X-ray diffraction study of the complex of the enzyme SAICAR synthase with substrate analogues

The three-dimensional structure of the complex of the enzyme SAICAR synthase with analogues of natural substrates, namely, phosphoribosylaminoimidazolecarboxamide (AICAR) and succinic acid, was determined and refined by methods of protein crystallography. Two AICAR-binding sites were revealed in the protein molecule. One of these sites is located in the active center of the enzyme in the vicinity of the ATP-binding site, which has been found in the complex of SAICAR synthase with ATP that had been studied earlier. The second AICAR-binding site is located at the periphery of the protein molecule and coincides with the additional ATP-binding site present in the complexes studied earlier. The binding site of succinic acid was revealed in the active center of the enzyme in the vicinity of the AICAR molecule. The electron density distribution for the AICAR molecule in the active center is indicative of the possible lability of the atomic group of the adenine base.     

Three-dimensional structure of Saccharomyces cerevisiae inorganic pyrophosphatase complexed with cobalt and phosphate ions

Crystals of Saccharomyces cerevisiae inorganic pyrophosphatase suitable for X-ray diffraction study were grown by cocrystallization of the enzyme with cobalt chloride and imidodiphosphate. Saccharomyces cerevisiae is a metal-dependent enzyme which catalyzes hydrolysis of inorganic pyrophosphate to orthophosphate. The three-dimensional structure of this enzyme was solved by the molecular-replacement method and refined at 1.8 Å resolution to an R factor of 19.5%. Cobalt and phosphate ions were revealed in the active centers of both identical subunits (A and B) of the pyrophosphatase molecule. In subunit B, a water molecule was found between two cobalt ions. It is believed that this water molecule acts as an attacking nucleophile in the enzymatic cleavage of the pyrophosphate bond. It was demonstrated that cobalt ions and a phosphate group occupy only part of the potential binding sites (two chemically identical and crystallographically independent subunits have different binding sites). The arrangement of ligands and the structure of the nucleophile-binding site are discussed in relation to the mechanism of action of the enzyme and the nature of the metal activator.     

Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI₂ with the coupled reduction of nicotinamide adenine dinucleotide (NAD⁺). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD⁺-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 Å resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.     

X-ray diffraction study of <Emphasis Type="Italic">Penicillium Vitale</Emphasis> catalase in the complex with aminotriazole

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.     

Comparative analysis of spatial organization of laccases from <Emphasis Type="Italic">Cerrena maxima</Emphasis> and <Emphasis Type="Italic">Coriolus zonatus</Emphasis>

Laccase (oxygen oxidoreductase, EC 1.10.3.2) belongs to the multicopper oxidase family. The main function of this enzyme is to perform electron transfer from the oxidized substrate through the mononuclear copper-containing site T1 to the oxygen molecule bound to the site T3 in the trinuclear T2/T3 cluster. The structures of two new fungal laccases from C. maxima and C. zonatus were solved on the basis of synchrotron X-ray diffraction data. Both laccases show high structural homology with laccases from other sources. The role of the carbohydrate component of laccases in structure stabilization and formation of ordered protein crystals was demonstrated. In the structures of C. maxima and C. zonatus laccases, two water channels of functional importance were found and characterized. The structural results reported in the present study characterize one of the functional states of the enzyme fixed in the crystal structure.     

Structural basis for the mechanism of inhibition of uridine phosphorylase from <Emphasis Type="Italic">Salmonella typhimurium</Emphasis>

The three-dimensional structures of three complexes of Salmonella typhimurium uridine phosphorylase with the inhibitor 2,2′-anhydrouridine, the substrate PO₄, and with both the inhibitor 2,2′-anhydrouridine and the substrate PO₄ (a binary complex) were studied in detail by X-ray diffraction. The structures of the complexes were refined at 2.38, 1.5, and 1.75 Å resolution, respectively. Changes in the three-dimensional structure of the subunits in different crystal structures are considered depending on the presence or absence of the inhibitor molecule and (or) the phosphate ion in the active site of the enzyme. The presence of the phosphate ion in the phosphate-binding site was found to substantially change the orientations of the side chains of the amino-acid residues Arg30, Arg91, and Arg48 coordinated to this ion. A comparison showed that the highly flexible loop L9 is unstable. The atomic coordinates of the refined structures of the complexes and the corresponding structure factors were deposited in the Protein Data Bank (their PDB ID codes are 3DD0 and 3C74). The experimental data on the spatial reorganization of the active site caused by changes in its functional state from the unligated to the completely inhibited state suggest the structural basis for the mechanism of inhibition of Salmonella typhimurium uridine phosphorylase.     

Synthesis and crystal and molecular structure of the [MoO2(L)(H2O)] · H2O complex (L 2− is the anion of 2-[N-(hydroxynaphtylidene)amino]propan-1,2,3-triol)

A new compound of dioxomolybdenum(VI)—[MoO₂(L)(H₂O)] · H₂O, where L ^2? = 2-[N-(hydroxynaphtylidene)amino]propan-1,2,3-triol)—is synthesized. Its structure is determined by X-ray diffraction. The Mo atom has an octahedral coordination formed by two oxo ligands located cis with respect to one another, two O atoms and the N atom of the tridentate bis(chelate) L ^2? ligand, and the O atom of a water molecule. The crystallization water molecule is connected with two complex molecules by O-H…O hydrogen bonds.     

Three-dimensional structure of laccase from Coriolus zonatus at 2.6 Å resolution

Laccase (oxygen oxidoreductase, EC 1.14.18.1) belongs to the copper-containing oxidases. This enzyme catalyzes reduction of molecular oxygen by different organic and inorganic compounds to water without the formation of hydrogen peroxide. The three-dimensional structure of native laccase from Coriolus zonatus was solved and refined at 2.6 Å resolution (R _factor = 21.23%, R _free = 23.82%, rms deviations for the bond lengths and bond angles are 0.008 Å and 1.19°, respectively). The primary structure of the polypeptide chain and the architecture of the active site were refined. The carbohydrate component of the enzyme was identified. The access and exit water channels providing the access of molecular oxygen to the active site and release of water, which is the reduction product of molecular oxygen, from the protein molecule were found in the structure.     

X-ray structures of uridine phosphorylase from <Emphasis Type="Italic">Vibrio cholerae</Emphasis> in complexes with uridine,thymidine, uracil,thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2′-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation     

Inclusion Compounds of Plant Growth Regulators in Cyclodextrins. Part VI. Study of the Inclusion Compound of MCPA in β-Cyclodextrin by X-Ray Crystallography

Abstract  

The structure of the 4-chloro-2-methylphenoxyacetic acid (MCPA) inclusion compound in β-Cyclodextrin (β-CD) has been investigated by X-ray crystallography. The inclusion complex crystallizes in the P2₁ space group with unit cell dimensions a = 15.860(2) ?, b = 24.275 (5) ?, c = 19.334(6) ? and β = 108.80(3)°. Its asymmetric unit contains two β-CD molecules which host two disordered MCPA guest molecules (2:2 host:guest stoichiometry) occupying overall five sites. It also contains 16.13 water molecules distributed over 36 sites. One water molecule is entrapped inside the dimeric cavity, forming a hydrogen bond with the chlorine atom of a guest. The two complexes of the asymmetric unit are located alongside and they form head-to-head dimers with the symmetry related complexes by the 2-fold screw axis (b-axis). The dimers form channels developed along the a-axis.     

Magnetic resonance study of the crystallization behavior of InF3-based glasses doped with Cu2+, Mn2+ and Gd3+

The crystallization of fluoroindate glasses doped with Gd³⁺, Mn²⁺ and Cu²⁺ heat treated at different temperatures, ranging from the glass transition temperature (T_g) to the crystallization temperature (T_c), are investigated by electron paramagnetic resonance (EPR) and ¹⁹F nuclear magnetic resonance (NMR). The EPR spectra indicate that the Cu²⁺ ions in the glass are located in axially distorted octahedral sites. In the crystallized glass, the g-values agreed with those reported for Ba₂ZnF₆, which correspond to Cu²⁺ in a tetragonal compressed F⁻ octahedron and to Cu²⁺ on interstitial sites with a square-planar F⁻ co-ordination. The EPR spectra of the Mn²⁺ doped glasses exhibit a sextet structure due to the Mn²⁺ hyperfine interaction. These spectra suggest a highly ordered environment for the Mn²⁺ ions (close to octahedral symmetry) in the glass. The EPR spectra of the recrystallized sample exhibit resonances at the same position, suggesting that the Mn²⁺ ions are located in sites of highly symmetric crystalline field. The increase of the line intensity of the sextet and the decrease of the background line in the thermal treated samples suggest that the Mn²⁺ ions move to the highly ordered sites which contribute to the sextet structure. The EPR spectra of the Gd³⁺ doped glasses exhibit the typical U-spectrum of a s-state ion in a low symmetry site in disordered systems. The EPR of the crystallized glasses, in contrast, have shown a strong resonance in g ≈ 2.0, suggesting Gd³⁺ ions in environment close to cubic symmetry. The ¹⁹F NMR spin–lattice relaxation rates were also strongly influenced by the crystallization process that takes over in samples annealed above T_c. For the glass samples (doped or undoped) the ¹⁹F magnetization recoveries were found to be adjusted by an exponential function and the spin–lattice relaxation was characterized by a single relaxation time. In contrast, for the samples treated above T_c, the ¹⁹F magnetization-recovery becomes non-exponential. A remarkable feature of our results is that the changes in the Cu²⁺, Mn²⁺, Gd³⁺ EPR spectra and NMR relaxation, are always observed for the samples annealed above T_c.     

Crystal structure and spectroscopic study of bis{1,3-bis[3-(5-amino-1,2,4-triazolyl)]triazenido-N′4,N2,N″4}nickel(II) tetrahydrate

The title compound [Ni(batt)₂]·4H₂O, in which Hbatt is 1,3-bis[3-(5-amino-1,2,4-triazolyl)]triazene, has been prepared and its crystal structure determined by X-ray diffraction methods. The compound crystallizes in the tetragonal space group I4/m (a = 10.5645(8) Å, c = 9.1336(6) Å, and Z = 2). The Ni(batt)₂ molecule has local 4¯ symmetry, but it is located on a crystallographic 4/m site and is disordered over the mirror plane. The ligand batt^– is tridentate with nitro-type coordination of the triazenido group and N⁴ coordination of the two outer triazolyl substituents. The complex has a distorted octahedral geometry with meridional configuration of the two nearly planar batt^– ligands. The geometry of the tridentate cavity is examined and a comparison is made with the Ni-terpyridyl system, which shows similar coordination around the nickel center. The FTIR, micro-Raman, and UV-vis spectra are analyzed in relation with the structure.     

57Fe Mössbauer effect studies in Y66(FExTM1−x)34 metallic glasses

⁵⁷Fe Mössbauer effect (ME) measurements in a variety of Y based metallic glasses are reported. The spectra are best described in terms of a model which assumes two Fe sites having nearly equal intensities. We find that the ME parameters are smooth and monotonic functions of composition (x) for the glasses Y₆₆(Fe_xTM_1?x)₃₄ (TM = Mn, Fe, Co, Ni, Cu Zn) leading to the conclusion that Fe randomly substitutes for the various TM in these glasses. The nature of the two sites we observe is radically different depending on whether TM is to the right or left of Ni. Those glasses containing Mn, Fe, Co, and Ni display a degree of chemical ordering. In these glasses (TM = Mn, Fe, Co, Ni) we identify site 1 as a Y-dominated Fe environment and site 2 as an Fe environment having a larger number of Fe(TM) near neighbors. A correlation between the isomer shifts [IS] of site 2 and Fe impurities in the corresponding crystalline compounds PTYM₂ is noted and discussed in terms of a volume dependence of IS.     

Crystal Structure of a Nickel(II) Complex with the Macrocyclic Azadibenzo-14-crown-4 Ether Ligand Containing the Embedded Di(α-pyridyl)bispidone Moiety

The crystal structure of the nickel(II) complex with substituted azadibenzo-14-crown-4 ether containing the embedded di(α-pyridyl)bispidone moiety having the formula [L(H₂O)Ni(NO₃) Ni(H₂O)L](ClO₄)₃ · 0.7EtOH was studied by X-ray diffraction (T = 150(2) K, R = 0.0628). In the complex cation two five-coordinate nickel complexes are bridged by the nitrate anion to form a dimer. The distorted octahedral environment of Ni atoms is formed by four nitrogen atoms of the molecule L and the oxygen atoms of the water molecule and the NO ₃ ^- anion. In the nickel complex, like in the cobalt and copper complexes studied previously, the bispidine moiety of the molecule L adopts a chair-chair conformation.     

Rare-earth-doped silica-based glasses for photonic applications

Two different silica-based glass systems with valuable optical and spectroscopic properties in the 1.5 μm band, exploited in optical microcavities, are presented. First, we report on Er³⁺-activated core–shell silica spheres prepared by sol–gel process. The core consists of a silica sphere of 270 nm in diameter, while the shell is an Er₂O₃–SiO₂ film. The second system is an Er³⁺-activated microcavity fabricated by rf-sputtering technique. The cavity is constituted of an Er³⁺-doped SiO₂ layer inserted between two Bragg mirrors, fabricated by alternately stacking five TiO₂ and five SiO₂ thin films. Optical and spectroscopic properties were assessed, and the two systems were characterized from morphological and structural point of view.     

Structure of octaheme cytochrome <Emphasis Type="Italic">c</Emphasis> nitrite reductase from <Emphasis Type="Italic">Thioalkalivibrio nitratireducens</Emphasis> in a complex with phosphate

Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of the oxidized complex of TvNiR with phosphate and of this complex reduced by europium(II) chloride (1.8- and 2.0-Å resolution, the R factors are 15.9 and 16.7%, respectively) and the structure of the enzyme in the complex with cyanide (1.76-Å resolution, the R factor is 16.5%), which was prepared by soaking a crystal of the oxidized phosphate complex of TvNiR. In the active site of the enzyme, the phosphate ion binds to the iron ion of the catalytic heme and to the side chains of the catalytic residues Arg131, Tyr303, and His361. The cyanide ion is coordinated to the heme-iron ion and is hydrogen bonded to the residue His361. In the structure of reduced TvNiR, the phosphate ion is bound in the same manner as in the structure of oxidized TvNiR, and the nine_coordinated europium ion is located on the surface of one of the crystallographically independent monomers of the enzyme.     

Crystal and molecular structure of two isomeric N-methyl iodides of thiobinupharidine:trans,trans-N,N′-dmethyl-thiobinupharidine diiodide dihydrate acetone solvate andcis,trans-N,N′-dimethylthiobinupharidine diiodide dihydrate methanol solvate

The crystal structures of two quaternary salts,trans,trans- andcis,trans-N,N-dimethylthiobinupharidine diiodide, whose stereochemistries have been previously characterized by¹³C NMR spectroscopy, have now been determined by X-ray analysis. Differences in the nitrogen atom configuration of the AB quinolizidine fragment result in different conformations of the central part of the cations, the spiro tetrahydrothiophene ring, and specific selectivity toward solvent molecules. Thetrans,trans isomer crystals obtained from an acetone/methanol/water solution contained two water and one acetone molecule, while thecis,trans cocrystallized from the same solvent mixture with methanol and two water molecules. Very weak hydrogen bonds of the C-HI^– type determine interactions between the quaternary cations and the I^– anions in the solid state. Water molecules form a dimer, and this dimer is hydrogen bonded to the I^– anions. Organic solvent molecules included in crystals show different type of interactions with surrounding molecules: (i) the acetone molecule is trapped in the cavity of thetrans,trans cation by very weak C-HO interactions; (ii) methanol is hydrogen bonded to a water molecule while with thecis,trans cation and I^– anion interacts only by van der Waals forces.     

Crystal and molecular structure of hydridodinitratobis(triphenylphosphine)iridium(III)

Crystals of hydridodinitratobis(triphenylphosphine) iridium(III), IrH(NO₃)2(PPh₃)₂, belong to the trigonal system, space groupP¯3e1, with hexagonal unit-cell dimensionsa = 16.33(1),c = 22.85(2) Å, andZ = 6. The six Ir atoms lie in special positions. Two (of molecule 1) have site symmetry 32 and four (of molecule 2) have site symmetry 3. Both types of molecule have trigonal bipyramidal coordination with phosphorus atoms axial but do not have sufficient nitrate groups (two instead of three) to satisfy the site symmetry. Thus both types of molecule have disordered nitrate groups and the mode of coordination appears to be somewhat different at the two sites.     

Crystal Structure of 9α,11-Epoxy-7α-(methoxycarbonyl)-3-oxo-17α-pregn-4-ene-21,17-carbolactone

Abstract  The title compound (common name eplerenone), C₂₄H₃₀O₆, is an aldosterone receptor antagonist. From the isopropyl acetate solution the compound crystallizes in monoclinic space group P 21 with a = 8.811(1) ?, b = 11.250(1) ?, c = 11.079(1) ?, β = 93.822(12)°, Z = 2. The molecule contains three six membered rings, two five membered rings and one three membered ring. Both five membered rings display envelope conformation, whereas three six membered rings show different conformation: chair, half-chair and envelope. In the crystal the eplerenone molecules link to one another via intermolecular weak C–H···O hydrogen bonding to form the smaller cavity of 12.0(1) ?³ between eplerenone molecules, no solvent molecule filled in this cavity. Index Abstract  In the title molecule three six-membered rings show different conformation. Weak C–H···O hydrogen bonding links adjacent molecules to form the small cavity 12.0(1) ?³, no solvent molecule filled in the cavity.      

Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from <Emphasis Type="Italic">E. coli</Emphasis> at 2.71 Å resolution

Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 Å resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sites were shown to be identical in both proteins.