Crystal and solution structures of N,N-dimethylthioformamide-solvated copper(I), silver(I), and gold(I) ions studied by X-ray diffraction, X-ray absorption, and vibrational spectroscopy.

Crystal structures of the solvated copper(I) and silver(I) perchlorate salts crystallizing from N,N-dimethylthioformamide solution have been determined by single-crystal X-ray diffraction at 295 K. Tetrakis(N,N-dimethylthioformamide)copper(I) perchlorate, [Cu(SCHN(CH(3))(2))(4)]ClO(4), crystallizes in the monoclinic space group P2/n (No. 13) with a = 8.428(2), b = 9.605(2), and c = 15.096(3) A, beta = 104.35(2) degrees, and Z = 2. The copper(I) ion in a site of C(2) symmetry coordinates four N,N-dimethylthioformamide ligands in a slightly distorted tetrahedral coordination with Cu-S bond distances of 2.3249(8) and 2.3494(8) A. The triclinic (P1, No. 2) tris(N,N-dimethylthioformamide)silver(I) perchlorate, Ag(SCHN(CH(3))(2))(3)ClO(4), with a = 7.4149(5), b = 7.7953(5), and c = 17.1482(1) A, alpha = 98.341(5), beta = 93.910(5), and gamma = 107.084(5) degrees, and Z = 2, contains centrosymmetric Ag(2)(SCHN(CH(3))(2))(6)(2+) dimers in which two almost planar AgS(3) units are held together by an asymmetric double sulfur bridge with one short and one long Ag-S bond, 2.529(1) and 2.930(1) A, respectively. The Ag-S bond distances to the two terminal N,N-dimethylthioformamide ligands are 2.469(1) and 2.543(1) A. The solvated copper(I) and silver(I) ions in solution were found by means of large-angle X-ray scattering (LAXS) to coordinate four N,N-dimethylthioformamide molecules with the mean Cu-S and Ag-S bond distances 2.36(1) and 2.58(1) A, respectively, probably with distorted tetrahedral coordination geometry, while an EXAFS study gave the Cu-S bond distance 2.34(1) A. EXAFS studies showed a linear S-Au-S entity with an Au-S bond distance of 2.290(5) A in the structure of the solid bis(N,N-dimethylthioformamide)gold(I) tetrafluoroborate, Au(SCHN(CH(3))(2))(2)BF(4). The structure in solution is similar with a mean Au-S bond distance of 2.283(4) A. Raman and infrared vibrational spectra of the solvated copper(I), silver(I), and gold(I) ions in the solid state and N,N-dimethylthioformamide solution have been recorded and assigned.

Kinetic and spectroscopic characterization of the gamma-carbonic anhydrase from the methanoarchaeon Methanosarcina thermophila.

The zinc and cobalt forms of the prototypic gamma-carbonic anhydrase from Methanosarcina thermophila were characterized by extended X-ray absorption fine structure (EXAFS) and the kinetics were investigated using steady-state spectrophotometric and (18)O exchange equilibrium assays. EXAFS results indicate that cobalt isomorphously replaces zinc and that the metals coordinate three histidines and two or three water molecules. The efficiency of either Zn-Cam or Co-Cam for CO(2) hydration (k(cat)/K(m)) was severalfold greater than HCO(3-) dehydration at physiological pH values, a result consistent with the proposed physiological function for Cam during growth on acetate. For both Zn- and Co-Cam, the steady-state parameter k(cat) for CO(2) hydration was pH-dependent with a pK(a) of 6.5-6.8, whereas k(cat)/K(m) was dependent on two ionizations with pK(a) values of 6.7-6.9 and 8.2-8.4. The (18)O exchange assay also identified two ionizable groups in the pH profile of k(cat)/K(m) with apparent pK(a) values of 6.0 and 8.1. The steady-state parameter k(cat) (CO(2) hydration) is buffer-dependent in a saturable manner at pH 8. 2, and the kinetic analysis suggested a ping-pong mechanism in which buffer is the second substrate. The calculated rate constant for intermolecular proton transfer is 3 x 10(7) M(-1) s(-1). At saturating buffer concentrations and pH 8.5, k(cat) is 2.6-fold higher in H(2)O than in D(2)O, suggesting that an intramolecular proton transfer step is at least partially rate-determining. At high pH (pH > 8), k(cat)/K(m) is not dependent on buffer and no solvent hydrogen isotope effect was observed, consistent with a zinc hydroxide mechanism. Therefore, at high pH the catalytic mechanism of Cam appears to resemble that of human CAII, despite significant structural differences in the active sites of these two unrelated enzymes.

X-ray absorption spectroscopic analysis of Fe(II) and Cu(II) forms of a herbicide-degrading alpha-ketoglutarate dioxygenase.

The first step in the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by Ralstonia eutropha JMP134 is catalyzed by the alpha-ketoglutarate (alpha-KG)-dependent dioxygenase TfdA. Previously, EPR and ESEEM studies on inactive Cu(II)-substituted TfdA suggested a mixture of nitrogen/oxygen coordination with two imidazole-like ligands. Differences between the spectra for Cu TfdA and alpha-KG- and 2,4-D-treated samples were interpreted as a rearrangement of the g-tensor principal axis system. Herein, we report the use of X-ray absorption spectroscopy (XAS) to further characterize the metal coordination environment of Cu TfdA as well as that in the active, wild-type Fe(II) enzyme. The EXAFS data are interpreted in terms of four N/O ligands (two imidazole-like) in the Cu TfdA sample and six N/O ligands (one or two imidazole-like) in the Fe TfdA sample. Addition of alpha-KG results in no significant structural change in coordination for Cu or Fe TfdA. However, addition of 2,4-D results in a decrease in the number of imidazole ligands in both Cu and Fe TfdA. Since this change is seen both in the Fe and Cu EXAFS, loss of one histidine ligand upon 2,4-D addition best describes the phenomenon. These XAS data clearly demonstrate that changes occur in the atomic environment of the metallocenter upon substrate binding.

Structural conservation of the isolated zinc site in archaeal zinc-containing ferredoxins as revealed by x-ray absorption spectroscopic analysis and its evolutionary implications.

The zfx gene encoding a zinc-containing ferredoxin from Thermoplasma acidophilum strain HO-62 was cloned and sequenced. It is located upstream of two genes encoding an archaeal homolog of nascent polypeptide-associated complex alpha subunit and a tRNA nucleotidyltransferase. This gene organization is not conserved in several euryarchaeoteal genomes. The multiple sequence alignments of the zfx gene product suggest significant sequence similarity of the ferredoxin core fold to that of a low potential 8Fe-containing dicluster ferredoxin without a zinc center. The tightly bound zinc site of zinc-containing ferredoxins from two phylogenetically distantly related Archaea, T. acidophilum HO-62 and Sulfolobus sp. strain 7, was further investigated by x-ray absorption spectroscopy. The zinc K-edge x-ray absorption spectra of both archaeal ferredoxins are strikingly similar, demonstrating that the same zinc site is found in T. acidophilum ferredoxin as in Sulfolobus sp. ferredoxin, which suggests the structural conservation of isolated zinc binding sites among archaeal zinc-containing ferredoxins. The sequence and spectroscopic data provide the common structural features of the archaeal zinc-containing ferredoxin family.

Cu XAS shows a change in the ligation of CuB upon reduction of cytochrome bo3 from Escherichia coli.

Copper X-ray absorption spectroscopy (XAS) has been used to examine the structures of the Cu(II) and Cu(I) forms of the cytochrome bo3 quinol oxidase from Escherichia coli. Cytochrome bo3 is a member of the superfamily of heme-copper respiratory oxidases. Of particular interest is the fact that these enzymes function as redox-linked proton pumps, resulting in the net translocation of one H+ per electron across the membrane. The molecular mechanism of how this pump operates and the manner by which it is linked to the oxygen chemistry at the active site of the enzyme are unknown. Several proposals have featured changes in the coordination of CuB during enzyme turnover that would result in sequential protonation or deprotonation events that are key to the functioning proton pump. This would imply lability of the ligands to CuB. In this work, the structure of the protein in the immediate vicinity of CuB, in both the fully oxidized and fully reduced forms of the enzyme, has been examined by Cu XAS, a technique that is particularly sensitive to changes in metal coordination. The results show that in the oxidized enzyme, CuB(II) is four-coordinate, consistent with three imidazoles and one hydroxyl (or water). Upon reduction of the enzyme, the coordination of CuB(I) is significantly altered, consistent with the loss of one of the histidine imidazole ligands in at least a substantial fraction of the population. These data add to the credibility that changes in the ligation of CuB might occur during catalytic turnover of the enzyme and, therefore, could, in principle, be part of the mechanism of proton pumping.