Chemically distinct Ni sites in the A-cluster in subunit beta of the acetyl-CoA decarbonylase/synthase complex from Methanosarcina thermophila: Ni L-edge absorption and X-ray magnetic circular dichroism analyses. 2004

Tobias Funk, and Weiwei Gu, and Stephan Friedrich, and Hongxin Wang, and Simonida Gencic, and David A Grahame, and Stephen P Cramer
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

The 5-subunit-containing acetyl-CoA decarbonylase/synthase (ACDS) complex plays an important role in methanogenic Archaea that convert acetate to methane, by catalyzing the central reaction of acetate C-C bond cleavage in which acetyl-CoA serves as the acetyl donor substrate reacting at the ACDS beta subunit active site. The properties of Ni in the active site A-cluster in the ACDS beta subunit from Methanosarcina thermophila were investigated. A recombinant, C-terminally truncated form of the beta subunit was employed, which mimics the native subunit previously isolated from the ACDS complex, and contains an A-cluster composed of an [Fe(4)S(4)] center bridged to a binuclear Ni-Ni site. The electronic structures of these two Ni were studied using L-edge absorption and X-ray magnetic circular dichroism (XMCD) spectroscopy. The L-edge absorption data provided evidence for two distinct Ni species in the as-isolated enzyme, one with low-spin Ni(II) and the other with high-spin Ni(II). XMCD spectroscopy confirmed that the species producing the high-spin signal was paramagnetic. Upon treatment with Ti(3+) citrate, an additional Ni species emerged, which was assigned to Ni(I). By contrast, CO treatment of the reduced enzyme converted nearly all of the Ni in the sample to low-spin Ni(II). The results implicate reaction of a high-spin tetrahedral Ni site with CO to form an enzyme-CO adduct transformed to a low-spin Ni(II) state. These findings are discussed in relation to the mechanism of C-C bond activation, in connection with the model of the beta subunit A-cluster developed from companion Ni and Fe K edge, XANES, and EXAFS studies.

UI MeSH Term Description Entries
D009097 Multienzyme Complexes Systems of enzymes which function sequentially by catalyzing consecutive reactions linked by common metabolic intermediates. They may involve simply a transfer of water molecules or hydrogen atoms and may be associated with large supramolecular structures such as MITOCHONDRIA or RIBOSOMES. Complexes, Multienzyme
D009532 Nickel A trace element with the atomic symbol Ni, atomic number 28, and atomic weight 58.69. It is a cofactor of the enzyme UREASE.
D011994 Recombinant Proteins Proteins prepared by recombinant DNA technology. Biosynthetic Protein,Biosynthetic Proteins,DNA Recombinant Proteins,Recombinant Protein,Proteins, Biosynthetic,Proteins, Recombinant DNA,DNA Proteins, Recombinant,Protein, Biosynthetic,Protein, Recombinant,Proteins, DNA Recombinant,Proteins, Recombinant,Recombinant DNA Proteins,Recombinant Proteins, DNA
D002942 Circular Dichroism A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Circular Dichroism, Vibrational,Dichroism, Circular,Vibrational Circular Dichroism
D000445 Aldehyde Oxidoreductases Oxidoreductases that are specific for ALDEHYDES. Aldehyde Oxidoreductase,Oxidoreductase, Aldehyde,Oxidoreductases, Aldehyde
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D013050 Spectrometry, Fluorescence Measurement of the intensity and quality of fluorescence. Fluorescence Spectrophotometry,Fluorescence Spectroscopy,Spectrofluorometry,Fluorescence Spectrometry,Spectrophotometry, Fluorescence,Spectroscopy, Fluorescence
D013052 Spectrometry, X-Ray Emission The spectrometric analysis of fluorescent X-RAYS, i.e. X-rays emitted after bombarding matter with high energy particles such as PROTONS; ELECTRONS; or higher energy X-rays. Identification of ELEMENTS by this technique is based on the specific type of X-rays that are emitted which are characteristic of the specific elements in the material being analyzed. The characteristic X-rays are distinguished and/or quantified by either wavelength dispersive or energy dispersive methods. Particle-Induced X-Ray Emission Spectrometry,Proton-Induced X-Ray Emission Spectrometry,Spectrometry, Particle-Induced X-Ray Emission,Spectrometry, Proton-Induced X-Ray Emission,Spectrometry, X-Ray Fluorescence,X-Ray Emission Spectrometry,X-Ray Emission Spectroscopy,X-Ray Fluorescence Spectrometry,Energy Dispersive X-Ray Fluorescence Spectrometry,Energy Dispersive X-Ray Fluorescence Spectroscopy,Energy Dispersive X-Ray Spectrometry,Energy Dispersive X-Ray Spectroscopy,Particle Induced X Ray Emission Spectrometry,Proton Induced X Ray Emission Spectrometry,Spectrometry, Particle Induced X Ray Emission,Spectrometry, Proton Induced X Ray Emission,Spectrometry, Xray Emission,Wavelength Dispersive X-Ray Fluorescence Spectrometry,Wavelength Dispersive X-Ray Fluorescence Spectroscopy,Wavelength Dispersive X-Ray Spectrometry,Wavelength Dispersive X-Ray Spectroscopy,X-Ray Fluorescence Spectroscopy,Xray Emission Spectroscopy,Emission Spectrometry, X-Ray,Emission Spectrometry, Xray,Emission Spectroscopy, X-Ray,Emission Spectroscopy, Xray,Energy Dispersive X Ray Fluorescence Spectrometry,Energy Dispersive X Ray Fluorescence Spectroscopy,Energy Dispersive X Ray Spectrometry,Energy Dispersive X Ray Spectroscopy,Fluorescence Spectrometry, X-Ray,Fluorescence Spectroscopy, X-Ray,Spectrometry, X Ray Emission,Spectrometry, X Ray Fluorescence,Spectroscopy, X-Ray Emission,Spectroscopy, X-Ray Fluorescence,Spectroscopy, Xray Emission,Wavelength Dispersive X Ray Fluorescence Spectrometry,Wavelength Dispersive X Ray Fluorescence Spectroscopy,Wavelength Dispersive X Ray Spectrometry,Wavelength Dispersive X Ray Spectroscopy,X Ray Emission Spectrometry,X Ray Emission Spectroscopy,X Ray Fluorescence Spectrometry,X Ray Fluorescence Spectroscopy,X-Ray Fluorescence Spectroscopies,Xray Emission Spectrometry
D017020 Methanosarcina A genus of anaerobic, irregular spheroid-shaped METHANOSARCINALES whose organisms are nonmotile. Endospores are not formed. These archaea derive energy via formation of methane from acetate, methanol, mono-, di-, and trimethylamine, and possibly, carbon monoxide. Organisms are isolated from freshwater and marine environments.
D021122 Protein Subunits Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly. Protomers,Protein Subunit,Protomer,Subunit, Protein,Subunits, Protein

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