration calorimetry are similar for zinc binding to E. coli ZiPD (K(d1)=2.2+/-0.2 microM and K(d2)=23.0+/-0.6 microM) and to the E. coli FlRd metallo-beta-lactamase domain (K(d1)=0.7+/-0.1 microM and K(d2)=26.0+/-0.1 microM). In good correspondence, apo-ZiPD requires incubation with 10 microM zinc for full reconstitution of the phosphodiesterase activity. Accordingly, metal selectivity of ZiPD and FlRd only partially relies on first shell metal ligands. Back mutation of the atypical glutamate in FlRd to a histidine unexpectedly resulted in an increased first zinc dissociation constant (K(d1)=30+/-4 microM and K(d2)=23+/-2 microM). In combination with a recent mutational study on ZiPD [Vogel, Schilling and Meyer-Klaucke (2004) Biochemistry 43, 10379-10386], we conclude that the atypical glutamate does not guide metal selectivity of the FlRd metallo-beta-lactamase domain but suppresses possible hydrolytic cross-activity.
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Affiliation(s)
- Oliver Schilling
- *EMBL Outstation Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Andreas Vogel
- *EMBL Outstation Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | - Hugo Natal da Luz
- †Institute for Experimental Physics II, University of Leipzig, Linnéstr. 5, D-04103 Leipzig, Germany
| | - Daniel Spemann
- †Institute for Experimental Physics II, University of Leipzig, Linnéstr. 5, D-04103 Leipzig, Germany
| | - Bettina Späth
- ‡Molekulare Botanik, Universität Ulm, D-89069 Ulm, Germany
| | | | - Wolfgang Tröger
- †Institute for Experimental Physics II, University of Leipzig, Linnéstr. 5, D-04103 Leipzig, Germany
| | - Wolfram Meyer-Klaucke
- *EMBL Outstation Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany
- To whom correspondence should be addressed (email )
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D'Angelo P, Chillemi G, Barone V, Mancini G, Sanna N, Persson I. Experimental Evidence for a Variable First Coordination Shell of the Cadmium(II) Ion in Aqueous, Dimethyl Sulfoxide, and N,N‘-Dimethylpropyleneurea Solution. J Phys Chem B 2005; 109:9178-85. [PMID: 16852093 DOI: 10.1021/jp050460k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A combined extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS) investigation has been performed to evaluate the coordination structure of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea (dmpu) solutions. This approach has singled out the existence of a flexible coordination shell around the cadmium(II) ion in aqueous and dimethyl sulfoxide solutions, whereas a regular octahedral complex is detected in dmpu. The EXAFS and LAXS techniques provide different values of the Cd-O first shell distance (2.27(1) A and 2.302(5) A, respectively) for the hydrated and dimethyl sulfoxide solvated complexes, and this discrepancy is originated by the simultaneous presence of hexa- and heptacoordinated complexes in solution, giving rise to a broad distribution of distances around the ion. These findings demonstrate that, in solution, the cadmium(II) ion forms quite flexible hydration and dimethyl sulfoxide solvate complexes undergoing a solvent exchange with unusually stable seven-coordinated intermediate complexes, and therefore the mean ion-solvent distance is longer in solution than in the solid state. In the dmpu solution, due to the bulkiness of the solvent molecules, the octahedral cadmium(II) solvate is extremely crowded and it is not possible for a seventh ligand to enter the inner-coordination shell. This investigation shows that the combined analysis of the EXAFS and LAXS data allows a reliable determination of the structural properties of electrolyte solutions, also in the presence of flexible coordination shell with a variable number of coordinating molecules.
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Affiliation(s)
- Paola D'Angelo
- Dipartimento di Chimica, Università di Roma "La Sapienza", P.le Aldo Moro 5, 00185 Roma, Italy.
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Buhrke T, Löscher S, Lenz O, Schlodder E, Zebger I, Andersen LK, Hildebrandt P, Meyer-Klaucke W, Dau H, Friedrich B, Haumann M. Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16. J Biol Chem 2005; 280:19488-95. [PMID: 15764814 DOI: 10.1074/jbc.m500601200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regulatory Ni-Fe hydrogenase (RH) from Ralstonia eutropha functions as a hydrogen sensor. The RH consists of the large subunit HoxC housing the Ni-Fe active site and the small subunit HoxB containing Fe-S clusters. The heterolytic cleavage of H(2) at the Ni-Fe active site leads to the EPR-detectable Ni-C state of the protein. For the first time, the simultaneous but EPR-invisible reduction of Fe-S clusters during Ni-C state formation was demonstrated by changes in the UV-visible absorption spectrum as well as by shifts of the iron K-edge from x-ray absorption spectroscopy in the wild-type double dimeric RH(WT) [HoxBC](2) and in a monodimeric derivative designated RH(stop) lacking the C-terminal 55 amino acids of HoxB. According to the analysis of iron EXAFS spectra, the Fe-S clusters of HoxB pronouncedly differ from the three Fe-S clusters in the small subunits of crystallized standard Ni-Fe hydrogenases. Each HoxBC unit of RH(WT) seems to harbor two [2Fe-2S] clusters in addition to a 4Fe species, which may be a [4Fe-3S-3O] cluster. The additional 4Fe-cluster was absent in RH(stop). Reduction of Fe-S clusters in the hydrogen sensor RH may be a first step in the signal transduction chain, which involves complex formation between [HoxBC](2) and tetrameric HoxJ protein, leading to the expression of the energy converting Ni-Fe hydrogenases in R. eutropha.
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Affiliation(s)
- Thorsten Buhrke
- Humboldt-Universität zu Berlin, Institut für Biologie/Mikrobiologie, Berlin, Germany
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40
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Burgdorf T, Löscher S, Liebisch P, Van der Linden E, Galander M, Lendzian F, Meyer-Klaucke W, Albracht SPJ, Friedrich B, Dau H, Haumann M. Structural and oxidation-state changes at its nonstandard Ni-Fe site during activation of the NAD-reducing hydrogenase from Ralstonia eutropha detected by X-ray absorption, EPR, and FTIR spectroscopy. J Am Chem Soc 2005; 127:576-92. [PMID: 15643882 DOI: 10.1021/ja0461926] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure and oxidation state of the Ni-Fe cofactor of the NAD-reducing soluble hydrogenase (SH) from Ralstonia eutropha were studied employing X-ray absorption spectroscopy (XAS) at the Ni K-edge, EPR, and FTIR spectroscopy. The SH comprises a nonstandard (CN)Ni-Fe(CN)(3)(CO) site; its hydrogen-cleavage reaction is resistant against inhibition by dioxygen and carbon monoxide. Simulations of the XANES and EXAFS regions of XAS spectra revealed that, in the oxidized SH, the Ni(II) is six-coordinated ((CN)O(3)S(2)); only two of the four conserved cysteines, which bind the Ni in standard Ni-Fe hydrogenases, provide thiol ligands to the Ni. Upon the exceptionally rapid reductive activation of the SH by NADH, an oxygen species is detached from the Ni; hydrogen may subsequently bind to the vacant coordination site. Prolonged reducing conditions cause the two thiols that are remote from the Ni in the native SH to become direct Ni ligands, creating a standardlike Ni(II)(CysS)(4) site, which could be further reduced to form the Ni-C (Ni(III)-H(-)) state. The Ni-C state does not seem to be involved in hydrogen cleavage. Two site-directed mutants (HoxH-I64A, HoxH-L118F) revealed structural changes at their Ni sites and were employed to further dissect the role of the extra CN ligand at the Ni. It is proposed that the predominant coordination by (CN),O ligands stabilizes the Ni(II) oxidation state throughout the catalytic cycle and is a prerequisite for the rapid activation of the SH in the presence of oxygen.
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Affiliation(s)
- Tanja Burgdorf
- Humboldt-Universität zu Berlin, Mikrobiologie, Chausseestr. 117, D-10115 Berlin, Germany
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41
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Abstract
Extended x-ray absorption fine structure (EXAFS) spectroscopy was combined with thermodynamic and kinetic approaches to investigate zinc binding to a zinc finger (C2H2) and a tetrathiolate (C4) peptide. Both peptides represent structural zinc sites of proteins and rapidly bind a single zinc ion with picomolar dissociation constants. In competition with EDTA the transfer of peptide-bound zinc ions proved to be 6 orders of magnitude faster than predicted for a dissociation-association mechanism thus requiring ligand exchange mechanisms via peptide-zinc-EDTA complexes. EXAFS spectra of C2H2 showed the expected Cys2His2-ligand geometry when fully loaded with zinc. For a 2-fold excess of peptide, however, the existence of zinc-bridged peptide-peptide complexes with dominating sulfur coordination could be clearly shown. Whereas zinc binding kinetics of C2H2 appeared as a simple second order process, the suggested mechanism for C4 comprises a zinc-bridged Zn-(C4)2 species as well as a Zn-C4 species with less than 4 metal-bound thiolates, which is supported by EXAFS results. A rapid equilibrium of bound and unbound states of individual ligands might explain the kinetic instability of zinc-peptide complexes, which enables fast ligand exchange during the encounter of occupied and unoccupied acceptor sites. Depending on relative concentrations and stabilities, this results in a rapid transfer of zinc ions in the virtual absence of free zinc ions, as seen for the zinc transfer to EDTA, or in the formation of zinc-bridged complexes, as seen for both peptides with excess of peptides over available zinc.
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Affiliation(s)
- Uwe Heinz
- Department of Natural Sciences, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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Mentler M, Weiss A, Grantner K, del Pino P, Deluca D, Fiori S, Renner C, Klaucke WM, Moroder L, Bertsch U, Kretzschmar HA, Tavan P, Parak FG. A new method to determine the structure of the metal environment in metalloproteins: investigation of the prion protein octapeptide repeat Cu2+ complex. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2004; 34:97-112. [PMID: 15452673 DOI: 10.1007/s00249-004-0434-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2004] [Revised: 07/02/2004] [Accepted: 07/05/2004] [Indexed: 10/26/2022]
Abstract
Since high-intensity synchrotron radiation is available, "extended X-ray absorption fine structure" spectroscopy (EXAFS) is used for detailed structural analysis of metal ion environments in proteins. However, the information acquired is often insufficient to obtain an unambiguous picture. ENDOR spectroscopy allows the determination of hydrogen positions around a metal ion. However, again the structural information is limited. In the present study, a method is proposed which combines computations with spectroscopic data from EXAFS, EPR, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). From EXAFS a first picture of the nearest coordination shell is derived which has to be compatible with EPR data. Computations are used to select sterically possible structures, from which in turn structures with correct H and N positions are selected by ENDOR and ESEEM measurements. Finally, EXAFS spectra are re-calculated and compared with the experimental data. This procedure was successfully applied for structure determination of the Cu(2+) complex of the octapeptide repeat of the human prion protein. The structure of this octarepeat complex is rather similar to a pentapeptide complex which was determined by X-ray structure analysis. However, the tryptophan residue has a different orientation: the axial water is on the other side of the Cu.
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Affiliation(s)
- Matthias Mentler
- Physik-Department E17, Technische Universität München, Garching, Germany
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43
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Vogel A, Schilling O, Meyer-Klaucke W. Identification of Metal Binding Residues for the Binuclear Zinc Phosphodiesterase Reveals Identical Coordination as Glyoxalase II. Biochemistry 2004; 43:10379-86. [PMID: 15301536 DOI: 10.1021/bi049703+] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Zinc phosphodiesterase (ZiPD) is a member of the metallo-beta-lactamase family with a binuclear zinc binding site. As an experimental attempt to identify the metal ligands of Escherichia coli ZiPD and to investigate their function in catalysis, we mutationally exchanged candidate metal coordinating residues and performed kinetic and X-ray absorption spectroscopic analysis of the mutant proteins. All mutants (H66E, H69A, H141A, D212A, D212C, H231A, H248A, and H270A) show significantly lower catalytic rates toward the substrate bis(p-nitrophenyl)phosphate. Substrate binding, represented by the kinetic value K', remains unchanged for six mutants, whereas it is increased 3-4-fold for H231A and H270A. Accordingly, these two residues are supposed to be involved in substrate binding, whereas the others are more important for catalytic turnover and thus are assumed to be involved in zinc ligation. Structural insight into the metal binding of D212 was gained by zinc K-edge extended X-ray absorption fine structure (EXAFS). The sulfur coordination number of the cysteine mutant was found to be 1, demonstrating binding to both zinc metals in a bridging mode. Taken together with two residues from a strictly conserved sequence region within the metallo-beta-lactamase family, the metal site of ZiPD is proposed with H64, H66, and H141 coordinating ZnA, D68, H69, and H248 coordinating ZnB, and D212 bridging both metals. Surprisingly, the same coordination sphere is found in glyoxalase II. This is further substantiated by comparable EXAFS spectra of both native enzymes. This is the first example of the same metal site in two members of the metallo-beta-lactamase domain proteins catalyzing different reactions. The kinetic analysis of mutants provides unexpected insights into the reaction mechanism of ZiPD.
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Affiliation(s)
- Andreas Vogel
- EMBL Outstation Hamburg, Notkestrasse 85, 22603 Hamburg, Germany
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44
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Banci L, Bertini I, Cantini F, Ciofi-Baffoni S, Gonnelli L, Mangani S. Solution structure of Cox11, a novel type of beta-immunoglobulin-like fold involved in CuB site formation of cytochrome c oxidase. J Biol Chem 2004; 279:34833-9. [PMID: 15181013 DOI: 10.1074/jbc.m403655200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytochrome c oxidase assembly process involves many accessory proteins including Cox11, which is a copper-binding protein required for Cu incorporation into the Cu(B) site of cytochrome c oxidase. In a genome wide search, a number of Cox11 homologs are found in all of the eukaryotes with complete genomes and in several Gram-negative bacteria. All of them possess a highly homologous soluble domain and contain an N-terminal fragment that anchors the protein to the membrane. An anchor-free construct of 164 amino acids was obtained from Sinorhizobium meliloti, and the first structure of this class of proteins is reported here. The apoform has an immunoglobulin-like fold with a novel type of beta-strand organization. The copper binding motif composed of two highly conserved cysteines is located on one side of the beta-barrel structure. The apoprotein is monomeric in the presence of dithiothreitol, whereas it dimerizes in the absence of the reductant. When copper(I) binds, NMR and extended x-ray absorption fine structure (EXAFS) data indicate a dimeric protein state with two thiolates bridging two copper(I) ions. The present results advance the knowledge on the poorly understood molecular aspects of cytochrome c oxidase assembly.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center CERM and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Florence, Italy
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Wenzel NF, Carenbauer AL, Pfiester MP, Schilling O, Meyer-Klaucke W, Makaroff CA, Crowder MW. The binding of iron and zinc to glyoxalase II occurs exclusively as di-metal centers and is unique within the metallo-beta-lactamase family. J Biol Inorg Chem 2004; 9:429-38. [PMID: 15067523 DOI: 10.1007/s00775-004-0535-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2003] [Accepted: 02/23/2004] [Indexed: 10/26/2022]
Abstract
Cytosolic glyoxalase 2 (GLX2-2) from Arabidopsis thaliana is a metalloenzyme that has been shown to bind a mixture of Zn, Fe, or Mn when produced in cells grown in rich media. In an effort to prepare metal-enriched samples, GLX2-2 was over-expressed in minimal media containing either Zn, Fe, or Mn. The resulting enzymes bound an average of 1 equivalent of metal ion and were partially enriched with a specific metal ion. The enzymes produced in minimal media were active towards the substrate S-D-lactoylglutathione, yielding kcat/ Km values similar to those of rich media GLX2-2. EPR studies on minimal media GLX2-2 samples revealed spectra which were identical to those over-expressed in rich media that contained nearly 2 equivalents of metal. The EPR spectra showed the presence of antiferromagnetically and ferromagnetically coupled, dinuclear metal centers. EXAFS spectra on the minimal media GLX2-2 samples over-expressed in the presence of Fe or Zn were also very similar to those of the rich media GLX2-2 samples, indicating the presence of dinuclear metal centers. The EXAFS studies also demonstrate that Zn(II) and Fe (in the Fe-enriched sample) are distributed in the dinuclear site. These data indicate that the minimal media GLX2-2 samples are a mixture of fully loaded, dinuclear metal-containing enzyme and metal-free enzyme. This characteristic of A. thaliana GLX2-2 makes it unique among the other members of the metallo-beta-lactamase family in that it does not ever appear to exist as a mononuclear metal ion containing enzyme and that it exhibits positive cooperativity in metal binding.
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Affiliation(s)
- Nathan F Wenzel
- Department of Chemistry and Biochemistry, Miami University, 112 Hughes Hall, Oxford, OH 45056, USA
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Slep LD, Mijovilovich A, Meyer-Klaucke W, Weyhermüller T, Bill E, Bothe E, Neese F, Wieghardt K. Mixed-valent [FeIV(mu-O)(mu-carboxylato)2FeIII]3+ core. J Am Chem Soc 2004; 125:15554-70. [PMID: 14664603 DOI: 10.1021/ja030377f] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The symmetrically ligated complexes 1, 2, and 3 with a (mu-oxo)bis(mu-acetato)diferric core can be one-electron oxidized electrochemically or chemically with aminyl radical cations [*NR3][SbCl6] in acetonitrile yielding complexes which contain the mixed-valent [(mu-oxo)bis(mu-acetato)iron(IV)iron(III)]3+ core: [([9]aneN3)(2FeIII2)(mu-O)(mu-CH3CO2)2](ClO4)2 (1(ClO4)2), [(Me3[9]aneN3)(2FeIII2)(mu-O)(mu-CH3CO2)2](PF6)2 (2(PF6)(2)), and [(tpb)(2FeIII2)(mu-O)(mu-CH3CO2)2] (3) where ([9]aneN3) is the neutral triamine 1,4,7-triazacyclononane and (Me3[9]aneN3) is its tris-N-methylated derivative, and (tpb)(-) is the monoanion trispyrazolylborate. The asymmetrically ligated complex [(Me3[9]aneN3)FeIII(mu-O)(mu-CH3CO2)2FeIII(tpb)](PF6) (4(PF6)) and its one-electron oxidized form [4ox]2+ have also been prepared. Finally, the known heterodinuclear species [(Me3[9]aneN3)CrIII(mu-O)(mu-CH3CO2)2Fe([9]aneN3)](PF6)2 (5(PF6)(2)) can also be one-electron oxidized yielding [5ox]3+ containing an iron(IV) ion. The structure of 4(PF6).0.5CH3CN.0.25(C2H5)2O has been determined by X-ray crystallography and that of [5ox]2+ by Fe K-edge EXAFS-spectroscopy (Fe(IV)-O(oxo): 1.69(1) A; Fe(IV)-O(carboxylato) 1.93(3) A, Fe(IV)-N 2.00(2) A) contrasting the data for 5 (Fe(III)-O(oxo) 1.80 A; Fe(III)-O(carboxylato) 2.05 A, Fe-N 2.20 A). [5ox]2+ has an St = 1/2 ground state whereas all complexes containing the mixed-valent [FeIV(mu-O)(mu-CH3CO2)2FeIII]3+ core have an St = 3/2 ground state. Mössbauer spectra of the oxidized forms of complexes clearly show the presence of low spin FeIV ions (isomer shift approximately 0.02 mm s(-1), quadrupole splitting approximately 1.4 mm s(-1) at 80 K), whereas the high spin FeIII ion exhibits delta approximately 0.46 mm s(-1) and DeltaE(Q) approximately 0.5 mm s(-1). Mössbauer, EPR spectral and structural parameters have been calculated by density functional theoretical methods at the BP86 and B3LYP levels. The exchange coupling constant, J, for diiron complexes with the mixed-valent FeIV-FeIII core (H = -2J S1.S2; S(1) = 5/2; S2 = 1) has been calculated to be -88 cm(-1) (intramolecular antiferromagnetic coupling) and for the reduced diferric form of -75 cm(-1) in reasonable agreement with experiment (J = -120 cm(-1)).
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Affiliation(s)
- Leonardo D Slep
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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Küpper H, Mijovilovich A, Meyer-Klaucke W, Kroneck PMH. Tissue- and age-dependent differences in the complexation of cadmium and zinc in the cadmium/zinc hyperaccumulator Thlaspi caerulescens (Ganges ecotype) revealed by x-ray absorption spectroscopy. PLANT PHYSIOLOGY 2004; 134:748-57. [PMID: 14966248 PMCID: PMC344550 DOI: 10.1104/pp.103.032953] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2003] [Revised: 09/24/2003] [Accepted: 11/11/2003] [Indexed: 05/17/2023]
Abstract
Extended x-ray absorption fine structure measurements were performed on frozen hydrated samples of the cadmium (Cd)/zinc (Zn) hyperaccumulator Thlaspi caerulescens (Ganges ecotype) after 6 months of Zn(2+) treatment with and without addition of Cd(2+). Ligands depended on the metal and the function and age of the plant tissue. In mature and senescent leaves, oxygen ligands dominated. This result combined with earlier knowledge about metal compartmentation indicates that the plants prefer to detoxify hyperaccumulated metals by pumping them into vacuoles rather than to synthesize metal specific ligands. In young and mature tissues (leaves, petioles, and stems), a higher percentage of Cd was bound by sulfur (S) ligands (e.g. phytochelatins) than in senescent tissues. This may indicate that young tissues require strong ligands for metal detoxification in addition to the detoxification by sequestration in the epidermal vacuoles. Alternatively, it may reflect the known smaller proportion of epidermal metal sequestration in younger tissues, combined with a constant and high proportion of S ligands in the mesophyll. In stems, a higher proportion of Cd was coordinated by S ligands and of Zn by histidine, compared with leaves of the same age. This may suggest that metals are transported as stable complexes or that the vacuolar oxygen coordination of the metals is, like in leaves, mainly found in the epidermis. The epidermis constitutes a larger percentage of the total volume in leaves than in stems and petioles. Zn-S interaction was never observed, confirming earlier results that S ligands are not involved in Zn resistance of hyperaccumulator plants.
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Affiliation(s)
- Hendrik Küpper
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, Postfach M665, D-78457 Konstanz, Germany.
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Svetlitchnyi V, Dobbek H, Meyer-Klaucke W, Meins T, Thiele B, Römer P, Huber R, Meyer O. A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans. Proc Natl Acad Sci U S A 2004; 101:446-51. [PMID: 14699043 PMCID: PMC327167 DOI: 10.1073/pnas.0304262101] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Indexed: 11/18/2022] Open
Abstract
In anaerobic microorganisms employing the acetyl-CoA pathway, acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH) form a complex (ACS/CODH) that catalyzes the synthesis of acetyl-CoA from CO, a methyl group, and CoA. Previously, a [4Fe-4S] cubane bridged to a copper-nickel binuclear site (active site cluster A of the ACS component) was identified in the ACS(Mt)/CODH(Mt) from Moorella thermoacetica whereas another study revealed a nickel-nickel site in the open form of ACS(Mt), and a zink-nickel site in the closed form. The ACS(Ch) of the hydrogenogenic bacterium Carboxydothermus hydrogenoformans was found to exist as an 82.2-kDa monomer as well as in a 1:1 molar complex with the 73.3-kDa CODHIII(Ch). Homogeneous ACS(Ch) and ACS(Ch)/CODHIII(Ch) catalyzed the exchange between [1-(14)C]acetyl-CoA and (12)CO with specific activities of 2.4 or 5.9 micromol of CO per min per mg, respectively, at 70 degrees C and pH 6.0. They also catalyzed the synthesis of acetyl-CoA from CO, methylcobalamin, corrinoid iron-sulfur protein, and CoA with specific activities of 0.14 or 0.91 micromol of acetyl-CoA formed per min per mg, respectively, at 70 degrees C and pH 7.3. The functional cluster A of ACS(Ch) contains a Ni-Ni-[4Fe-4S] site, in which the positions proximal and distal to the cubane are occupied by Ni ions. This result is apparent from a positive correlation of the Ni contents and negative correlations of the Cu or Zn contents with the acetyl-CoA/CO exchange activities of different preparations of monomeric ACS(Ch), a 2.2-A crystal structure of the dithionite-reduced monomer in an open conformation, and x-ray absorption spectroscopy.
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Affiliation(s)
- Vitali Svetlitchnyi
- Lehrstuhl für Mikrobiologie, Universität Bayreuth, D-95440 Bayreuth, Germany.
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Korbas M, Rokita E, Meyer-Klaucke W, Ryczek J. Bone tissue incorporates in vitro gallium with a local structure similar to gallium-doped brushite. J Biol Inorg Chem 2003; 9:67-76. [PMID: 14648284 DOI: 10.1007/s00775-003-0497-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Accepted: 10/08/2003] [Indexed: 10/26/2022]
Abstract
During mineral growth in rat bone-marrow stromal cell cultures, gallium follows calcium pathways. The dominant phase of the cell culture mineral constitutes the poorly crystalline hydroxyapatite (HAP). This model system mimics bone mineralization in vivo. The structural characterization of the Ga environment was performed by X-ray absorption spectroscopy at the Ga K-edge. These data were compared with Ga-doped synthetic compounds (poorly crystalline hydroxyapatite, amorphous calcium phosphate and brushite) and with strontium-treated bone tissue, obtained from the same culture model. It was found that Sr(2+) substitutes for Ca(2+) in the HAP crystal lattice. In contrast, the replacement by Ga(3+) yielded a much more disordered local environment of the probe atom in all investigated cell culture samples. The coordination of Ga ions in the cell culture minerals was similar to that of Ga(3+), substituted for Ca(2+), in the Ga-doped synthetic brushite (Ga-DCPD). The Ga atoms in the Ga-DCPD were coordinated by four oxygen atoms (1.90 A) of the four phosphate groups and two oxygen atoms at 2.02 A. Interestingly, the local environment of Ga in the cell culture minerals was not dependent on the onset of Ga treatment, the Ga concentration in the medium or the age of the mineral. Thus, it was concluded that Ga ions were incorporated into the precursor phase to the HAP mineral. Substitution for Ca(2+ )with Ga(3+) distorted locally this brushite-like environment, which prevented the transformation of the initially deposited phase into the poorly crystalline HAP.
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Affiliation(s)
- M Korbas
- Institute of Physics, Jagiellonian University, Reymonta 4, 30059, Krakow, Poland.
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Schilling O, Wenzel N, Naylor M, Vogel A, Crowder M, Makaroff C, Meyer-Klaucke W. Flexible Metal Binding of the Metallo-β-lactamase Domain: Glyoxalase II Incorporates Iron, Manganese, and Zinc in Vivo†. Biochemistry 2003; 42:11777-86. [PMID: 14529289 DOI: 10.1021/bi034672o] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glyoxalase II belongs to the metallo-beta-lactamase superfamily of proteins, possessing the characteristic dinuclear active site. Within this protein family, glyoxalase II from Arabidopsis thaliana is the first member to be isolated with significant amounts of iron, manganese, and zinc when being recombinantly produced in Escherichia coli. Enzyme preparations with different ratios of these three metals all yield k(cat)/K(M) values in the range of 1.5-1.9 s(-1) microM(-1) with the substrate S-d-lactoylglutathione. X-ray absorption spectroscopy reveals binding of all three metals to the dinuclear active site with 5-6-fold coordination consisting of 2.5 +/- 0.5 histidine and 2.5 +/- 0.5 oxygen ligands. This model does not distinguish site-specific or distributed binding. The metal-metal distance is determined to be 3.18 +/- 0.06 A. Electron paramagnetic resonance spectroscopy gives evidence for several different types of dimetal sites, including spin-coupled Fe(III)Fe(II), Fe(III)Zn(II), and Mn(II)Mn(II) centers. The metal-ligand distances measured by X-ray absorption spectroscopy vary depending on the metal type and comply with their element-specific, characteristic values. This reflects a high degree of structural flexibility within the glyoxalase II dinuclear active site, which is considered as the structural basis for its broad metal selectivity.
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Affiliation(s)
- Oliver Schilling
- EMBL Outstation Hamburg, Notkestrasse 85, 22603 Hamburg, Germany
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