Substrate, substrate analogue, and inhibitor interactions with the ferrous active site of catechol 2,3-dioxygenase monitored through XAS studies.

The interactions of catechol (substrate), 2-hydroxy-pyridine-N-oxide (substrate analogue), and 2-bromophenol (inhibitor) with the extradiol cleaving catechol-2,3-dioxygenase from Pseudomonas putida mt-2 have been monitored through X-ray absorption spectroscopy (XAS). The analysis of the data provides details about the mode of coordination of the substrate and of the inhibitors to the active site of the enzyme.

Kinetic and spectroscopic characterization of native and metal-substituted beta-lactamase from Aeromonas hydrophila AE036.

Two metal ion binding sites are conserved in metallo-beta-lactamase from Aeromonas hydrophila. The ligands of a first zinc ion bound with picomolar dissociation constant were identified by EXAFS spectroscopy as one Cys, two His and one additional N/O donor. Sulfur-to-metal charge transfer bands are observed for all mono- and di-metal species substituted with Cu(II) or Co(II) due to ligation of the single conserved cysteine residue. Binding of a second metal ion results in non-competitive inhibition which might be explained by an alternative kinetic mechanism. A possible partition of metal ions between the two binding sites is discussed.

Zn-ligation in inorganic deposits in the wall of the human aorta determined by X-ray absorption spectroscopy.

X-ray absorption spectra were recorded at the K edge of Zn from inorganic deposits present in the human aortic wall. The interatomic distances and coordination numbers obtained indicate that Zn atoms probably occupy selected Ca positions in the lattice of the octacalcium phosphate crystals localized at the surface of the deposit.

X-ray absorption spectroscopy study of native and phenylphosphorodiamidate-inhibited Bacillus pasteurii urease.

X-ray absorption spectroscopy (XAS) has been applied to urease from Bacillus pasteurii, a highly ureolytic soil bacterium, with the aim of elucidating the structural details of the nickel-containing active site. The results indicate the presence of octahedrally coordinated Ni2+, in a sphere of six N/O donors at an average distance of 0.203 nm. An average of two histidine residues are bound to nickel. The experimental evidence suggests direct binding of the urease inhibitor phenylphosphorodiamidate to Ni2+. These spectroscopic results are in agreement with previous findings on both plant and microbial ureases, but differ in some respect from the results obtained by X-ray crystallography analysis of Klebsiella aerogenes urease.

X-ray absorption studies on catechol 2,3-dioxygenase from Pseudomonas putida mt2.

X-ray absorption spectroscopy has been utilized to investigate the structure of the active site of iron(II) catechol 2,3-dioxygenase from Pseudomonas putida mt2 both in the native and the 2-chlorophenol inhibited forms. XANES (X-ray absorption near edge structure) and EXAFS (extended X-ray absorption fine structure) results allow us to discuss the coordination number and geometry of the ferrous ion in the native enzyme. The metal geometry is not significantly affected by the binding of the inhibitor. The EXAFS spectrum is consistent with an iron(II) bound to six N/O atoms at an average distance of 2.05 A or to five N/O at an average distance of 2.04 A. The stimulation of the experimental data is greatly enhanced by considering the iron ligands divided in two different shells. Analysis of the outer shells performed using multiple scattering theory shows that there are histidines in the coordination sphere. The best fitting is obtained assuming the presence of two of them. Similar results are obtained for the inhibited enzyme, which, however, are indicative of a slight shortening of the average metal-donor bond distances. The direct binding of inhibitors to the metal center is confirmed by 1H NMR data.

EXAFS investigation of the active site of iron superoxide dismutase of Escherichia coli and Propionibacterium shermanii.

The local structure of the iron site in ferric superoxide dismutase from P. shermanii was analyzed by X-ray absorption spectroscopy. The metal-ligand cluster of the enzyme is found to be similar to the crystallographically investigated ferric superoxide dismutase from E. coli. At pH 6.4 the enzyme is five-fold coordinated with three histidines, an aspartate and a water molecule. The average bond lengths between the metal and the histidines are about 2.10 A, between metal and aspartate they are about 1.86 A and between metal and water 1.96 A. With an increase in pH a change in the coordination number from five to six is observed both in pre-edge peak and EXAFS spectra analysis. However, the bond lengths of the ligands do not change dramatically, they are conserved for the aspartate and increase slightly to 2.13 A for the average metal-histidine distance at pH 9.3. The observation of the increase in coordination number is correlated with a decrease in enzymatic activity which occurs in the high pH range. The zinc EXAFS spectra of P. shermanii superoxide dismutase have shown that zinc can be incorporated in the active center instead of the iron.

Mössbauer, electron-paramagnetic-resonance and X-ray-absorption fine-structure studies of the iron environment in recombinant human tyrosine hydroxylase.

Isoforms (1-4) of human tyrosine hydroxylase (TH) have been expressed in Escherichia coli and purified as apoenzymes (metal-free). Apo-human TH binds 1.0 atom Fe(II)/enzyme subunit, and iron binding is associated with an immediate and dramatic (40-fold) increase in specific activity. For X-ray absorption fine structure (XAFS) and electron paramagnetic resonance (EPR) measurements the apoenzyme was reconstituted with 56Fe and for Mössbauer measurements with 57Fe. XAFS measurements at the Fe-K edge of human TH were performed on the native form [Fe(II)-human TH], as well as after addition of stoichiometric amounts of the substrate tetrahydropterin, the inhibitor dopamine and of H2O2. The addition of dopamine or H2O2 oxidizes the ferrous iron of the native human TH to the ferric state. In both redox states the iron is octahedrally coordinated by low-Z backscatterers, thus sulfur coordination can be excluded. From the multiple scattering analysis of the EXAFS region is was surmised that part of the iron coordination is due to (3 +/- 1) imidazols. Addition of tetrahydropterin does not significantly change the iron coordination of the Fe(II) enzyme. The Mössbauer results confirm the valence states and the octahedral coordination of iron as well as the exclusion of sulfur ligation. Both the EPR spectra and the Mössbauer magnetic hyperfine pattern of dopamine- and H2O2-treated native human TH, were analyzed with the spin-Hamiltonian formalism. This analysis provides significantly different features for the two forms of human TH: the ferric iron (S = 5/2) of the H2O2-treated form exhibits a rhombic environment while that of the dopamine-treated form exhibits near-axial symmetry. The specific spectroscopic signature of dopamine-treated human TH, including that of an earlier resonance-Raman study [Michaud-Soret, I., Andersson, K. K., Que, L. Jr & Haavik, J. (1995) Biochemistry 34, 5504-5510] is most likely due to the bidentate binding of dopamine to iron.

Cloning and expression of Saccharomyces cerevisiae copper-metallothionein gene in Escherichia coli and characterization of the recombinant protein.

The gene sequences for intact and truncated forms of copper-binding metallothionein from Saccharomyces cerevisiae were cloned and overexpressed in Escherichia coli BL21(DE3)pLysE cells. In contrast to several other genes, the intact and truncated metallothionein genes are amplified in the polymerase chain reaction when Mg2+ is replaced by Co2+. The recombinant truncated protein binds copper in vivo and in vitro. A ratio of 8 Cu/12 cysteines was determined from atomic absorption, X-ray fluorescence and amino acid analysis. Extended X-ray absorption spectroscopy indicates that all Cu is in Cu(I) form and coordinated to three S atoms.

Evidence for polynuclear aggregates of ferric daunomycin. A Mössbauer, EPR, X-ray absorption spectroscopy and magnetic susceptibility study.

The interaction of the antitumor agent daunomycin (DN) with ferric iron has been analysed by Mössbauer spectroscopy, EPR, extended X-ray absorption fine structure (EXAFS), and magnetic susceptibility measurements. In contrast to literature data, at millimolar iron and anthracycline concentrations no solitary Fe(DN)3 complexes are formed in appreciable amounts. The Mössbauer spectroscopic analysis revealed severe dependencies on temperature, on the preparation procedure, the time allowed for equilibration, and on the metal/ligand ratio. The Mössbauer spectra exhibit two components: a broad magnetic sextet and a quadrupole doublet at an Fe/DN molar ratio of 1:3 and exclusively a doublet at a molar ratio of 1:20, indicating an equilibrium of these two spectral components. The EPR spectra are dominated by a signal at g(eff) = 2. Double integration of the EPR signals enabled the determination of their spin density and a correlation between EPR and Mössbauer spectra. The Mössbauer sextet species is EPR invisible and corresponds to magnetically ordered polynuclear aggregates with high magnetic anisotropy. EXAFS and susceptibility measurements provide additional evidence for the formation of polynuclear aggregates of ferric daunomycin. The quadrupole doublet species in the Mössbauer spectra correlates with the g = 2 signal in EPR. This species is also related to a magnetically ordered system, exhibiting, however, superparamagnetic behavior due to less magnetic anisotropy. Since daunomycin forms dimers in aqueous solution at millimolar concentrations, we conclude that the cooperative phenomena observed in EPR and Mössbauer spectra are a consequence of its stacking effects.

Changes in the iron coordination sphere of Fe(II) lipoxygenase-1 from soybeans upon binding of linoleate or oleate.

Fe K-edge X-ray absorption spectra of the non-heme iron constituent of lipoxygenase-1 from soybeans were obtained. The spectrum of 2.5 mM Fe(II) lipoxygenase, mixed with 1.2 M linoleate in the absence of O2, was compared to the spectrum of the native (i.e. untreated) enzyme. In the lipoxygenase-linoleate complex, an edge shift to lower energy was observed. This indicated that the iron-ligand distances in this complex are slightly longer than those in the untreated enzyme species. The extended X-ray absorption fine structure spectrum of Fe(II) lipoxygenase, prepared by anaerobic reduction of 2.5 mM Fe(II) lipoxygenase with 1.2 M linoleate, was very similar to the spectrum of the anaerobic lipoxygenase-linoleate complex. We conclude that the conformational differences between the iron coordination spheres of native and cycled Fe(II) lipoxygenase must be ascribed to the presence of linoleate, and not to changes in the enzyme that occur only after one cycle of oxidation and reduction. Furthermore, spectra of 2.5 mM Fe(II) lipoxygenase mixed with 1.2 M oleate, either in the absence or in the presence of O2, were also identical to the spectrum of the Fe(II) lipoxygenase-linoleate complex. This finding is in agreement with our observation that oleate is a competitive inhibitor of the lipoxygenase reaction. Moreover, the similarity of the lipoxygenase-oleate complexes in the presence and absence of O2 excludes the possibility that O2 binding to the iron cofactor is induced upon binding of a fatty acid to lipoxygenase.

Extended X-ray absorption fine structure (EXAFS) investigations of model compounds for zinc enzymes.

A test of the ability of extended X-ray absorption fine structure (EXAFS) to determine structural information with specific reference to zinc sites in enzymes has been made. X-ray absorption spectra of 18 compounds of zinc have been measured and the nearest-neighbour scattering has been interpreted using a Fourier transform and an ab initio technique. Empirical Zn-N, Zn-O, Zn-S and Zn-Cl amplitude and phase functions have been extracted from Zn(C3H4N2)4(ClO4)2, ZnO, Zn(S2COC2H5)2 and [N(CH3)4]2[ZnCl4], respectively and tabulated as a function of the wavevector with respect to 9660.0 eV X-ray energy. These amplitude and phase functions were then tested with respect to the other 14 compounds. For a single species of atoms in the first coordination shell the interatomic distances can be established to +/- 0.5 pm (+/- 5 x 10(-3) A) whilst when mixed shells exist errors in distances are +/-4 pm (+/- 40 x 10(-3) A). Coordination numbers are given to +/- 16% for the single species case a and +/- 25% for the mixed coordination case. Using the theoretical amplitude and phase functions of McKale et al. [(1988) J. Am. Chem. Soc. 110, 3763-3768] the deduced distances are systematically too small by an average of 0.6 pm (6 x 10(-3) A). The errors in the coordination numbers are 18%.

X-ray absorption spectroscopy of soybean lipoxygenase-1. Influence of lipid hydroperoxide activation and lyophilization on the structure of the non-heme iron active site.

X-ray absorption spectra at the Fe K-edge of the non-heme iron site in Fe(II) as well as Fe(III) soybean lipoxygenase-1, in frozen solution or lyophilized, are presented; the latter spectra were obtained by incubation of the Fe(II) enzyme with its product hydroperoxide. An edge shift of about 2-3 eV to higher energy occurs upon oxidation of the Fe(II) enzyme to the Fe(III) species, corresponding to the valence change. The extended X-ray absorption fine structure shows clear differences in active-site structure as a result of this conversion. Curve-fitting on the new data of the Fe(II) enzyme, using the EXCURV88 program, leads to a coordination sphere that is in agreement with the active-site structure proposed earlier (6 +/- 1 N/O ligands at 0.205-0.209 nm with a maximum variance of 0.009 nm, including 4 +/- 1 imidazole ligands) [Navaratnam, S., Feiters, M. C., Al-Hakim, M., Allen, J. C., Veldink, G. A. and Vliegenthart, J. F. G. (1988) Biochim. Biophys. Acta 956, 70-76], while for the Fe(III) enzyme a shortening in ligand distances occurs (6 +/- 1 N/O ligands at 0.200-0.203 nm with maximum variance of 0.008 nm) and one imidazole is replaced by an oxygen ligand of unknown origin. Lyophilization does not lead to any apparent differences in the iron coordination of either species and gives a much better signal/noise ratio, allowing analysis of a larger range of data.