The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase

The active-site geometry of the first crystal structure of a Delta(3)-Delta(2)-enoyl-coenzyme A (CoA) isomerase (the peroxisomal enzyme from the yeast Saccharomyces cerevisiae) shows that only one catalytic base, Glu158, is involved in shuttling the proton from the C2 carbon atom of the substrate, Delta(3)-enoyl-CoA, to the C4 atom of the product, Delta(2)-enoyl-CoA. Site-directed mutagenesis has been performed to confirm that this glutamate residue is essential for catalysis. This Delta(3)-Delta(2)-enoyl-CoA isomerase is a hexameric enzyme, consisting of six identical subunits. It belongs to the hydratase/isomerase superfamily of enzymes which catalyze a wide range of CoA-dependent reactions. The members of the hydratase/ isomerase superfamily have only a low level of sequence identity. Comparison of the crystal structure of the Delta(3)-Delta(2)-enoyl-CoA isomerase with the other structures of this superfamily shows only one region of large structural variability, which is in the second turn of the spiral fold and which is involved in defining the shape of the binding pocket.     

The crystal and molecular structure of diethylenetriammonium hexachloro-antimonate(III)

A compound of the type [DenH₃]SbCl₆ (DenH₃ = diethylenetriammonium cation) was prepared and characterized by means of structural and vibrational measurements. The structure consists of monomeric SbCl₆^3? anions and triprotonated diethylenetriam-monium cations. The SbCl₆^3? anion has a strongly distorted octahedral geometry, presenting three short (2.415–2.495 Å) and three long (2.836–3.114 Å) SbCl bonds. The presence of multiple hydrogen bonds, mainly involving the counterion and the three long-bonded chlorine atoms, is considered to be responsible for the octahedral distortion. Vibrational properties of the complex are discussed in the light of its known crystal structure.     

Amine free crystal structure: the crystal structure of d(CGCGCG)2 and methylamine complex crystal

We succeeded in the crystallization of d(CGCGCG)2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2Fo-Fc map was much clear and easily traced. It is the first time monoamine co-crystallizes with d(CGCGCG)2. However, methylamine was not found from the complex crystal of d(CGCGCG)2 and methylamine. Five Mg ions were found around d(CGCGCG)2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg2+. DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG)2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this.     

The crystal and molecular structure of tetrakis(biuret)strontium(II) perchlorate

Crystals of tetrakis(biuret)strontium(II) perchlorate, [Sr((NH₂CO)₂NH)₄](ClO₄)₂, are monoclinic with a = 11.21(1), b = 7.30(1), c = 14.52(1) A, β = 98.2(2)°, D_obs = 1.976, D_calcd(Z = 2) = 1.973 g/cm³, space group P2/c. 1526 independent reflections recorded photographically by the equi-inclination. Weissenberg technique using CuKα, the intensities of which were estimated visually, were used in the structure determination. The structure was solved by Patterson and Fourier methods and refined anisotropically by diagonal least squares to an R factor of 0.094. The strontium atoms are located at special positions related by inversion. The perchlorate moieties are ionic although extensive hydrogen bonding exists between them and the primary and secondary amines of biuret. The two biuret ligands in the asymmetric unit are bonded to strontium as bidentates via the carbonyl oxygens with a small twist (10.9, 12.0°) about the oxygen-oxygen line. The six membered rings formed by the chelate ligands with strontium are folded (49.6, 1.8°) about the oxygen-oxygen line. This is attributed to packing considerations. The co-ordination polyhedron is best described as approximately D₂-222 distorted square antiprism with the bidentate ligands spanning opposite edges of the rectangular faces. To our knowledge this complex presents the first case of an eight co-ordinate non-transition metal complex, characterized by x-rays, where all of the ligands are non-ionic chemically identical oxygen donor bidentates.     

Single crystals of alpha-chitin.

Single crystals of alpha-chitin were grown by the addition of precipitants to dilute solutions of low molecular weight chitin fractions dissolved in aqueous LiSCN. At temperatures around 200 degrees C, bundles of thin needle-shaped crystals were obtained. Each of these needles was an alpha-chitin single crystal, characterized by a spot electron diffraction pattern which could be indexed along the hk0 reciprocal net corresponding to the Minke and Blackwell unit cell [a = 0.474 nm, b = 1.88 nm, c (fibre axis) = 1.032 nm, space group P2(1)2(1)2(1)]. In a crystal, the a* parameter was along the crystal axis and the b* perpendicular to it.     

The crystal structure of the human co-chaperone P58(IPK)

P58^IPK is one of the endoplasmic reticulum- (ER-) localised DnaJ (ERdj) proteins which interact with the chaperone BiP, the mammalian ER ortholog of Hsp70, and are thought to contribute to the specificity and regulation of its diverse functions. P58^IPK, expression of which is upregulated in response to ER stress, has been suggested to act as a co-chaperone, binding un- or misfolded proteins and delivering them to BiP. In order to give further insights into the functions of P58^IPK, and the regulation of BiP by ERdj proteins, we have determined the crystal structure of human P58^IPK to 3.0 Å resolution using a combination of molecular replacement and single wavelength anomalous diffraction. The structure shows the human P58^IPK monomer to have a very elongated overall shape. In addition to the conserved J domain, P58^IPK contains nine N-terminal tetratricopeptide repeat motifs, divided into three subdomains of three motifs each. The J domain is attached to the C-terminal end via a flexible linker, and the structure shows the conserved Hsp70-binding histidine-proline-aspartate (HPD) motif to be situated on the very edge of the elongated protein, 100 Å from the putative binding site for unfolded protein substrates. The residues that comprise the surface surrounding the HPD motif are highly conserved in P58^IPK from other organisms but more varied between the human ERdj proteins, supporting the view that their regulation of different BiP functions is facilitated by differences in BiP-binding.     

The crystal structure of potassium (1S)-D-galactit-1-ylsulfonate

The structure of the crystalline addition product (1) formed between d-galactose and potassium bisulfite (potassium hydrogen sulfite) has been determined by X-ray diffraction analysis and compared with those structures reported for the related addition products from d-glucose and d-mannose. As with the latter two sulfonates, the d-galactose derived compound has an open-chain structure, with the carbon chain adopting a near planar zigzag conformation extending to the sulfur atom, similar to the d-mannose derivative but in contrast to the sickle conformation adopted by the d-glucose derivative. This last compound also differs in crystallising as a monohydrate. Inter-chain linking through cation coordination leads to a three dimensional network in the crystal.     

Enzymatic hydrolysis of alpha-chitin

It was shown that the enzymatic preparation Celloviridin G20x can be used for the hydrolysis of alpha-chitin of various origin. The purity of the final product of hydrolysis, N-acetylglucosamine, was monitored using HPLC.     

The crystal structure of N(10)-formyltetrahydrofolate synthetase from Moorella thermoacetica

The structure was solved at 2.5 A resolution using multiwavelength anomalous dispersion (MAD) scattering by Se-Met residues. The subunit of N(10)-formyltetrahydrofolate synthetase is composed of three domains organized around three mixed beta-sheets. There are two cavities between adjacent domains. One of them was identified as the nucleotide binding site by homology modeling. The large domain contains a seven-stranded beta-sheet surrounded by helices on both sides. The second domain contains a five-stranded beta-sheet with two alpha-helices packed on one side while the other two are a wall of the active site cavity. The third domain contains a four-stranded beta-sheet forming a half-barrel. The concave side is covered by two helices while the convex side is another wall of the large cavity. Arg 97 is likely involved in formyl phosphate binding. The tetrameric molecule is relatively flat with the shape of the letter X, and the active sites are located at the end of the subunits far from the subunit interface.     

The molecular crystal structure and self-assembly behavior of 6(I)-O-(3-nitrophenyl)cyclomaltoheptaose

The mono-modified beta-cyclodextrin derivative, 6(I)-O-(3-nitrophenyl)cyclomaltoheptaose{mono[6-O-(3-nitrophenyl)]-beta-cyclodextrin} was synthesized, and its crystal structure was determined by single-crystal X-ray analysis. The crystal structure suggests that the 3-nitrophenyl substituent group is inserted into the adjacent beta-cyclodextrin cavity from the secondary hydroxyl side, and the molecules are stacked along the twofold screw axis to form an infinite one-dimensional polymeric chain.     

The crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859) from Helicobacter pylori

Helicobacter pylori, the human pathogen that affects about half of the world population and that is responsible for gastritis, gastric ulcer and adenocarcinoma and MALT lymphoma, owes much of the integrity of its outer membrane on lipopolysaccharides (LPSs). Together with their essential structural role, LPSs contribute to the bacterial adherence properties, as well as they are well characterized for the capability to modulate the immuno-response. In H. pylori the core oligosaccharide, one of the three main domains of LPSs, shows a peculiar structure in the branching organization of the repeating units, which displayed further variability when different strains have been compared. We present here the crystal structure of ADP-L-glycero-D-manno-heptose-6-epimerase (HP0859, rfaD), the last enzyme in the pathway that produces L-glycero-D-manno-heptose starting from sedoheptulose-7-phosphate, a crucial compound in the synthesis of the core oligosaccharide. In a recent study, a HP0859 knockout mutant has been characterized, demonstrating a severe loss of lipopolysaccharide structure and a significant reduction of adhesion levels in an infection model to AGS cells, if compared with the wild type strain, in good agreement with its enzymatic role. The crystal structure reveals that the enzyme is a homo-pentamer, and NAD is bound as a cofactor in a highly conserved pocket. The substrate-binding site of the enzyme is very similar to that of its orthologue in Escherichia coli, suggesting also a similar catalytic mechanism.     

DNA-drug interactions. The crystal structure of d(CGATCG) complexed with daunomycin

The structure of a d(CGATCG)-daunomycin complex has been determined by single crystal X-ray diffraction techniques. Refinement, with the location of 40 solvent molecules, using data up to 1.5 A, converged with a final crystallographic residual, R = 0.25 (RW = 0.22). The tetragonal crystals are in space group P4(1)2(1)2, with cell dimensions of a = 27.98 A and c = 52.87 A. The self-complementary d(CGATCG) forms a distorted right-handed helix with a daunomycin molecule intercalated at each d(CpG) step. The daunomycin aglycon chromophore is oriented at right-angles to the long axis of the DNA base-pairs. This head-on intercalation is stabilized by direct hydrogen bonds and indirectly via solvent-mediated, hydrogen-bonding interactions between the chromophore and its intercalation site base-pairs. The cyclohexene ring and amino sugar substituent lie in the minor groove. The amino sugar N-3' forms a hydrogen bond with O-2 of the next neighbouring thymine. This electrostatic interaction helps position the sugar in a way that results in extensive van der Waals contacts between the drug and the DNA. There is no interaction between daunosamine and the DNA sugar-phosphate backbone. We present full experimental details and all relevant conformational parameters, and use the comparison with a d(CGTACG)-daunomycin complex to rationalize some neighbouring sequence effects involved in daunomycin binding.     

The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1)

Cyclophilins comprise one of the three classes of peptidylprolyl isomerases found in all eukaryotic and prokaryotic organisms, as well as viruses. Many of the 17 annotated human cyclophilins contain the catalytic domain in tandem with other domains, and many of the specific functions of a particular cyclophilin or its associated domains remain unknown. The structure of the isomerase domain from a spliceosome-associated cyclophilin, PPWD1 (peptidylprolyl isomerase containing WD40 repeat), has been solved to 1.65 A. In the crystal, the N-terminus of one isomerase domain is bound in the active site of a neighboring isomerase molecule in a manner analogous to substrate. NMR solution studies show that this sequence binds to the active site of the cyclophilin, but cannot be turned over by the enzyme. A pseudo-substrate immediately N-terminal to the cyclophilin domain in PPWD1 could have wider implications for the function of this cyclophilin in the spliceosome, where it is located in human cells.     

The crystal structure of L-chiro-inositol

The crystal structure of L-chiro-inositol is monoclinic, P21, with a = 6.867(3), b = 9.133(4), c = 6.217(3) A, beta = 106.59(4) degrees, Z = 2. The structure was solved by using MULTAN, and refined to R = 0.028 for 1065 intensities observed with Ni-filtered MoK alpha radiation. The molecule has the expected chair conformation, with puckering parameters Q = 0.561 A, theta = 4.4 degrees, phi = 51.2 degrees. The non-hydrogen molecular symmetry is close to C2, with deviations of less than 0.07 A from a weighted fit. The intramolecular hydrogen-bonding forms infinite chains which are cross-linked through the weaker component of a three-center bond. The C-C bond lengths range from 1.515 to 1.528 A, and the C-O bond lengths from 1.418 to 1.436 A. The C-C-C angles range from 109.7 to 113.1 degrees, and the C-C-O angles from 106.5 to 112.0 degrees.