Three-Dimensional Structure of Recombinant Thermophilic Ribokinase from Thermus speсies 2.9 in Complex with Adenosine Diphosphate

Crystallography Reports - The three-dimensional structure of recombinant thermophilic ribokinase from Thermus speсies 2.9 was determined at 2.4 Å resolution using crystals, which were...     

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.     

Structure of a new crystalline modification of 4-amino-5-ethoxymethyl-1,2-dimethylpyrimidinium iodide

The structure of a new crystalline modification (II) of 4-amino-5-ethoxymethyl-1,2-dimethylpyrimidinium iodide, C₉H₁₆IN₃O, the major product of methylation of 4-amino-5-ethoxymethyl-2-methylpyrimidine has been determined. The lattice parameters are a = 6.528(4) Å, b = 15.325(7) Å, c = 12.653(6) Å, γ = 97.57(50)°, sp. gr. P2₁/b, Z = 4, R = 0.0348 (over 1480 independent reflections). The molecule is planar. Its pyrimidine ring has the 2,5-diene structure and shows a weak tendency to adopt the C(2)-sofa conformation. Molecules in the crystal structure are linked into centrosymmetric dimers by N(8)-H?N(3) hydrogen bonds. These dimers, in turn, are linked into a three-dimensional framework by I^?-ions. The structure of modification II is compared with the structures of other 4-aminopyrimidines.     

Crystal and molecular structure of the membrane-active antibiotic enniatin C

The crystal structure of the cyclic hexadepsipeptide antibiotic enniatin C c[-(L-MeLeu-D-Hyi)₃-], C₃₄H₅₉N₃O₉, was established by X-ray structure analysis (sp. gr. P2₁, a = 20.205(5) Å, b = 8.702(2) Å, c = 25.587(6) Å, γ = 97.0(5)°, V = 4465.3(18) ų, Z = 4, R = 0.089 for 3601 reflections with I > 2σ(I)). The unit cell contains two independent molecules of enniatin C, one ethanol molecule disordered over two positions, and approximately two water molecules occupying four positions and forming hydrogen bonds with each other. The independent antibiotic molecules adopt virtually identical conformations similar to those observed in the structures of enniatin B and its Na,Ni-complex. These conformations are characterized by alternating upward and downward orientations of the carbonyl groups and pseudoequatorial orientations of side radicals. The Leu residues have stretched conformations. The N-methylamide groups of the independent antibiotic molecules face each other, whereas the molecules are displaced by approximately 8.4 Å with respect to each other along the mean planes of the rings.     

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.     

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.     

Three-dimensional organization of three-domain copper oxidases: A review

“Blue” copper-containing proteins are multidomain proteins that utilize a unique redox property of copper ions. Among other blue multicopper oxidases, three-domain oxidases belong to the group of proteins that exhibit a wide variety of compositions in amino acid sequences, functions, and occurrences in organisms. This paper presents a review of the data obtained from X-ray diffraction investigations of the three-dimensional structures of three-domain multicopper oxidases, such as the ascorbate oxidase catalyzing oxidation of ascorbate to dehydroascorbate and its three derivatives; the multicopper oxidase CueO (the laccase homologue); the laccases isolated from the basidiomycetes Coprinus cinereus, Trametes versicolor, Coriolus zonatus, Cerrena maxima, and Rigidoporus lignosus and the ascomycete Melanocarpus albomyces; and the bacterial laccases CotA from the endospore coats of Bacillus subtilis. A comparison of the molecular structures of the laccases of different origins demonstrates that, structurally, these objects are highly conservative. This obviously indicates that the catalytic activity of the enzymes under consideration is characterized by similar mechanisms.     

Crystal Packing of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in Two Crystal Modifications

Crystallography Reports - Crystals of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPATMt), which were grown using 2-methyl-2,4-pentanediol (MPD) or ammonium sulfate as...     

Molecular and crystal structures of 2,4,6-trinitro-N-methyl-N-nitroaniline

The structure of single crystals of 2,4,6-trinitro-N-methyl-N-nitroaniline C₇H₅N₅O₈ (I) is determined by X-ray diffraction analysis. The unit cell parameters are a = 14.137(3) Å, b = 10.621(2) Å, c = 7.376(2) Å, γ = 95.19 (5)°, space group P2₁/b, and Z = 4. The structure is solved by the direct method and refined in the anisotropic approximation to R = 0.051 for 1917 reflections with I > 2σ(I). All hydrogen atoms are located and refined in the isotropic approximation. The carbon skeleton of the aromatic nucleus of the molecule tends to adopt the C(2),C(5)-boat conformation. The angle of rotation of the planar NNO₂ group with respect to the plane of the six-membered ring is 123.1(2)°. The NO₂groups that are bonded to the aromatic nucleus of the molecule are also rotated relative to this plane.     

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).