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One Dimer (one + dimer)
Selected AbstractsNovel dimer structure of a membrane-bound protease with a catalytic Ser,Lys dyad and its linkage to stomatinJOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Hideshi Yokoyama Membrane-bound proteases are involved in various regulatory functions. A previous report indicates that the N-terminal region of PH1510 (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser,Lys dyad (Ser97 and Lys138), and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511. According to the crystal structure of the wild-type 1510-N in dimeric form, the active site around Ser97 is in a hydrophobic environment suitable for the hydrophobic substrates. This article reports the crystal structure of the K138A mutant of 1510-N at 2.3,Å resolution. The determined structure contains one molecule per asymmetric unit, but 1510-N is active in dimeric form. Two possible sets of dimer were found from the symmetry-related molecules. One dimer is almost the same as the wild-type 1510-N. Another dimer is probably in an inactive form. The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2. [source] Proton-transfer dynamics in the (HCO3,)2 dimer of KHCO3 from Car,Parrinello and path-integrals molecular dynamics calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010Przemyslaw D. Dopieralski The proton motion in the (HCO)2 dimer of KHCO3 at 298,K has been studied with Car,Parrinello molecular dynamics (CPMD) and path-integrals molecular dynamics (PIMD) simulations. According to earlier neutron diffraction studies at 298,K hydrogen is disordered and occupies two positions with an occupancy ratio of 0.804/0.196. A simulation with only one unit cell is not sufficient to reproduce the disorder of the protons found in the experiments. The CPMD results with four cells, 0.783/0.217, are in close agreement with experiment. The motion of the two protons along the O...O bridge is highly correlated inside one dimer, but strongly uncoupled between different dimers. The present results support a mechanism for the disorder which involves proton transfer from donor to acceptor and not orientational disordering of the entire dimer. The question of simultaneous or successive proton transfer in the two hydrogen bonds in the dimer remains unanswered. During the simulation situations with almost simultaneous proton transfer with a time gap of around 1,fs were observed, as well as successive processes where first one proton is transferred and then the second one with a time gap of around 20,fs. The calculated vibrational spectrum is in good agreement with the experimental IR spectrum, but a slightly different assignment of the bands is indicated by the present simulations. [source] Crystallization and preliminary X-ray crystallographic studies of mouse autocrine motility factorACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004Noriko Naba Mouse autocrine motility factor (mAMF), a tumour-secreted cytokine that stimulates cell migration in vitro and metastasis in vivo, has been crystallized by the hanging-drop vapour-diffusion method. The crystals belong to the monoclinic space group P21, with unit-cell parameters a = 69.97, b = 115.88, c = 73.27,Å, , = 101.76°. There are two subunits (one dimer) per asymmetric unit. Complexes with four-, five- and six-carbon carbohydrate phosphate inhibitors have also been crystallized. The crystals diffract to at least 1.8,Å resolution and are suitable for X-ray structure analyses at high resolution. [source] Structure of SurE protein from Aquifex aeolicus VF5 at 1.5,Å resolutionACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Svetlana V. Antonyuk SurE is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. The structure of the SurE protein from the hyperthermophile Aquifex aeolicus has been solved at 1.5,Å resolution using molecular replacement with one dimer in the asymmetric unit and refined to an R factor of 15.6%. The crystal packing reveals that two dimers assemble to form a tetramer, although gel-filtration chromatography showed the presence of only a dimer in solution. The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium. [source] | ||||||||||