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.     

Recombinant formate dehydrogenase from <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>: Preparation,crystal growth in microgravity,and preliminary X-ray diffraction study

Crystals of high-purity recombinant NAD⁺-dependent formate dehydrogenase from the higher plant Arabidopsis thaliana (AraFDH) were grown in microgravity in the Modul’-1 protein crystallization apparatus on the International Space Station. The space-grown crystals have larger sizes than those grown on Earth. X-ray diffraction data suitable for determining the three-dimensional structure were collected from the space-grown crystals to a resolution of 1.22 Å using an X-ray synchrotron source. The crystals belong to sp. gr. P4₃2₁2; the unit-cell parameters are a = b = 107.865 Å, c = 71.180 Å, α = β = γ = 90°.     

Effect of plastic deformation on physical properties and structure of the shape memory alloy Ti<Subscript>49.5</Subscript>Ni<Subscript>50.5</Subscript>

The effect of severe plastic deformation by torsion (SPDT) in Bridgman anvils at a high pressure (6 GPa) on the physical properties and crystal structure of the shape memory alloy Ti_49.5Ni_50.5 has been studied. The behavior of the thermal expansion, electrical resistivity, absolute differential thermopower, Hall coefficient, magnetic properties, and optical characteristics of the amorphous/nanocrystalline and submicrocrystalline alloys obtained by the SPDT with subsequent heat treatment at 800 K has been discussed.     

Three-dimensional structure of Erwinia carotovora L-asparaginase

Three-dimensional structure of Erwinia carotovora L-asparaginase, which has antitumor activity and is used for the treatment of acute lymphoblastic leukemia, was solved at 3 Å resolution and refined to R _cryst = 20% and R _free = 28%. Crystals of recombinant Erwinia carotovora L-asparaginase were grown by the hanging-drop vapor-diffusion method from protein solutions in a HEPES buffer (pH 6.5) and PEG MME 5000 solutions in a cacodylate buffer (pH 6.5) as the precipitant. Three-dimensional X-ray diffraction data were collected up to 3 Å resolution from one crystal at room temperature. The structure was solved by the molecular replacement method using the coordinates of Erwinia chrysanthemi L-asparaginase as the starting model. The coordinates refined with the use of the CNS program package were deposited in the Protein Data Bank (PDB code 1ZCF).     

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.     

Effect of cobalt doping on thermoelastic martensitic transformations and physical properties of magnetic shape memory alloys Ni50 − x Co x Mn29Ga21

The magnetic and thermoelastic martensitic transformations and physical properties (magnetization, electrical resistivity, thermoelectric power, relative elongation, and thermal expansion coefficient) of multicomponent magnetic shape memory alloys Ni_{50 ? x} Co _x Mn₂₉Ga₂₁ (x = 0, 1, 2, 3, 10 at %) have been investigated. The critical temperatures of thermoelastic martensitic transformation and magnetic transitions have been determined. It has been found that the alloy with 10 at % Co undergoes a martensitic transformation in the temperature range of 6–10 K.     

Peculiarities of the phase composition and structure of the high-entropy FeWMoCrVSiMnC multicomponent steel

We report on the results of analysis of the phase composition, structure, and hardness of high-entropy FeWMoCrVSiMnC multicomponent steel subjected to synthesis and subsequent thermal treatment. Analysis is carried out using the methods of analytic transmission and scanning structural and orientational electron microscopy, optical metallography, X-ray energy-dispersive spectroscopy, X-ray phase and structural analyses, and Rockwell measurements of hardness. It is found that steel has a high hardness (62 HRC) and is in ultra-fine-disperse composite martensite-multicarbide state. All carbides are distributed uniformly over the steel volume and have nano- and submicrometer scales depending on the carbide type.

     

Application of Isothermal Upset for Megaplastic Deformation of Cu–Al–Ni β Alloys

Technical Physics - Cu–14 wt% Al–4 wt% Ni alloy demonstrating the shape memory effect has been subjected to plastic deformation by means of uniaxial compression (upset). The process has...     

Modeling of Phosphoribosylpyrophosphate Synthetase from Thermus Thermophilus in Complex with ATP and Ribose 5-Phosphate

Crystallography Reports - The positions of the substrates (ATP and ribose 5 phosphate) of phosphoribosylpyrophosphate synthetase from Thermus thermophilus were determined by molecular dynamics...