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Central Channel (central + channel)
Selected AbstractsVirus DNA translocation: progress towards a first ascent of Mount Pretty DifficultMOLECULAR MICROBIOLOGY, Issue 1 2006Nasib K. Maluf Summary Virion DNA molecules of large dsDNA viruses are highly condensed. To pack the DNA, an ATP hydrolysis-powered motor translocates the DNA into a preformed empty protein shell, the prohead. The icosahedral prohead has a special fivefold vertex, the portal vertex, where the translocation machinery acts. The portal vertex contains the portal protein, a gear-shaped dodecamer of radially disposed subunits with a central channel for DNA entry. The symmetry mismatch between the fivefold symmetry of the shell vertex and the 12-fold symmetry of the portal protein has prompted DNA packaging models in which ATP-driven portal protein rotation drives DNA translocation. In this issue of Molecular Microbiology, Baumann and colleagues test portal rotation models using bacteriophage T4. A fusion between the gp20 portal protein and the HOC external shell decoration protein is used to create a block to portal rotation. Finding that DNA packaging is unimpeded in proheads containing the fusion argues that portal rotation is not crucial to DNA translocation. The paper is a landmark for describing direct testing of the mechanism of DNA translocation. [source] Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ionsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2007Christophe Creze A parallel 5,-d(TGGGGT)-3, quadruplex was formed in Na+ solution and crystallized using lithium sulfate as the main precipitating agent. The X-ray structure was determined to 1.5,Å resolution in space group P21 by molecular replacement. The asymmetric unit consists of a characteristic motif of two quadruplexes stacked at their 5, ends. All nucleotides are clearly defined in the density and could be positioned. A single bound Li+ ion is observed at the surface of the column formed by the two joined molecules. Thus, this small alkali metal ion appears to be unsuitable as a replacement for the Na+ ion in the central channel of G-quartets, unlike K+ or Tl+ ions. A well conserved constellation of water molecules is observed in the grooves of the dimeric structure. [source] Structures of vaccinia virus dUTPase and its nucleotide complexesACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2007Alexandra Samal Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate in the presence of Mg2+ ions. The enzyme plays multiple cellular roles by maintaining a low dUTP:dTTP ratio and by synthesizing the substrate for thymidylate synthase in the biosynthesis of dTTP. Although dUTPase is an essential enzyme and has been established as a valid target for drug design, the high degree of homology of vaccinia virus dUTPase to the human enzyme makes the identification of selective inhibitors difficult. The crystal structure of vaccinia virus dUTPase has been solved and the active site has been mapped by crystallographic analysis of the apo enzyme and of complexes with the substrate-analog dUMPNPP, with the product dUMP and with dUDP, which acts as an inhibitor. Analyses of these structures reveal subtle differences between the viral and human enzymes. In particular, the much larger size of the central channel at the trimer interface suggests new possibilities for structure-based drug design. Vaccinia virus is a prototype of the poxviruses. [source] Crystallization and preliminary X-ray analysis of FliJ, a cytoplasmic component of the flagellar type III protein-export apparatus from Salmonella sp.ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 1 2009Tatsuya Ibuki The axial component proteins of the bacterial flagellum are synthesized in the cytoplasm and then translocated into the central channel of the flagellum by the flagellar type III protein-export apparatus for self-assembly at the distal growing end of the flagellum. FliJ is an essential cytoplasmic component of the export apparatus. In this study, Salmonella FliJ with an extra three residues (glycine, serine and histidine) attached to the N-terminus as the remainder of a His tag (GSH-FliJ) was purified and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion technique using PEG 300 as a precipitant. GSH-FliJ crystals grew in the hexagonal space group P6122 or P6522. While the native crystals diffracted to 3.3,Å resolution, the diffraction resolution limit of mercury derivatives was extended to 2.1,Å. Anomalous and isomorphous difference Patterson maps of the mercury-derivative crystal showed significant peaks in their Harker sections, indicating the usefulness of the derivative data for structure determination. [source] Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal formACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2008Jacqueline Vitali Crystals of the catalytic subunit of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form contain four crystallographically independent trimers which associate in pairs to form stable staggered complexes that are similar to each other and to a previously determined monoclinic C2 form. Each subunit has a sulfate in the central channel. The catalytic subunits in these complexes show flexibility, with the elbow angles of the monomers differing by up to 7.4° between crystal forms. Moreover, there is also flexibility in the relative orientation of the trimers around their threefold axis in the complexes, with a difference of 4° between crystal forms. [source] | ||||||||||