Substitution of asparagine 76 by a tyrosine residue induces domain swapping in Helicobacter pylori phosphopantetheine adenylyltransferase

References

• Atherton, J.C. , 2006. The pathogenesis of Helicobacter pylori-induced gastro-duodenal diseases , Annual Review Pathology: Mechanisms of Disease 1 (2006), pp. 63–96.
   PubMed Web of Science ®Google Scholar
• Begley, T.P. , Kinsland, C. , and Strauss, E. , 2001. The biosynthesis of coenzyme A in bacteria , Vitamins and Hormones Series 61 (2001), pp. 157–171.
   PubMed Web of Science ®Google Scholar
• Bennett, M.J. , and Eisenberg, D. , 2004. The evolving role of 3D domain swapping in proteins , Structure 12 (2004), pp. 1339–1341.
   PubMed Web of Science ®Google Scholar
• Berendsen, H.J.C. , Postma, J.P.M. , van Gunsteren, W.F. , Di Nola, A. , and Haak, J.R. , 1984. Molecular dynamics with coupling to an external bath , Journal of Chemical Physics 81 (1984), pp. 3684–3690.
   Web of Science ®Google Scholar
• Berendsen, H.J.C. , Postma, J.P.M. , van Gunsteren, W.F. , and Hermans, J. , 1981. "Interaction models for water in relation to protein hydration". In: Pullman, B. , ed. Intermolecular forces . Dordrecht: D. Reidel; 1981. pp. 331–342.
   Google Scholar
• Blaser, M. , 2011. Antibiotic overuse: Stop the killing of beneficial bacteria , Nature 476 (2011), pp. 393–394.
   PubMed Web of Science ®Google Scholar
• Brown, K.L. , Morris, V.K. , and Izard, T. , 2004. Rhombohedral crystals of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase , Acta Crystallographica Section D: Biological Crystallography 60 (2004), pp. 195–196.
   PubMedGoogle Scholar
• Carson, M. , Johnson, D.H. , McDonald, H. , Brouillette, C. , and Delucas, L.J. , 2007. Rhombohedral crystals of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase , Acta Crystallographica Section D: Biological Crystallography 63 (2007), pp. 295–301.
   PubMed Web of Science ®Google Scholar
• Cheng, C.-S. , Chen, C.-H. , Luo, Y.-C. , Chen, W.-C. , Chang, S.-Y. , Lyu, P.-C. , …, , and Yin, H.-S. , 2011. Crystal structure and biophysical characterisation of Helicobacter pylori phosphopantetheine adenylyltransferase , Biochemical and Biophysical Research Communications 408 (2011), pp. 356–361.
   PubMed Web of Science ®Google Scholar
• Cheng, C.-S. , Lu, W.-S. , Tu, I.-F. , Lyu, P.-C. , and Yin, H.-S. , 2011. Comparative analysis of receptor binding by chicken and human interleukin-1β , Journal of Molecular Modeling 17 (2011), pp. 1283–1294.
   PubMed Web of Science ®Google Scholar
• Darden, T. , York, D. , and Pedersen, L. , 1993. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , Journal of Chemical Physics 98 (1993), pp. 10089–10092.
   Web of Science ®Google Scholar
• Ding, F. , Prutzman, K.C. , Campbell, S.L. , and Dokholyan, N.V. , 2006. Topological determinants of protein domain swapping , Structure 14 (2006), pp. 5–14.
   PubMed Web of Science ®Google Scholar
• Emsley, P. , and Cowtan, K. , 2004. Coot: Model-building tools for molecular graphics , Acta Crystallographica Section D: Biological Crystallography 60 (2004), pp. 2126–2132.
   PubMed Web of Science ®Google Scholar
• Fenstermacher, D.K. , and Rose, R.C. , 1986. Absorption of pantothenic acid in rat and chick intestine , American Journal of Physiology: Gastrointestinal and Liver Physiology 250 (1986), pp. G155–G160.
   Web of Science ®Google Scholar
• Finlayson, H.J. , and Seeley, R.C. , 1983. The synthesis and absorption of pantothenic acid in the gastrointestinal tract of the adult sheep , Journal of the Science of Food and Agriculture 34 (1983), pp. 427–432.
   PubMed Web of Science ®Google Scholar
• Geerlof, A. , Lewendon, A. , and Shaw, W.V. , 1999. Purification and characterization of phosphopantetheine adenylyltransferase from Escherichia coli , Journal of Biological Chemistry 274 (1999), pp. 27105–27111.
   PubMed Web of Science ®Google Scholar
• Gerdes, S.Y. , Scholle, M.D. , D’Souza, M. , Bernal, A. , Baev, M.V. , Farrell, M. , …, , and Osterman, A.L. , 2002. From genetic footprinting to antimicrobial drug targets: Examples in cofactor biosynthetic pathways , Journal of Bacteriology 184 (2002), pp. 4555–4572.
   PubMed Web of Science ®Google Scholar
• Gibbons, A.H. , 2003. Helicobacter pylori: A clinician’s view , Hospital Medicine 64 (2003), pp. 535–538.
   PubMedGoogle Scholar
• Haugland, G.T. , Sakakibara, N. , Pey, A.L. , Rollor, C.R. , Birkeland, N.K. , and Kelman, Z. , 2008. Thermoplasma acidophilum Cdc6 protein stimulates MCM helicase activity by regulating its ATPase activity , Nucleic Acids Research 36 (2008), pp. 5602–5609.
   PubMed Web of Science ®Google Scholar
• Hess, B. , Bekker, H. , Berendsen, H.J.C. , and Fraaije, J.G.E. , 1997. LINCS: A linear constraint solver for molecular simulations , Journal of Computational Chemistry 18 (1997), pp. 1463–1472.
   Web of Science ®Google Scholar
• Hirai, Y. , Hayashi, S. , Shimomura, H. , Oguma, K. , and Yokota, K. , 1999. Association of Helicobacter pylori with gastroduodenal diseases , Japanese Journal of Infectious Diseases 52 (1999), pp. 183–197.
   PubMed Web of Science ®Google Scholar
• Izard, T. , 2002. The crystal structures of phosphopantetheine adenylyltransferase with bound substrates reveal the enzyme’s catalytic mechanism , Journal of Molecular Biology 315 (2002), pp. 487–495.
   PubMed Web of Science ®Google Scholar
• Izard, T. , 2003. A novel adenylate binding site confers phosphopantetheine adenylyltransferase interactions with coenzyme A , Journal of Bacteriology 185 (2003), pp. 4074–4080.
   PubMed Web of Science ®Google Scholar
• Izard, T. , and Geerlof, A. , 1999. The crystal structure of a novel bacterial adenylyltransferase reveals half of sites reactivity , EMBO Journal 18 (1999), pp. 2021–2030.
   PubMed Web of Science ®Google Scholar
• Jackowski, S. , and Rock, C.O. , 1981. Regulation of coenzyme A biosynthesis , Journal of Bacteriology 148 (1981), pp. 926–932.
   PubMed Web of Science ®Google Scholar
• Kabsch, W. , and Sander, C. , 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features , Biopolymers 22 (1983), pp. 2577–2637.
   PubMed Web of Science ®Google Scholar
• Kusters, J.G. , van Vliet, A.H. , and Kuipers, E.J. , 2006. Pathogenesis of Helicobacter pylori infection , Clinical Microbiology Reviews 19 (2006), pp. 449–490.
   PubMed Web of Science ®Google Scholar
• Laemmli, U.K. , 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4 , Nature 227 (1970), pp. 680–685.
   PubMed Web of Science ®Google Scholar
• Laskowski, R.A. , Macarthur, M.W. , Moss, D.S. , and Thornton, J.M. , 1993. Main-chain bond lengths and bond angles in protein structures , Journal of Applied Crystallography 26 (1993), pp. 283–291.
   Web of Science ®Google Scholar
• Lebowitz, J. , Lewis, M.S. , and Schuck, P. , 2002. Modern analytical ultracentrifugation in protein science: A tutorial review , Protein Science 11 (2002), pp. 2067–2079.
   PubMed Web of Science ®Google Scholar
• Liu, Y. , and Eisenberg, D. , 2002. 3D domain swapping: As domains continue to swap , Protein Science 11 (2002), pp. 1285–1299.
   PubMed Web of Science ®Google Scholar
• Miller, J.R. , Ohren, J. , Sarver, R.W. , Mueller, W.T. , de Dreu, P. , Case, V. , and Thanabal, H. , 2007. Phosphopantetheine adenylyltransferase from Escherichia coli: Investigation of the kinetic mechanism and role in regulation of coenzyme A biosynthesis , Journal of Bacteriology 189 (2007), pp. 8196–8205.
   PubMed Web of Science ®Google Scholar
• Murshudov, G.N. , Vagin, A.A. , and Dodson, E.J. , 1997. Refinement of macromolecular structures by the maximum-likelihood method , Acta Crystallographica Section D: Biological Crystallography 53 (1997), pp. 240–255.
   PubMed Web of Science ®Google Scholar
• Ogihara, N.L. , Ghirlanda, G. , Bryson, J.W. , Gingery, M. , DeGrado, W.F. , and Eisenberg, D. , 2001. Design of three-dimensional domain-swapped dimers and fibrous oligomers , Proceeding of the National Academy of Sciences USA 98 (2001), pp. 1404–1409.
   PubMed Web of Science ®Google Scholar
• Otwinowski, Z. , and Minor, W. , 1997. Processing of X-ray diffraction data collected in oscillation mode , Methods in Enzymology 276 (1997), pp. 307–326.
   PubMed Web of Science ®Google Scholar
• Proenca-Modena, J.L. , Acrani, G.O. , and Brocchi, M. , 2009. Helicobacter pylori: Phenotypes, genotypes and virulence genes , Future Microbiology 4 (2009), pp. 223–240.
   PubMed Web of Science ®Google Scholar
• Robishaw, J.D. , and Neely, J.R. , 1985. Coenzyme A metabolism , American Journal of Physiology: Endocrinology and Metabolism 248 (1985), pp. E1–E9.
   PubMedGoogle Scholar
• Rock, C.O. , Park, H.W. , and Jackowski, S. , 2003. Role of feedback regulation of pantothenate kinase (CoaA) in control of coenzyme A levels in Escherichia coli , Journal of Bacteriology 185 (2003), pp. 3410–3415.
   PubMed Web of Science ®Google Scholar
• Rousseau, F., Schymkowitz, J., & Itzhaki, L.S. (2007). Implications of 3D domain swapping for protein folding, misfolding and function. In J. Matthews (Ed.), Protein dimerization (and oligomerization) in biology (pp. 137–152). Georgetown, TX: LANDES Bioscience..
   Google Scholar
• Sassetti, C.M. , Boyd, D.H. , and Rubin, E.J. , 2003. Genes required for mycobacterial growth defined by high density mutagenesis , Molecular Microbiology 48 (2003), pp. 77–84.
   PubMed Web of Science ®Google Scholar
• Schulman, B.A. , Kim, P.S. , Dobson, C.M. , and Redfield, C. , 1997. A residue-specific NMR view of the non-cooperative unfolding of a molten globule , Natural Structural Biology 4 (1997), pp. 630–634.
   PubMedGoogle Scholar
• Seeliger, M.A. , Spichty, M. , Kelly, S.E. , Bycroft, M. , Freund, S.M. , Karplus, M. , and Itzhaki, L.S. , 2005. Role of conformational heterogeneity in domain swapping and adapter function of the Cks proteins , Journal of Biological Chemistry 280 (2005), pp. 30448–30459.
   PubMed Web of Science ®Google Scholar
• Shaw, W.V., & Lewendon, A. (2000). PCT International Patent WO 00/17387. Germany..
   Google Scholar
• Spry, C. , Kirk, K. , and Saliba, K.J. , 2008. Coenzyme A biosynthesis: An antimicrobial drug target , FEMS Microbiology Reviews 32 (2008), pp. 56–106.
   PubMed Web of Science ®Google Scholar
• Vagin, A. , and Teplyakov, A. , 1997. Refinement of macromolecular structures by the maximum-likelihood method , Journal of Applied Crystallography 30 (1997), pp. 1022–1025.
   Web of Science ®Google Scholar
• Van Der Spoel, D. , Lindahl, E. , Hess, B. , Groenhof, G. , Mark, A.E. , and Berendsen, H.J. , 2005. GROMACS: Fast, flexible, and free , Journal of Computational Chemistry 26 (2005), pp. 1701–1718.
   PubMed Web of Science ®Google Scholar
• Wallace, A.C. , Laskowski, R.A. , and Thornton, J.M. , 1995. LIGPLOT: A program to generate schematic diagrams of protein–ligand interactions , Protein Engineering 8 (1995), pp. 127–134.
   PubMedGoogle Scholar
• Winn, M.D. , Ballard, C.C. , Cowtan, K.D. , Dodson, E.J. , Emsley, P. , Evans, P.R. , …, , and Wilson, K.S. , 2011. Overview of the CCP4 suite and current developments , Acta Crystallographica Section D: Biological Crystallography 67 (2011), pp. 235–242.
   PubMed Web of Science ®Google Scholar
• Wubben, T.J. , and Mesecar, A.D. , 2010. Kinetic, thermodynamic, and structural insight into the mechanism of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis , Journal of Molecular Biology 404 (2010), pp. 202–219.
   PubMed Web of Science ®Google Scholar