Crystal structures of MKK4 kinase domain reveal that substrate peptide binds to an allosteric site and induces an auto-inhibition state.

MKK4 activates both JNKs and p38s. We determined the crystal structures of human non-phosphorylated MKK4 kinase domain (npMKK4) complexed with AMP-PNP (npMKK4/AMP) and a ternary complex of npMKK4, AMP-PNP and p38α peptide (npMKK4/AMP/p38). These crystal structures revealed that the p38α peptide-bound npMKK4 at the allosteric site rather than at the putative substrate binding site and induced an auto-inhibition state. While the activation loop of the npMKK4/AMP complex was disordered, in the npMKK4/AMP/p38 complex it configured a long α-helix, which prevented substrate access to the active site and αC-helix movement to the active configuration of MKK4.

Vaccinium ashei leaves extract alleviates insulin resistance via AMPK independent pathway in C2C12 myotube model.

Blueberry (Vaccinium ashei) leaf has recently attracted attention as an anti-obesity food component. In this study, we examined the effects of blueberry leaf extract (BLEx) on insulin signaling in C2C12 differentiated myoblasts. The results showed that BLEx promotes the intracellular uptake of 2-[N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-D-glucose (2-NBDG) and phosphorylation of Akt under insulin stimulation. In addition, pretreatment with BLEx ameliorated TNF-α-nduced insulin resistance with regard to 2-NBDG uptake and Akt phosphorylation. Moreover, BLEx prevented the TNF-α-induced activation of JNK and NF-kB pathways and phosphorylation of IRS-1 at serine residue. BLEx failed to induce phosphorylation of AMPK as well as did not prevent the restoration of 2-NBDG uptake under TNF-α-induced insulin resistance. Overall, skeletal muscle is a putative target for the anti-diabetic effect of BLEx by amelioration of insulin resistance.

Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

Chitosanases belong to glycoside hydrolase families 5, 7, 8, 46, 75 and 80 and hydrolyse glucosamine polymers produced by partial or full deacetylation of chitin. Herein, we determined the crystal structure of chitosanase from the ß-proteobacterium, Mitsuaria chitosanitabida, (McChoA) at 1.75 Å resolution; the first structure of a family 80 chitosanase. McChoA is a 34 kDa extracellular protein of 301 amino acids that fold into two (upper and lower) globular domains with an active site cleft between them. Key substrate-binding features are conserved with family 24 lysozymes and family 46 chitosanases. The distance between catalytic residues E41 and E61 (10.8 Å) indicates an inverting type mechanism. Uniquely, three disulphide bridges and the C terminus might contribute to enzyme activity.

Crystal structure of the solute-binding protein BxlE from Streptomyces thermoviolaceus OPC-520 complexed with xylobiose.

BxlE from Streptomyces thermoviolaceus OPC-520 is a xylo-oligosaccharide (mainly xylobiose)-binding protein that serves as the initial receptor for the bacterial ABC-type xylo-oligosaccharide transport system. To determine the ligand-binding mechanism of BxlE, X-ray structures of ligand-free (open form) and ligand (xylobiose)-bound (closed form) BxlE were determined at 1.85 Å resolution. BxlE consists of two globular domains that are linked by two ß-strands, with the cleft at the interface of the two domains creating the ligand-binding pocket. In the ligand-free open form, this pocket consists of a U-shaped and negatively charged groove located between the two domains. In the xylobiose-bound closed form of BxlE, both the N and C domains move to fold the ligand without conformational changes in either domain. Xylobiose is buried in the groove and wrapped by the N-domain mainly via hydrogen bond interactions and by the C-domain primarily via non-polar interactions with Trp side chains. In addition to the concave shape matching the binding of xylobiose, an inter-domain salt bridge between Asp-47 and Lys-294 limits the space in the ligand-binding site. This domain-stabilized mechanism of ligand binding to BxlE is a unique feature that is not observed with other solute-binding proteins.

Crystallization and preliminary crystallographic analysis of endo-1,3-beta-glucanase from alkaliphilic Nocardiopsis sp. strain F96.

Endo-1,3-beta-glucanase, an enzyme that hydrolyzes the 1,3-beta-glycosyl linkages of beta-glucan, belongs to the family 16 glycosyl hydrolases, which are widely distributed among bacteria, fungi and higher plants. Crystals of a family 16 endo-1,3-beta-glucanase from the alkaliphilic Nocardiopsis sp. strain F96 were obtained by the hanging-drop vapour-diffusion method. The crystals belonged to space group P2(1), with unit-cell parameters a = 34.59, b = 71.84, c = 39.67 A, beta = 90.21 degrees, and contained one molecule per asymmetric unit. The Matthews coefficient (VM) and solvent content were 1.8 A3 Da(-1) and 31.8%, respectively. Diffraction data were collected to a resolution of 1.3 A and gave a data set with an overall Rmerge of 6.4% and a completeness of 99.3%.

Near IR Emitting Red-Shifting Ratiometric Fluorophores Based on Borondipyrromethene.

Two distyryl-BODIPY-based NIR red-shifting ratiometric fluorescent probes are reported: KBHR-1 for pH and KBAHgR-1 for Ag(+) and Hg(2+). KBHR-1 showed a red-shifting ratiometric response to pH in the NIR region. The identical fluorophore core structure applied to KBAHgR-1 with a different recognition moiety resulted in a ratiometric response to Ag(+) and Hg(2+) in the NIR region.

Cloning, structural analysis and expression of the gene encoding aspartate aminotransferase from the thermophilic cyanobacterium Phormidium lapideum.

The aspartate aminotransferase gene from the thermophilic cyanobacterium Phormidium lapideum was cloned and expressed in Escherichia coli. The ORF of 1167 nucleotides encodes a protein of 388 amino acids having a molecular weight of 42,099. A molecular model of PIAspAT shows structural features similar to those of the Thermus thermophilus AspAT.

Analysis of sugar epimers using mass spectrometry: N-acetyllactosamine-6,6'-disulfate and the 2'-epimer.

Galbeta1-4GlcNAc-6,6'-disulfate and 2'-epimer corresponding to Galbeta1- 4ManNAc-6,6'-disulfate were distinguished by mass spectrometry by utilizing fast atom bombardment (FAB), electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) methods. As for the steric information, negative-ion ESI mass spectrometry/mass spectrometry (MS/MS) provides the most extensive data, but FAB MS/MS also reveals detailed structural information of interest in our case, where MALDI MS is not yet fully equipped with post-source decay.

Expression, purification, crystallization and preliminary X-ray studies of geranylgeranyl diphosphate synthase from Thermus thermophilus HB8.

Geranylgeranyl diphosphate (GGPP) synthase from Thermus thermophilus HB8 was expressed in Escherichia coli, purified to homogeneity and crystallized both as the recombinant native protein and its selenomethionine (SeMet) derivative. Well diffracting crystals of these proteins were obtained belonging to the tetragonal space group P4(1) or P4(3), with unit-cell parameters a = b = 139.88, c = 73.37 A. There were two homodimers in the asymmetric unit. A native data set was collected to 1.55 A resolution and a data set suitable for MAD phasing was collected to 2.40 A resolution on beamline BL40B2 at SPring-8.