X-ray structural studies of the entire extracellular region of the serine/threonine kinase PrkC from Staphylococcus aureus(510 views) Ruggiero A, Squeglia F, Marasco D, Marchetti R, Molinaro A, Berisio R
Keywords: Cell Wall, Penicillin Binding-Associated And Serine Threonine Kinase-Associated Domain (pasta Domain), Peptidoglycan, Prkc, Staphylococcus Aureus, Bacterial Enzyme, Prkc Protein, Protein Serine Threonine Kinase, Unclassified Drug, Article, Carboxy Terminal Sequence, Controlled Study, Enzyme Activation, Enzyme Structure, Extracellular Matrix, Nonhuman, Oligomerization, Priority Journal, Protein Domain, Regulatory Mechanism, Upregulation, X Ray Crystallography, Bacterial Proteins, X-Ray, Dimerization, Penicillin-Binding Proteins, Protein Conformation, Protein Interaction Domains And Motifs, Protein Kinase C, Recombinant Proteins, Bacillus Subtilis, Bacteria (microorganisms),
Affiliations: *** IBB - CNR ***
Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134, Napoli, Italy
Department of Organic Chemistry and Biochemistry, University of Naples Federico II, I-80134, Via Cinthia 4, I-80126, Napoli, Italy
References: Munoz-Dorado, J., Inouye, S., Inouye, M., A gene encoding a protein serine/threonine kinase is required for normal development of M. xanthus, a gram-negative bacterium (1991) Cell, 67 (5), pp. 995-100
Madec, E., Laszkiewicz, A., Iwanicki, A., Obuchowski, M., Seror, S., Characterization of a membrane-linked Ser/Thr protein kinase in Bacillus subtilis, implicated in developmental processes (2002) Mol. Microbiol., 46, pp. 571-586
Fiuza, M., Canova, M.J., Zanella-Cleon, I., Becchi, M., Cozzone, A.J., Mateos, L.M., Kremer, L., Molle, V., From the characterization of the four serine/threonine protein kinases (PknA/B/G/L) of Corynebacterium glutamicum toward the role of PknA and PknB in cell division (2008) J. Biol. Chem., 283, pp. 18099-18112
Madec, E., Stensballe, A., Kjellstrom, S., Cladiere, L., Obuchowski, M., Jensen, O.N., Seror, S.J., Mass spectrometry and site-directed mutagenesis identify several autophosphorylated residues required for the activity of PrkC, a Ser/Thr kinase from Bacillus subtilis (2003) J. Mol. Biol., 330, pp. 459-472
Absalon, C., Obuchowski, M., Madec, E., Delattre, D., Holland, I.B., Seror, S.J., CpgA, EF-Tu and the stressosome protein YezB are substrates of the Ser/Thr kinase/phosphatase couple, PrkC/PrpC, in Bacillus subtilis (2009) Microbiology, 155, pp. 932-943
Shah, I.M., Laaberki, M.H., Popham, D.L., Dworkin, J., A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments (2008) Cell, 135, pp. 486-496
Shah, I.M., Dworkin, J., Induction and regulation of a secreted peptidoglycan hydrolase by a membrane Ser/Thr kinase that detects muropeptides (2010) Mol. Microbiol., 75, pp. 1232-1243
Kana, B.D., Mizrahi, V., Resuscitation-promoting factors as lytic enzymes for bacterial growth and signaling (2010) FEMS Immunol. Med. Microbiol., 58, pp. 39-50
Warner, D.F., Mizrahi, V., The survival kit of Mycobacterium tuberculosis (2007) Nat. Med., 13, pp. 282-284
Keep, N.H., Ward, J.M., Cohen-Gonsaud, M., Henderson, B., Wake up! Peptidoglycan lysis and bacterial non-growth states (2006) Trends in Microbiology, 14 (6), pp. 271-276. , DOI 10.1016/j.tim.2006.04.003, PII S0966842X06000953
Hett, E.C., Rubin, E.J., Bacterial growth and cell division: A mycobacterial perspective (2008) Microbiol. Mol. Biol. Rev., 72, pp. 126-156
Ruggiero, A., Marasco, D., Squeglia, F., Soldini, S., Pedone, E., Pedone, C., Berisio, R., Structure and functional regulation of RipA, a mycobacterial enzyme essential for daughter cell separation (2010) Structure, 18, pp. 1184-1190
Gaidenko, T.A., Kim, T.J., Price, C.W., The PrpC serine-threonine phosphatase and PrkC kinase have opposing physiological roles in stationary-phase Bacillus subtilis cells (2002) J. Bacteriol., 184, pp. 6109-6114
McGahee, W., Lowy, F.D., Staphylococcal infections in the intensive care unit (2000) Semin. Respir. Infect., 15, pp. 308-313
Ohlsen, K., Donat, S., The impact of serine/threonine phosphorylation in Staphylococcus aureus (2010) Int. J. Med. Microbiol., 300, pp. 137-141
Yeats, C., Finn, R.D., Bateman, A., The PASTA domain: A β-lactam-binding domain (2002) Trends Biochem. Sci., 27, pp. 438-440
Gordon, E., Mouz, N., Duee, E., Dideberg, O., The crystal structure of the penicillin-binding protein 2x from Streptococcus pneumoniae and its acyl-enzyme form: Implication in drug resistance (2000) J. Mol. Biol., 299, pp. 477-485
Dessen, A., Mouz, N., Gordon, E., Hopkins, J., Dideberg, O., Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: A mosaic framework containing 83 mutations (2001) J. Biol. Chem., 276, pp. 45106-45112
Ruggiero, A., Squeglia, F., Izzo, V., Silipo, A., Vitagliano, L., Molinaro, A., Berisio, R., Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the peptidoglycan binding region of the Ser/Thr kinase PrkC from Staphylococcus aureus (2010) Protein Pept. Lett., 17, pp. 1296-1299
Otwinowski, Z., Minor, W., Processing of X-ray diffraction data collected in oscillation mode (1997) Methods in Enzymology, 276, pp. 307-326. , DOI 10.1016/S0076-6879(97)76066-X
Panjikar, S., Parthasarathy, V., Lamzin, V.S., Weiss, M.S., Tucker, P.A., Auto-Rickshaw: An automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment (2005) Acta Crystallogr. Sect. D Biol. Crystallogr., 61, pp. 449-457
Sheldrick, G.M., A short history of SHELX (2008) Acta Crystallogr. Sect. A Found Crystallogr., 64, pp. 112-122
Terwilliger, T., SOLVE and RESOLVE: Automated structure solution, density modification and model building (2004) J. Synchrotron Radiat., 11, pp. 49-52
Langer, G., Cohen, S.X., Lamzin, V.S., Perrakis, A., Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 (2008) Nat. Protoc., 3, pp. 1171-1179
Potterton, E., Briggs, P., Turkenburg, M., Dodson, E., A graphical user interface to the CCP4 program suite (2003) Acta Crystallogr. Sect. D Biol. Crystallogr., 59, pp. 1131-1137
Laskowski, R.A., Rullmannn, J.A., MacArthur, M.W., Kaptein, R., Thornton, J.M., AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR (1996) J. Biomol. NMR, 8, pp. 477-486
Hu, J., Yan, C., HMM-RA: An improved method for α-helical transmembrane protein topology prediction (2008) Bioinform. Biol. Insights, 2, pp. 67-74
Bertaccini, E., Trudell, J.R., Predicting the transmembrane secondary structure of ligand-gated ion channels (2002) Protein Eng., 15, pp. 443-454
Girardin, S.E., Boneca, I.G., Carneiro, L.A.M., Antignac, A., Jehanno, M., Viala, J., Tedin, K., Philpott, D.J., Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan (2003) Science, 300 (5625), pp. 1584-1587. , DOI 10.1126/science.1084677
Erbs, G., Silipo, A., Aslam, S., De Castro, C., Liparoti, V., Flagiello, A., Pucci, P., Molinaro, A., Peptidoglycan and muropeptides from pathogens Agrobacterium and Xanthomonas elicit plant innate immunity: Structure and activity (2008) Chem. Biol., 15, pp. 438-448
Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.-R., Ceric, G., Bateman, A., The Pfam protein families database (2008) Nucleic Acids Research, 36 (SUPPL. 1), pp. D281-D288. , DOI 10.1093/nar/gkm960
Pares, S., Mouz, N., Petillot, Y., Hakenbeck, R., Dideberg, O., X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme (1996) Nat. Struct. Biol., 3, pp. 284-289
Barthe, P., Mukamolova, G.V., Roumestand, C., Cohen-Gonsaud, M., The structure of PknB extracellular PASTA domain from Mycobacterium tuberculosis suggests a ligand-dependent kinase activation (2010) Structure, 18, pp. 606-615
Holm, L., Sander, C., Dali: A network tool for protein structure comparison (1995) Trends Biochem. Sci., 20, pp. 478-480
Bork, P., Holm, L., Sander, C., The immunoglobulin fold: Structural classification, sequence patterns and common core (1994) J. Mol. Biol., 242, pp. 309-320
Lemmon, M.A., Schlessinger, J., Cell signaling by receptor tyrosine kinases (2010) Cell, 141, pp. 1117-1134
Bowden, M.G., Heuck, A.P., Ponnuraj, K., Kolosova, E., Choe, D., Gurusiddappa, S., Narayana, S.V., Hook, M., Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG (2008) J. Biol. Chem., 283, pp. 638-647
Ganesh, V.K., Rivera, J.J., Smeds, E., Ko, Y.P., Bowden, M.G., Wann, E.R., Gurusiddappa, S., Hook, M., A structural model of the Staphylococcus aureus ClfA - Fibrinogen interaction opens new avenues for the design of anti-staphylococcal therapeutics (2008) PLoS Pathog., 4, pp. e1000226
Carafoli, F., Saffell, J.L., Hohenester, E., Structure of the tandem fibronectin type 3 domains of neural cell adhesion molecule (2008) J. Mol. Biol., 377, pp. 524-534
Richardson, J.S., Richardson, D.C., Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation (2002) Proc. Natl. Acad. Sci. U.S.A., 99, pp. 2754-2759
Kline, K.A., Dodson, K.W., Caparon, M.G., Hultgren, S.J., A tale of two pili: Assembly and function of pili in bacteria (2010) Trends Microbiol., 18, pp. 224-232
Vitagliano, L., Ruggiero, A., Pedone, C., Berisio, R., A molecular dynamics study of pilus subunits: Insights into pilus biogenesis (2007) J. Mol. Biol., 367, pp. 935-941
Dodson, K.W., Pinkner, J.S., Rose, T., Magnusson, G., Hultgren, S.J., Waksman, G., Structural basis of the interaction of the pyelonephritic E. coli adhesin to its human kidney receptor (2001) Cell, 105 (6), pp. 733-743. , DOI 10.1016/S0092-8674(01)00388-9
Imberty, A., Mitchell, E.P., Wimmerova, M., Structural basis of high-affinity glycan recognition by bacterial and fungal lectins (2005) Curr. Opin. Struct. Biol., 15, pp. 525-534
Krissinel, E., Henrick, K., Inference of macromolecular assemblies from crystalline state (2007) J. Mol. Biol., 372, pp. 774-797
Chung, I., Akita, R., Vandlen, R., Toomre, D., Schlessinger, J., Mellman, I., Spatial control of EGF receptor activation by reversible dimerization on living cells (2010) Nature, 464, pp. 783-787
Mieczkowski, C., Iavarone, A.T., Alber, T., Auto-activation mechanism of the Mycobacterium tuberculosis PknB receptor Ser/Thr kinase (2008) EMBO J., 27, pp. 3186-3197
Debarbouille, M., Dramsi, S., Dussurget, O., Nahori, M.A., Vaganay, E., Jouvion, G., Cozzone, A., Duclos, B., Characterization of a serine/threonine kinase involved in virulence of Staphylococcus aureus (2009) J. Bacteriol., 191, pp. 4070-4081
Schlessinger, J., Plotnikov, A.N., Ibrahimi, O.A., Eliseenkova, A.V., Yeh, B.K., Yayon, A., Linhardt, R.J., Mohammadi, M., Crystal structure of a ternary FGF - FGFR - heparin complex reveals a dual role for heparin in FGFR binding and dimerization (2000) Mol. Cell, 6, pp. 743-750
D'Andrea, L.D., Iaccarino, G., Fattorusso, R., Sorriento, D., Carannante, C., Capasso, D., Trimarco, B., Pedone, C., Targeting angiogenesis: Structural characterization and biological properties of a de novo engineered VEGF mimicking peptide (2005) Proc. Natl. Acad. Sci. U.S.A., 102, pp. 14215-14220
Shah, I. M., Laaberki, M. H., Popham, D. L., Dworkin, J., A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments (2008) Cell, 135, pp. 486-496
Shah, I. M., Dworkin, J., Induction and regulation of a secreted peptidoglycan hydrolase by a membrane Ser/Thr kinase that detects muropeptides (2010) Mol. Microbiol., 75, pp. 1232-1243
Kana, B. D., Mizrahi, V., Resuscitation-promoting factors as lytic enzymes for bacterial growth and signaling (2010) FEMS Immunol. Med. Microbiol., 58, pp. 39-50
Warner, D. F., Mizrahi, V., The survival kit of Mycobacterium tuberculosis (2007) Nat. Med., 13, pp. 282-284
Keep, N. H., Ward, J. M., Cohen-Gonsaud, M., Henderson, B., Wake up! Peptidoglycan lysis and bacterial non-growth states (2006) Trends in Microbiology, 14 (6), pp. 271-276. , DOI 10. 1016/j. tim. 2006. 04. 003, PII S0966842X06000953
Hett, E. C., Rubin, E. J., Bacterial growth and cell division: A mycobacterial perspective (2008) Microbiol. Mol. Biol. Rev., 72, pp. 126-156
Gaidenko, T. A., Kim, T. J., Price, C. W., The PrpC serine-threonine phosphatase and PrkC kinase have opposing physiological roles in stationary-phase Bacillus subtilis cells (2002) J. Bacteriol., 184, pp. 6109-6114
Sheldrick, G. M., A short history of SHELX (2008) Acta Crystallogr. Sect. A Found Crystallogr., 64, pp. 112-122
Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., Thornton, J. M., AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR (1996) J. Biomol. NMR, 8, pp. 477-486
Girardin, S. E., Boneca, I. G., Carneiro, L. A. M., Antignac, A., Jehanno, M., Viala, J., Tedin, K., Philpott, D. J., Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan (2003) Science, 300 (5625), pp. 1584-1587. , DOI 10. 1126/science. 1084677
Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H. -R., Ceric, G., Bateman, A., The Pfam protein families database (2008) Nucleic Acids Research, 36 (SUPPL. 1), pp. D281-D288. , DOI 10. 1093/nar/gkm960
Lemmon, M. A., Schlessinger, J., Cell signaling by receptor tyrosine kinases (2010) Cell, 141, pp. 1117-1134
Bowden, M. G., Heuck, A. P., Ponnuraj, K., Kolosova, E., Choe, D., Gurusiddappa, S., Narayana, S. V., Hook, M., Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG (2008) J. Biol. Chem., 283, pp. 638-647
Ganesh, V. K., Rivera, J. J., Smeds, E., Ko, Y. P., Bowden, M. G., Wann, E. R., Gurusiddappa, S., Hook, M., A structural model of the Staphylococcus aureus ClfA - Fibrinogen interaction opens new avenues for the design of anti-staphylococcal therapeutics (2008) PLoS Pathog., 4, pp. e1000226
Richardson, J. S., Richardson, D. C., Natural -sheet proteins use negative design to avoid edge-to-edge aggregation (2002) Proc. Natl. Acad. Sci. U. S. A., 99, pp. 2754-2759
Kline, K. A., Dodson, K. W., Caparon, M. G., Hultgren, S. J., A tale of two pili: Assembly and function of pili in bacteria (2010) Trends Microbiol., 18, pp. 224-232
Dodson, K. W., Pinkner, J. S., Rose, T., Magnusson, G., Hultgren, S. J., Waksman, G., Structural basis of the interaction of the pyelonephritic E. coli adhesin to its human kidney receptor (2001) Cell, 105 (6), pp. 733-743. , DOI 10. 1016/S0092-8674 (01) 00388-9
D'Andrea, L. D., Iaccarino, G., Fattorusso, R., Sorriento, D., Carannante, C., Capasso, D., Trimarco, B., Pedone, C., Targeting angiogenesis: Structural characterization and biological properties of a de novo engineered VEGF mimicking peptide (2005) Proc. Natl. Acad. Sci. U. S. A., 102, pp. 14215-14220
X-ray structural studies of the entire extracellular region of the serine/threonine kinase PrkC from Staphylococcus aureus