Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: The zinc co-ordination in 5-aminolaevulinate dehydratase (5-aminolaevulinate hydro-lyase, EC 4.2.1.24) was investigated by recording and interpreting the extended X-ray-absorption fine structure (e.x.a.f.s.) associated with the zinc K-edge. The enzyme has a molecular mass of 280 000 Da and consists of eight subunits of 35 000 Da each; the samples studied contained approx. 1 g-atom of zinc/mol of subunit. Four forms of the enzyme were investigated and details of the zinc environment were elucidated, as follows. In the native enzyme, zinc is considered to be co-ordinated to three sulphur atoms at 0.228(2)nm [2.28(2)A] and a lower-Z atom at 0.192(5)nm [1.92(5)A] (if nitrogen) or 0.189(5)nm [1.89(5)A] (if oxygen). Reaction of the enzyme with the inhibitor 2-bromo-3-(imidazol-5-yl)propionic acid produced significant changes in the e.x.a.f.s., the nature of which are consistent with co-ordination by about three sulphur atoms at 0.222(2)nm [2.22(2)A], a nitrogen atom at 0.193(5)nm [1.93(5)A] and a nitrogen atom from the inhibitor at 0.214(5)nm [2.14(5)A]. Inactivation of the enzyme by air-oxidation of essential thiol groups and binding of the substrate produce slight changes in the e.x.a.f.s. consistent with slight re-arrangement of ligands with additional lighter ligands (nitrogen or oxygen). These results, when combined with previous findings, are taken to indicate that zinc has a structural rather than a direct catalytic role in 5-aminolaevulinate dehydratase.

SUBMITTER: Hasnain SS

PROVIDER: S-EPMC1152664 | biostudies-other | 1985 Sep

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

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

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

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).

| S-EPMC1152194 | biostudies-other

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.

| S-EPMC1152871 | biostudies-other

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

Extended X-Ray Absorption Fine Structure of ZrW2O8: 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

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

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

Extended X-ray absorption fine structure spectroscopy measurements and ab initio molecular dynamics simulations reveal the hydration structure of the radium(II) ion.

Project description:Radium is refocused from the viewpoint of an environmental pollutant and cancer therapy using alpha particles, where it mainly exists as a hydrated ion. We investigated the radium hydration structure and the dynamics of water molecules by extended X-ray absorption fine structure (EXAFS) spectroscopy and ab initio molecular dynamics (AIMD) simulation. The EXAFS experiment showed that the coordination number and average distance between radium ion and the oxygen atoms in the first hydration shell are 9.2 ± 1.9 and 2.87 ± 0.06 Å, respectively. They are consistent with those obtained from the AIMD simulations, 8.4 and 2.88 Å. The AIMD simulations also revealed that the water molecules in the first hydration shell of radium are less structured and more mobile than those of barium, which is an analogous element of radium. Our results indicate that radium can be more labile than barium in terms of interactions with water.

| S-EPMC9386089 | biostudies-literature

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

Project description: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.

| S-EPMC1144072 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data