Substrate specificity of pyrimidine nucleoside phosphorylases of NP-II family probed by X-ray crystallography and molecular modeling

Pyrimidine nucleoside phosphorylases, which are widely used in the biotechnological production of nucleosides, have different substrate specificity for pyrimidine nucleosides. An interesting feature of these enzymes is that the three-dimensional structure of thymidine-specific nucleoside phosphorylase is similar to the structure of nonspecific pyrimidine nucleoside phosphorylase. The three-dimensional structures of thymidine phosphorylase from Salmonella typhimurium and nonspecific pyrimidine nucleoside phosphorylase from Bacillus subtilis in complexes with a sulfate anion were determined for the first time by X-ray crystallography. An analysis of the structural differences between these enzymes demonstrated that Lys108, which is involved in the phosphate binding in pyrimidine nucleoside phosphorylase, corresponds to Met111 in thymidine phosphorylases. This difference results in a decrease in the charge on one of the hydroxyl oxygens of the phosphate anion in thymidine phosphorylase and facilitates the catalysis through S_N2 nucleophilic substitution. Based on the results of X-ray crystallography, the virtual screening was performed for identifying a potent inhibitor (anticancer agent) of nonspecific pyrimidine nucleoside phosphorylase, which does not bind to thymidine phosphorylase. The molecular dynamics simulation revealed the stable binding of the discovered compound—2-pyrimidin-2-yl-1H-imidazole-4-carboxylic acid—to the active site of pyrimidine nucleoside phosphorylase.     

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     

Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3′-azido-2′-fluoro-2′,3′-dideoxyuridine

The three-dimensional structures of thymidine phosphorylase from E. coli containing the bound sulfate ion in the phosphate-binding site and of the complex of thymidine phosphorylase with sulfate in the phosphate-binding site and the inhibitor 3′-azido-2′-fluoro-2′,3′-dideoxyuridine (N₃F-ddU) in the nucleoside-binding site were determined at 1.55 and 1.50 Å resolution, respectively. The amino-acid residues involved in the ligand binding and the hydrogen-bond network in the active site occupied by a large number of bound water molecules are described. A comparison of the structure of thymidine phosphorylase in complex with N₃F-ddU with the structure of pyrimidine nucleoside phosphorylase from St. Aureus in complex with the natural substrate thymidine (PDB_ID: 3H5Q) shows that the substrate and the inhibitor in the nucleoside-binding pocket have different orientations. It is suggested that the position of N₃F-ddU can be influenced by the presence of the azido group, which prefers a hydrophobic environment. In both structures, the active sites of the subunits are in the open conformation.     

Structural and Functional Analysis of Pyrimidine Nucleoside Phosphorylases of the NP-I and NP-II Families in Complexes with 6-Methyluracil

The structure of bacterial uridine phosphorylase (UPh) belonging to the NP-I family in complex with 6-methyluracil was determined for the first time at 1.17 Å resolution. The structural features of bacterial UPh from the bacterium Vibrio cholerae (VchUPh) responsible for selectivity toward 6-methyluracil acting as a pseudosubstrate were revealed. The repulsion between the hydrophilic hydroxyl group of the active-site residue Thr93 of VchUPh and the hydrophobic methyl group of 6-methyluracil prevents the oxygen atom O4' of the ribose moiety and the phosphate oxygen atom O3P of ribose 1-phosphate from forming hydrogen bonds with OG1_Thr93, which are essential for the enzymatic reaction. This, apparently, makes VchUPh inactive in the enzymatic synthesis of 6-methyluridine from 6-methyluracil. Hence, Thr93 is the residue, the modification of which will allow VchUPh to catalyze the biotechnologically important synthesis of 6-methyluridine from 6-methyluracil. Taking into account high structural homology of the functionally significant regions of bacterial UPhs, this conclusion is also true for other bacterial UPhs. It was demonstrated that bacterial thymidine phosphorylases of the NP-II family cannot bind 6-methyluracil in a proper conformation required for the catalysis because of a close contact between the 6-methyl group and Phe210.     

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.     

Oxophosphoryl Complexes of Dipyrrin: Spectral and Aggregation Characteristics of Solutions and Thin Films

Crystallography Reports - The spectral characteristics of a compound representing a new class of organic luminescent materials—dipyrrin oxophosphoryl complex (PODIPY)—in organic...     

Study of the complex vibrational spectra of natural mesolite

The vibrational spectra of the natural zeolite, mesolite (locality Akureyri-Island) were measured in the infrared (200—400 cm⁻¹) and the far infrared — FIR (40—400 cm⁻¹) regions: the infrared reflectance (200—1400 cm⁻¹) and Raman scattering (50—3600 cm⁻¹) spectra of the polycrystalline material were also measured. The Schimanouchi GCCC, BGLZ, and LSMA programs were used to calculate the force constants and vibrational frequencies of the Si O, Al O, O H, cation-oxygen, O Si O, O Al O, H O H bonds and libration of H₂O and Si(Al) O Si on the basis of the symmetry coordinates. The KKK-1 program (Petzelt, Kroupa) was used to calculate the dispersion curves of the complex refractive index for both parts of the complex dielectric permittivity in the whole measured wavenumber region. The bands in the spectra were assigned to the vibrations of the individual bonds and structural groups of the mesolite on the basis of theoretical calculations.     

Anion Cluster: Assembly of Dihydrogen Phosphates for the Formation of a Cyclic Anion Octamer

Structural characterization of a dihydrogen phosphate complex of triprotonated tris[2-(2-thienylmethylamino)ethyl] amine shows that eight dihydrogen phosphate anions are assembled around the host by strong interactions of H-bond donors and acceptors to form a new type of cyclic anion octamer as (H(2)PO(4) (-))(8), an analogy of cyclic water octamer. The presence of an anion cluster has also been identified by electrospray ionization mass spectrometry and (31)P NMR experiments.     

Three-dimensional structure of <Emphasis Type="Italic">E. Coli</Emphasis> purine nucleoside phosphorylase at 0.99 Å resolution

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 Å resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment of the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB_ID: 4RJ2).     

New phosphate Fe0.5Nb1.5(PO4)3 with an electrically neutral framework. Synthesis and crystal structure

A new iron-niobium phosphate, Fe_0.5Nb_1.5(PO₄)₃, has been prepared and studied by X-ray diffraction, electron microprobe analysis, IR spectroscopy, and neutron powder diffraction. On the basis of X-ray powder data, it was found that the synthesized phosphate crystallizes into the sp. gr. R $\bar 3$ c and corresponds to the structural type of sodium-zirconium phosphate NaZr₂(PO₄)₃. The structure was refined by the Rietveld method based on a powder neutron diffraction experiment. The obtained phosphate belongs to complex niobium orthophosphates and has a framework structure with a zero framework charge.     

Synthesis and crystallographic characterization of a six coordinate Cu(II) complex based on hexamethylenetetramine ligand

The title compound, Cu(H₂O)₆]Cl₂.2{(CH₂)₆N₄}.4H₂O ( 1 ), has been prepared under mild hydrothermal conditions. Each Cu^II atom, located on a centre of symmetry, is coordinated by six water molecules in distorted octahedral coordination geometry. The hexamethylenetetramine molecule does not coordinate to the Cu atom but links with the Cu complex via three O—H…N hydrogen bonds. The remaining N atom of the hexamethylenetetramine is hydrogen‐bonded to the solvent water molecule. In the crystal structure, intermolecular O—H…O, O—H…N and O—H…Cl hydrogen bonds link the components into a three‐dimensional network. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Topological Soft Matter for Optics and Photonics

Liquid crystal colloids are interesting for a variety of mechanisms—including self-assembly, optical-tweezers assisted assembly, topology, and material flow—that can be used to create various complex optical and photonic structures. Here, we present a brief overview of liquid crystal colloidal structures, as recently achieved by numerical modeling and experiments. Central to the structures are complex conformations of topological defects, as they can bind, stabilize, or distort the structure. Using topological and geometrical arguments, we show that the defects can be controllably rewired and imprinted, for example by using optical tweezers. We show that 3D colloidal crystals can be assembled from elastic dipoles of spherical beads in nematic liquid crystals or via inherently inhomogeneous order profiles in bulk and confined cholesteric blue phases. Colloidal crystals are generalized to close-packed colloidal lattices, which we show can serve as natural templates for defect networks. Finally, photonic bands are calculated for selected structures and possible defects in the structure are discussed.     

Zur Integration der Grundgleichungen für bewegte Eigenspannungsquellen in kubischen Kristallen

Solutions of the equations of dislocation theory are given being based on a mathematical method which decouples the system of differential equations for the displacement vector. The solutions regard elastic anisotropy of crystalline matter not only in statics but also in dynamics. — The method succeeds in the case of plane strain in cubic or hexagonal crystals, allowing most general plastic distorsions as well as processes of arbitrary timedependence. Decoupling is the basis for using complex variable methods which may be applied when dislocations move in a uniform way.     

The Influence of Interstitials and Growth Conditions on the X-Ray Colorability of Synthetic Quartz Crystals

The saturation colorability of quartz crystals depends not only on the contamination of the material but also on the regarded growth sector. But even in the same sector the colorability varies locally. Investigations of crystals with induced growth striations and defined local growth rate showed that the dependence of the colorability on the growth conditions is very complex. The growth rate to colorability characteristics may have positive or negative slopes regarding e.g. —x-or z-sections. Optical investigations of —x-sections prove that under certain circumstances light and/or dark striations may occur or even uncolorable regions may be observed, althought the contamination is sure. We explain this by the interaction of the coloration centres with interstitials. That effect might be of importance for the evaluation of the impurity by means of the coloration of natural or synthetic quartz crystals.     

Nitrilotris(methylenephosphonato)potassium K[μ<Superscript>6</Superscript>-NH(CH<Subscript>2</Subscript>PO<Subscript>3</Subscript>)<Subscript>3</Subscript>H<Subscript>4</Subscript>]: Synthesis,structure, and the nature of the K–O chemical bond

The crystal structure of nitrilotris(methylenephosphonato)potassium K[μ⁶-NH(CH₂PO₃)₃H₄]—a three-dimensional coordination polymer—was determined. The potassium atom is coordinated by seven oxygen atoms belonging to the six nearest ligand molecules, resulting in distorted monocapped octahedral coordination geometry. The complex contains the four-membered chelate ring K–O–P–O. The K–O chemical bond is predominantly ionic. Meanwhile, the bonds of the potassium atom with some oxygen atoms have a noticeable covalent component. In addition to coordination bonds, the molecules in the crystal packing are linked by hydrogen bonds.     

Keggin型多酸基超分子化合物H3[{H(4-AP)}6(PMoⅤ6MoⅥ6O40)]的结构和电催化性能

通过水热合成方法,以钼酸铵、氯化镍和4-氨基吡啶为原料成功合成了一个Keggin型多酸基超分子化合物H₃[{H(4-AP)}₆(PMo^V₆Mo^VI₆O₄₀)] (4-AP=4-氨基吡啶)。该化合物的结构单元包含一个[PMo^V₆Mo^VI₆O₄₀]^9-阴离子和6个质子化的配体。而[PMo^V₆Mo^VI₆O₄₀]^9-阴离子与配体之间通过N(1)—H(1)…O(3)、N(2)—H(2A)…O(5)和N(2)—H(2B)…O(1)三种氢键相互作用,进而形成二维超分子层。通过X射线单晶衍射、IR和粉末X射线衍射对其进行表征。晶体结构分析表明:该标题化合物属于三方晶系,R-3空间群,a=2.191 2 (10) nm, b=2.191 2 (10) nm, c=1.042 3(5) nm, α=β=90°, γ=120°, V=4.333 8(4) nm³, Z=3, R₁=0.036 2, wR₂=0.095 6, 电催化性质研究表明该标题化合物对H₂O₂和K₂Cr₂O₇具有良好的电催化还原效果,以及对抗坏血酸具有良好的电催化氧化效果。     

Density and Ultrasonic Velocity Measurements in Hexyloxybenzylidene Phenylazoaniline

The temperature variation of density and ultrasonic velocity of the liquid crystal hexyloxybenzylidene phenylazoaniline are reported. The density across the smectic A—smectic B transition is more predominant than the other transitions. The density variation with temperature and the calculated thermal expansion coefficients suggest that the transitions isotropic liquid—nematic, nematic—smectic A and smectic A—smectic B are of first order. Anomalous behaviour of ultrasonic velocity is observed across the isotropic liquid—nematic transition and prominent dips in velocity are observed at the nematic—smectic A and smectic A—smectic B transitions. The adiabatic compressibility (β _ad ) Rao number (R _a ) and molar compressibility (B) are estimated using the experimental density and ultrasonic velocity.     

The Base of the Computation of Quantitative Changes Running in Technological Processes in the Multicomponent Systems with Mixed Crystals

The three multicomponent systems (KCl—KBr—H₂O, K₂SO₄—(NH₄)₂SO₄—H₂O, KNO₃—NH₄NO₃— H₂O) with mixed crystals in their solid phases have been studied. The isotherms of solubility and the curves of distribution have been mathematically described. The system of equations, which allows to calculate the quantitative changes running in technological processes in the multicomponent systems with mixed crystals has been proposed.     

Local structure around phosphorus and silicon in the CaO–SiO2–PO2.5 system

The local structure of phosphorus and silicon in the molten CaO–SiO₂–PO_2.5 slag system was investigated by magic angle spinning nuclear magnetic resonance (MAS-NMR). The ³¹P MAS-NMR spectra revealed that phosphorus was present primarily as the monophosphate complex ion PO₄^3?, with a small amount of diphosphate ion also present. Their relative ratio to total phosphorus was independent of the phosphate concentration of the sample. In the case of the ²⁹Si MAS-NMR, the mean number of the non-bridging oxygen atoms associated with tetrahedrally coordinated silicon decreased as the phosphate concentration increased at a fixed CaO/SiO₂ ratio. This indicates that the nonbridging oxygen atoms around the silicon were replaced by bridging oxygen atoms around the phosphorus as the phosphate concentration in the samples increased.To elucidate the basicity dependence of the structure of slag, the relationship between the structure and optical basicity was also investigated. The relative ratio of Qⁿ (Qⁿ means the silicon atoms tetrahedrally bonded with “n” number of bridging oxygen atoms) strongly depends on the optical basicity. These optical basicity dependencies of the structures of phosphorus and silicon can be explained clearly by the basicity equalization concept (Duffy and Ingram, 1976) [12].     

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.