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Direct structural information for the copper site of dopamine beta-mono-oxygenase obtained by using extended X-ray-absorption fine structure.

ABSTRACT: Copper K-edge e.x.a.f.s (extended X-ray-absorption fine structure) was measured for dopamine beta-mono-oxygenase in aqueous solution. Comparison with the Cu K-edge e.x.a.f.s. of bovine erythrocyte superoxide dismutase shows a close resemblance. Detailed analysis of the e.x.a.f.s. indicates that the copper atom is bound to four imidazole groups at 0.201 nm with one or two oxygen atoms at 0.23 nm.

SUBMITTER: Hasnain SS

PROVIDER: S-EPMC1144072 | biostudies-other | 1984 Jul

REPOSITORIES: biostudies-other

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Structural study of the copper and zinc sites in metallothioneins by using extended X-ray-absorption fine structure.

Project description:Zn-metallothionein 1 from rabbit liver was investigated by means of Zn K-edge extended X-ray-absorption fine structure (e.x.a.f.s.). Also, the Cu and Zn K-edge e.x.a.f.s. were measured for two samples of mixed Cu Zn-metallothionein 2, with Cu/Zn ratios of 5:2 and 6:3, from pig liver. Detailed simulation of the Cu sites shows a primary co-ordination with three sulphur atoms, presumably from cysteine residues at 0.225 nm +/- 0.001 nm (2.25 +/- 0.01 A). The data for the Zn sites are best reproduced by four Zn-S separations at 0.233 +/- 0.001 nm (2.33 +/- 0.01 A). The Zn K-edge e.x.a.f.s. recorded for rabbit metallothionein 1 at 77 K shows, in addition to the primary co-ordination shell, evidence for two Zn-Zn separations at approx. 0.50 nm (5.0 A). This latter result provides the first information concerning the internal arrangement of zinc atoms in Zn7-metallothionein.

| S-EPMC1146879 | biostudies-other

Geometric structure determination of N694C lipoxygenase: a comparative near-edge X-ray absorption spectroscopy and extended X-ray absorption fine structure study.

Project description:The mononuclear nonheme iron active site of N694C soybean lipoxygenase (sLO1) has been investigated in the resting ferrous form using a combination of Fe-K-pre-edge, near-edge (using the minuit X-ray absorption near-edge full multiple-scattering approach), and extended X-ray absorption fine structure (EXAFS) methods. The results indicate that the active site is six-coordinate (6C) with a large perturbation in the first-shell bond distances in comparison to the more ordered octahedral site in wild-type sLO1. Upon mutation of the asparagine to cysteine, the short Fe-O interaction with asparagine is replaced by a weak Fe-(H(2)O), which leads to a distorted 6C site with an effective 5C ligand field. In addition, it is shown that near-edge multiple scattering analysis can give important three-dimensional structural information, which usually cannot be accessed using EXAFS analysis. It is further shown that, relative to EXAFS, near-edge analysis is more sensitive to partial coordination numbers and can be potentially used as a tool for structure determination in a mixture of chemical species.

| S-EPMC2736335 | biostudies-literature

An extended X-ray-absorption-fine-structure study of the copper and zinc sites of freeze-dried bovine superoxide dismutase.

Project description:Copper and zinc K-edge-extended X-ray-absorption fine structures were measured for the metal sites of freeze-dried bovine superoxide dismutase and the model compounds tetrakis(imidazole)cupric nitrate and tetrakis(imidazole)zinc perchlorate. Detailed simulation of the spectra indicates that the copper site of the enzyme is best fit by co-ordination of four imidazole groups with Cu-N(alpha) distances of 0.198 nm (1.98 A). The zinc site is best fit by three imidazole groups at 0.201 nm (2.01 A) and an oxygen (from aspartate) at 0.203 nm (2.03 A).

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Extended-X-ray-absorption-fine-structure investigations of zinc in 5-aminolaevulinate dehydratase.

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An extended-X-ray-absorption-fine-structure (e.x.a.f.s.) study of coenzyme F430 from Methanobacterium thermoautotrophicum.

Project description:Coenzyme F430 is a nickel porphinoid found in all methanogenic bacteria. Extended-X-ray-absorption-fine-structure (e.x.a.f.s.) spectra have been recorded above the nickel K-edge of coenzyme F430 and two model compounds, (5,10,15,20-tetramethylporphinato) nickel(II) and (5,10,15,20-tetramethylchlorinato)-nickel(II). The results show that the four nickel-nitrogen distances in F430 are split, with two nitrogen atoms at 0.192 nm and two at 0.210 nm.

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Combining reverse Monte Carlo analysis of X-ray scattering and extended X-ray absorption fine structure spectra of very small nanoparticles.

Project description:Finite size effects in partial pair distribution functions generate artefacts in the scattering structure factor and scattering intensity. It is shown how they can be overcome using a binned version of the Debye scattering equation. Accordingly, reverse Monte Carlo simulations are used for very small nanoparticles of LaFeO3 with diameters below 10 nm to simultaneously analyse X-ray scattering data and extended X-ray absorption fine structure spectra at the La K and Fe K edges. The structural information obtained is consistent regarding local structure and long-range order.

| S-EPMC9901930 | biostudies-literature

An extended-X-ray-absorption-fine-structure investigation of diferric transferrins and their iron-binding fragments.

Project description:Iron K-edge extended-X-ray-absorption-fine-structure (e.x.a.f.s.) spectra were recorded for diferric human and rabbit serum transferrins and for diferric chicken ovotransferrin in aqueous solution; for ovotransferrin e.x.a.f.s. spectra from the N-terminal and C-terminal domain fragments were also measured. The overall spectral profiles closely resemble one another, indicating similar iron-binding sites. The simulation of the diferric ovotransferrin spectrum suggests a first co-ordination shell consisting of six low-Z ligands (nitrogen/oxygen), two ligands at a distance of approx. 0.185 nm (1.85 A) and four ligands at approx. 0.204 nm (2.04 A). The two shorter distances may correspond to Fe-O (tyrosine), whereas the longer distance is consistent with Fe-N (histidine) and Fe-O (water). Detailed analysis of the spectra of the N-terminal and C-terminal fragments indicates a difference in the short ligand distance.

| S-EPMC1153050 | biostudies-other

Extended X-Ray Absorption Fine Structure of ZrW<sub>2</sub>O<sub>8</sub>: Theory vs. Experiment.

Project description:Extended x-ray absorption fine structure (EXAFS) is well-suited for investigations of structure and disorder of complex materials. Recently, experimental measurements and analysis of EXAFS have been carried out to elucidate the mechanisms responsible for the negative thermal expansion (NTE) in zirconium tungstate (ZrW2O8). In contrast to previous work suggesting that transverse O-displacements are largely responsible, the EXAFS analysis suggested that correlated rotations and translations of octahedra and tetrahedra within the structure are a major source. In an effort to resolve this controversy, we have carried out ab initio calculations of the structure, lattice vibrations, and EXAFS of ZrW2O8 based on real-space multiple-scattering calculations using the FEFF9 code and auxiliary calculations of structure and Debye-Waller factors. We find that the theoretical simulations are consistent with observed EXAFS, and show that both of the above mechanisms contribute to the dynamical structure of ZrW2O8.

| S-EPMC6115524 | biostudies-literature

Kinetic and e.p.r. studies of cyanide and azide binding to the copper sites of dopamine (3,4-dihydroxyphenethylamine) beta-mono-oxygenase.

Project description:The kinetics of inhibition of dopamine (3,4-dihydroxyphenethylamine) beta-mono-oxygenase by cyanide (CN-) and azide (N3-) ions have been investigated by using steady-state methods. Both anions show complex non-competitive-inhibition patterns with respect to ascorbate, suggestive of anion binding at two different sites on the oxidized enzyme. To further investigate this finding, e.p.r. titrations of CN- and N3- binding to the 63Cu-reconstituted enzyme were carried out. Addition of approx. 2 equiv. of CN- to copper elicits a new signal with g = 2.217, g = 2.025, A = 17.0 mT characteristic of a copper (II)-cyano complex. Simulations show that this signal accounts for half the copper (II) in the enzyme. The remainder of the enzyme-bound copper is expressed by a signal close to, but not identical with, that of native enzyme. Further addition of CN- induces a simultaneous decrease in intensity of both of these signals so that their 1:1 ratio is maintained. Binding of N3-, on the other hand, changes the e.p.r. spectrum to a form different from either that of the native or CN- -treated enzyme, and integrates to 100% of the copper in the enzyme (g = 2.252, g = 2.050, A = 16.5 mT). Resolved superhyperfine structure is apparent in the g region. N3- binding is also accompanied by the appearance of a broad charge-transfer band centred at 387 nm. Neither 9 nor 35 GHz e.p.r. spectra show evidence for more than one (non-interacting) species of Cu(II) in native enzyme and N3- derivatives. The binding and reactivity of CN-, on the other hand, argues against independent copper sites in the enzyme.

| S-EPMC1153646 | biostudies-other

Ab initio self-consistent x-ray absorption fine structure analysis for metalloproteins.

Project description:X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.

| S-EPMC1635686 | biostudies-literature

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