Erratum: Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori

Abstract

Ubx-homeodomain electron density, and polyalanine helices were placed into the Exd-homeodomain density. The MIRAS map was further improved by cycles of solvent¯attening with program DM 24 . Using these and F o 2 F c and 2F o 2 F c maps, interspersed with positional and individual B-factor re®nement using X-PLOR 26 , the model was rebuilt, side chains were added, and the Exd loops and N-terminal arms were built with the program O (ref. 27). The ®rst four residues of Exd, the residues from -7 to 4 of Ubx and the ®rst 6 residues of Ubx were disordered. There was clear density for the YPWM motif, but it was not readily interpretable for residues other than the tryptophan side chain. To obtain a more interpretable map, we re®ned and improved the MIRAS phases by solvent¯attening and extended them to 2.8 A Ê using the program SHARP 28 . This map was greatly improved and showed us how to ®t the YPWM motif. The YPWM ®t was further veri®ed by an anomalous-difference Fourier map calculated with data measured from selenomethionine (SeMet)-substituted protein; this map showed the positions of the three substituted seleniums, including the one in the YPWM motif. The re®nement of the structure was extended to 2.4 A Ê resolution using the native 1 data, and the structure veri®ed through extensive simulated annealing omit maps. Finally, 110 water molecules were added from the inspection of F o 2 F c maps. The ®nal re®ned structure has good stereochemistry, with the Ramachandran plot showing 84.5% of the residues in the core allowed regions and no residues in the disallowed or generously allowed regions.Received 18 December 1998; accepted 3 February 1999. The giant muscle protein titin (connectin) is essential in the temporal and spatial control of the assembly of the highly ordered sarcomeres (contractile units) of striated muscle. Here we present the crystal structure of titin's only catalytic domain, an autoregulated serine kinase (titin kinase). The structure shows how the active site is inhibited by a tyrosine of the kinase domain. We describe a dual mechanism of activation of titin kinase that consists of phosphorylation of this tyrosine and binding of calcium/calmodulin to the regulatory tail. The serine kinase domain of titin is the first known non-arginine-aspartate kinase to be activated by phosphorylation. The phosphorylated tyrosine is not located in the activation segment, as in other kinases, but in the P þ 1 loop, indicating that this tyrosine is a binding partner of the titin kinase substrate. Titin kinase phosphorylates the muscle protein telethonin in early differentiating myocytes, indicating that this kinase may act in myofibrillogenesis.Protein kinases are important in controlling cell proliferation and differentiation and they require specific mechanisms of regulation and substrate recognition [1][2][3] . Tight control of the enzymatic activity of protein kinases is achieved by phosphorylation of specific residues in the activation segment of the catalytic domain, sometimes combined with reversible conforma...

The Role of microRNAs in Helicobacter pylori Pathogenesis and Gastric Carcinogenesis

“…Additionally, VacA can induce apoptosis of host cells (Kuck et al, 2001; Xia and Talley, 2001) and suppress proliferation of T and B lymphocytes (Boncristiano et al, 2003; Gebert et al, 2003; Sundrud et al, 2004), which may contribute to the persistence of H. pylori through dysregulation of the host immune response. The cag pathogenicity island is present in ∼60% of all H. pylori strains and its presence is strongly associated with an increased risk of severe gastritis, ulcer disease, and gastric cancer (Censini et al, 1996; Tomb et al, 1997; Akopyants et al, 1998; Alm et al, 1999). The cag island encodes a type 4 secretion system (T4SS), which injects effector molecules, such as CagA, into host cells.…”

Conserved Transcriptional Unit Organization of the Cag Pathogenicity Island among Helicobacter pylori Strains

“…Here we sought to determine the conservation of operon structure in the cag PAI among H. pylori strains, and to identify promoters responsible for the transcription of cag PAI genes in strains 26695, J99, and G27, whose genomes are sequenced (Tomb et al, 1997; Alm et al, 1999), and in strain J166 that we and others have used to infect rhesus macaques (Hornsby et al, 2008). Operon structure was first predicted by a gene expression analysis that used quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) for both open reading frames (ORFs) and intergenic regions.…”

Mechanism of H. pylori Intracellular Entry: An in vitro Study

“…Helicobacter pylori appears to be a suitable system to study the biological role of Nudix hydrolases since the NudA protein is the only dinucleoside polyphosphate hydrolase homolog present in the two first strains that were sequenced (Tomb et al, 1997; Alm et al, 1999). J99 H. pylori harbors one Nudix hydrolase ortholog, Nud ix hydrolase A , nudA , with the gene numbers JHP1149 (Alm et al, 1999), 26,695 strain harbors HP1228 (named invA ; Tomb et al, 1997), and a GenBank search showed that a nudA gene is present in 30 additional completely sequenced H. pylori strains.…”

“…J99 H. pylori harbors one Nudix hydrolase ortholog, Nud ix hydrolase A , nudA , with the gene numbers JHP1149 (Alm et al, 1999), 26,695 strain harbors HP1228 (named invA ; Tomb et al, 1997), and a GenBank search showed that a nudA gene is present in 30 additional completely sequenced H. pylori strains. Due to the functional heterogeneity within this group of proteins, H. pylori NudA may be involved in (1) DNA repair, (2) oxidative stress and/or heat shock response, or (3) bacterial invasion of epithelial cells through degradation of toxic substances induced during invasion (Lundin et al, 2003).…”