Crystallization and preliminary crystallographic analysis of tetrahydrodipicolinate-N-succinyltransferase

Crystals of tetrahydrodipicolinate-N-succinyltransferase have been obtained from solutions containing 2-propanol and polyethylene glycol 4,000. These crystals belong to the monoclinic space group P2₁, diffract X-rays to a resolution of 2.2 Å, and contain one trimer per asymmetric unit. © 1996 Wiley-Liss, Inc.     

Crystallization and preliminary crystallographic analysis of transgelin

Transgelin was solubly expressed in E. coli. Crystals of transgelin have been grown at 291K using sodium formate or PEG-4000 as precipitants. X-ray diffraction by the crystal extends to 2.3 A resolution. The crystal belongs to the space group P2(1), with the unit cell parameters a=39.3, b=61.9, c=56.0 A and beta=90.2 degrees .     

Crystallization and preliminary X-ray crystallographic analysis of verotoxin-1 B-subunit

The B-subunit of verotoxin-1, which is believed to form a pentamer (monomer Mr = 7691), has been crystallized by vapor diffusion over a wide range of conditions. The best crystals, obtained with polyethylene glycol 8000 as the precipitant, belong to the orthorhombic space group P2(1)2(1)2(1), with cell dimensions a = 59.2 A, b = 102.7 A, c = 56.3 A. The cell dimensions are consistent with one B-subunit pentamer per asymmetric unit, and the crystals diffract to at least 2.0 A resolution. Data collected using synchrotron radiation at a wavelength of 2.070 A may allow the structure to be solved using the anomalous signal from three sulfur atoms in the monomer, combined with averaging over the non-crystallographic symmetry.     

Crystallization and preliminary crystallographic analysis of allograft inflammatory factor 1

Allograft inflammatory factor-1 (AIF-1) is a 17-kDa IFN-gamma inducible Ca2+-binding EF-hand protein involved in immune dysfunction and smooth muscle cell activation. AIF-1 was solubly expressed in E. coli and purified. Crystals of AIF-1 were grown at 291 K using PEG-8000 as precipitant. Diffraction by the AIF-1 crystal extends to 3.3 A resolution, and the crystal belongs to the space group P4(3) with unit cell parameters a=b=73.4, c=49.1 A.     

Crystallization and preliminary x-ray crystallographic studies of trichosanthin delta C7

Trichosanthin (TCS) is a type I ribosome-inactivating protein (RIP) which possesses rRNA N-glycosidase activity. TCS has various pharmacological properties. It is possible to reduce the antigenicity of TCS by deleting up to seven C-terminal residues of TCS (TCS-C7) with minimal effect on its activity. TCS-C7 has been crystallized and the crystal diffracted to 1.8 A. It belongs to space group P2(1), with unit-cell parameters a=71.6A, b=74.4A, c=87.6A, beta=97.0 degrees. It is given that there are four molecules per asymmetric unit.     

Caenorhabditis elegans galectins LEC-6 and LEC-10 interact with similar glycoconjugates in the intestine

Galectins are a family of metazoan proteins that show binding to various β-galactoside-containing glycans. Because of a lack of proper tools, the interaction of galectins with their specific glycan ligands in the cells and tissues are largely unknown. We have investigated the localization of galectin ligands in Caenorhabditis elegans using a novel technology that relies on the high binding specificity between galectins and their endogenous ligands. Fluorescently labeled recombinant galectin fusions are found to bind to ligands located in diverse tissues including the intestine, pharynx, and the rectal valve. Consistent with their role as galactoside-binding proteins, the interaction with their ligands is inhibited by galactose or lactose. Two of the galectins, LEC-6 and LEC-10, recognize ligands that co-localize along the intestinal lumen. The ligands for LEC-6 and LEC-10 are absent in three glycosylation mutants bre-1, fut-8, and galt-1, which have been shown to be required to synthesize the Gal-β1,4-Fuc modifications of the core N-glycans unique to C. elegans and several other invertebrates. Both galectins pull down the same set of glycoproteins in a manner dependent on the presence of these carbohydrate modifications. Endogenous LEC-6 and LEC-10 are expressed in the intestinal cells, but they are localized to different subcellular compartments that do not appear to overlap with each other or with the location of their glycan targets. An altered subcellular distribution of these ligands is found in mutants lacking both galectins. These results suggest a model where LEC-6 and LEC-10 interact with glycoproteins through specific glycans to regulate their cellular fate.     

Caenorhabditis elegans galectins LEC-1-LEC-11: structural features and sugar-binding properties

Galectins form a large family of beta-galactoside-binding proteins in metazoa and fungi. This report presents a comparative study of the functions of potential galectin genes found in the genome database of Caenorhabditis elegans. We isolated full-length cDNAs of eight potential galectin genes (lec-2-5 and 8-11) from a lambdaZAP cDNA library. Among them, lec-2-5 were found to encode 31-35-kDa polypeptides containing two carbohydrate-recognition domains similar to the previously characterized lec-1, whereas lec-8-11 were found to encode 16-27-kDa polypeptides containing a single carbohydrate-recognition domain and a C-terminal tail of unknown function. Recombinant proteins corresponding to lec-1-4, -6, and 8-10 were expressed in Escherichia coli, and their sugar-binding properties were assessed. Analysis using affinity adsorbents with various beta-galactosides, i.e., N-acetyllactosamine (Galbeta1-4GlcNAc), lacto-N-neotetraose (Galbeta1-4GlcNAcbeta1-3Galbeta1-4Glc), and asialofetuin, demonstrated that LEC-1-4, -6, and -10 have a significant affinity for beta-galactosides, while the others have a relatively lower affinity. These results indicate that the integrity of key amino acid residues responsible for recognition of lactose (Galbeta1-4Glc) or N-acetyllactosamine in vertebrate galectins is also required in C. elegans galectins. However, analysis of their fine oligosaccharide-binding properties by frontal affinity chromatography suggests their divergence towards more specialized functions.     

Caenorhabditis elegans N-glycans containing a Gal-Fuc disaccharide unit linked to the innermost GlcNAc residue are recognized by C. elegans galectin LEC-6

We report a detailed structural analysis of the N-glycans of Caenorhabditis elegans recognized by C. elegans galectin LEC-6. Glycoproteins of C. elegans captured by an immobilized LEC-6 affinity adsorbent were isolated. The N-glycans of these glycoproteins were then liberated by hydrazinolysis and labeled with the fluorophore 2-aminopyridine (PA). The derived pyridylaminated (PA)-sugars were further fractionated by rechromatography on immobilized LEC-6 adsorbent and by reversed-phase high-performance liquid chromatography (HPLC). The structures of the PA-sugars thus obtained were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS/MS) in conjunction with glycosidase digestion. We confirmed that all PA-sugars having affinity for LEC-6 contain a Gal-Fuc disaccharide unit, and that this unit is bound to the innermost GlcNAc residue of the N-glycan chain. The dissociation constants of LEC-6 for these glycans were measured by frontal affinity chromatography. LEC-6 exhibited higher affinity for oligosaccharides having a Gal-Fuc unit linked to position 6 of the innermost GlcNAc residue than for those having Galbeta1-4GlcNAc units. Affinity for the former disappeared, however, following treatment with beta-galactosidase. If the glycan contained a Hex-Fuc disaccharide linked to the penultimate GlcNAc residue, the affinity would be diminished. We propose, therefore, that the galectins of C. elegans utilize the Gal-Fuc disaccharide unit for recognition instead of the Gal-GlcNAc unit that is common in vertebrates.     

Crystallization and preliminary X-ray crystallographic analysis of arylesterase from Pseudomonas fluorescens

Large crystals of arylesterase from Pseudomonas fluorescens have been grown at room temperature using ammonium sulfate as a precipitant. They grow to dimensions of 0.7 × 0.7 × 0.6 mm³ within a month. The crystals belong to the trigonal space group P3₁ (or P3₂), with unit cell dimensions of a= 147.12 Å and c= 131.08 Å. The asymmetric unit seems to contain six molecules of dimeric aryles-terase, with corresponding crystal volume per protein mass (VM ) of 2.53 ų/Da and solvent fraction of 51.5% by volume. The crystals diffract to at least 2.2 Å Bragg spacing when exposed to X-rays from a rotating-anode source. X-ray data have been collected to 2.9 Å Bragg spacing from native crystals. © 1993 Wiley-Liss, Inc.     

Crystallization and preliminary X-ray crystallographic analysis of chitinase from barley seeds

Chitinase from barley seeds has been crystallized at room temperature using polyethylene glycol as precipitant. The crystal is monoclinic, belonging to the space group P2₁, with unit cell parameters of a = 69.43 Å, b = 44.55 Å, c = 81.41 Å, and β = 111.95 Å. The asymmetric unit seems to contain two molecules of chitinase with a corresponding crystal volume per protein mass (V_M) of 2.25 ų/Da and a solvent content of 45% by volume. The crystal diffracts to at least 2.0 Å with X-rays from a rotating anode source and is very stable in the X-ray beam. X-ray data have been collected to better than 2.2 Å Bragg spacing from a native crystal. © 1993 Wiley-Liss, Inc.     

Crystallization and preliminary x-ray crystallographic study of NADH-cytochrome b5 reductase from pig liver microsomes

Crystals of the hydrophilic, catalytic domain (30 kDa) of pig liver NADH-cytochrome b5 reductase solubilized by the protease (cathepsin D) have been grown in a solution of polyethylene glycol by the vapor-diffusion procedure. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1) with unit-cell dimensions of a = 87.1, b = 73.2, and c = 49.0 A. The asymmetric unit contains one molecule of the enzyme. The x-ray diffraction patterns extend to 2.0-A resolution. On the other hand, the intact enzyme (35 kDa) containing the hydrophobic membrane-binding domain solubilized by the detergent (Triton N-101) has been crystallized also from the polyethylene glycol solution. The crystals are needle-shaped and still too small for x-ray diffraction study.     

Crystallization and preliminary x-ray crystallographic data of dienelactone hydrolase from Pseudomonas sp. B13

Dienelactone hydrolase (EC 3.1.1.45) from Pseudomonas sp. B13 has been crystallized in a form suitable for high resolution x-ray diffraction study. The crystals are orthorhombic, the space group being P212121, with unit cell dimensions a = 48.9 A, b = 71.2 A, and c = 77.5 A. There appears to be 1 molecule in the asymmetric unit.     

Crystallization and preliminary crystallographic analysis of Bacillus thuringiensis AHL-lactonase

The quorum sensing (QS) systems in Gram-negative bacteria are mostly associated with diffusible N-acyl-L-homoserine lactones (AHLs). AHL-degrading enzymes hydrolyze the AHLs into inactive molecules, thereby blocking the QS systems that are closely linked to virulence factor production and biofilm formation. Consequently, these enzymes have recently attracted intense interest for the development of anti-infection therapies for plants and animals. However, despite significant progress in the investigation of AHL-degrading enzymes, no structure is yet available. Accordingly, this study reports on the expression and purification of the AHL-lactonase from Bacillus thuringiensis subsp. kurstaki HD263, as well as the successful crystallization of the enzyme. High-quality native crystals were obtained and a complete data set collected at 2.0 A resolution. The native crystal was found to belong to the space group P2(1)2(1)2(1), with unit cell parameters a=52.7 A, b=55.9 A, and c=74.1 A and one molecule in the asymmetric unit. MAD data were also collected at 2.4 A resolution for a SeMet-substituted crystal.     

Crystallization and preliminary X-ray crystallographic analysis of plant ferritin from Glycine max

The iron storage protein ferritin from soybean (Glycine max) was expressed in E. coli and crystallized using the hanging drop vapor diffusion method with sodium tartrate as the precipitant. The crystals belong to the tetragonal I4(1)22 space group, with unit cell parameters a=b=324.0, c=182.7 A. The diffraction data were collected up to a resolution of 3.0 A with a multi-wire area detector.     

Crystallization and preliminary X-ray crystallographic analysis of lipase from Pseudomonas cepacia.

Large crystals of lipase from Pseudomonas cepacia have been grown at room temperature from solutions containing 2-methyl-2,4-pentanediol and sodium citrate. They grow within two weeks to typical dimensions of 1.0 mm x 0.5 mm x 0.3 mm. The crystals belong to the monoclinic space group P2(1), with unit cell parameters a = 84.91 A, b = 47.33 A, c = 86.00 A, and beta = 116.09 degrees. And they diffract to about 1.6 A upon exposure to synchroton X-rays. X-ray data have been collected to 2.2 A Bragg spacing from a native crystal.     

Crystallization and preliminary X-ray crystallographic analysis of orotate phosphoribosyltransferase from Helicobacter pylori

Orotic acid phosphoribosyltransferase (PyrE) (EC 2.4.2.10) is a key enzyme in de novo uridine monophosphate (UMP) biosynthesis. It catalyzes the reaction between orotic acid and 5-phosphoribosyl-1-pyrophosphate (PRPP) to yield orotidine monophosphate (OMP), which is transformed to uridine monophosphate by decarboxylation. H. pylori PyrE was crystallized at 294 +/- 1 K by the hanging drop vapor-diffusion method. The crystals belong to the space group P2(1)2(1)2(1) with unit-cell dimensions a = 95.8, b = 104.9, c = 281.1 A, alpha = beta = gamma = 90 degrees. A set of diffraction data was collected to 3.29 A resolution using synchrotron X-ray radiation.     

Crystallization and preliminary X-ray crystallographic analysis of PAS factor from Vibrio vulnificus

Plasmid Achromobacter secretion (PAS) factor is a putative secretion factor that induces the secretion of periplasmic proteins. PAS factor from Vibrio vulnificus was crystallized at 294 K by the hanging drop vapor-diffusion method. It was isolated as a monomer during the purification procedures. The native crystal belongs to the F222 space group with unit cell parameters a=56.1, b=74.4, c=80.0 A, a=b=g=90 degrees. The crystal was soaked in cryoprotectant containing 1 M NaBr for 1 h for MAD phasing. The diffraction limit of the Br-MAD data set was 1.9 A using synchrotron X-ray irradiation at beam line BL-18B at the Photon Factory, Japan.     

Crystallization and preliminary X-ray crystallographic analysis of arylesterase from Vibrio mimicus.

Single crystals of arylesterase (EC 3.1.1.2) from Vibrio mimicus have been obtained from ammonium sulfate as a precipitant at room temperature for 2 months. The present crystals diffract up to 2.2 A resolution and belong to monoclinic space group P2(1). The cell dimensions are a = 55.65(1) A, b = 53.46(1) A, c = 65.79(1) A, and beta = 106.54(1) degrees. There are two molecules of molecular weight 22 kDa in an asymmetric unit with a solvent content of 43%.     

Crystallization and preliminary crystallographic analysis of aspartate-beta-semialdehyde dehydrogenase from Escherichia coli.

Aspartate-beta-semialdehyde dehydrogenase catalyzes the NADPH-mediated reductive dephosphorylation of beta-aspartylphosphate at a branch point in the biosynthesis of several amino acids. The enzyme from Escherichia coli has been crystallized by the vapor diffusion method from Tris buffer (pH 8.5) using polyethylene glycol 4000 as a precipitant. The crystals are orthorhombic and have the symmetry of space group P222(1), with unit cell dimensions of a = 177.8 A, b = 59.9 A, c = 118.65 A, and alpha = beta = gamma = 90 degrees. The dimensions and space group are indicative of two enzyme dimers (40 kDa per subunit) in the asymmetric unit. The crystals show strong diffraction, and a native data set has been collected to 2.5 A resolution.     

Crystallization and preliminary X-ray crystallographic analysis of phosphoribulokinase from Rhodobacter sphaeroides.

A recombinant form of Rhodobacter sphaeroides phosphoribulokinase (PRK), expressed in Escherichia coli and isolated by affinity chromatography, was crystallized by the sitting drop vapor diffusion technique using NH4H2PO4 (pH 5.6) as the precipitating agent. PRK crystallizes in the cubic space group P432, with unit cell parameters a = b = c = 129.55 A. Based on the assumption of one 32-kDa monomer per asymmetric unit, the Vm value is 2.83 A3/Da. The octameric molecular symmetry is consistent with two planar tetramers stacked in a nearly eclipsed arrangement. A native data set has been collected to 2.6 A resolution.