Crystal Structure of the Resuscitation-Promoting Factor (Delta DUF)RpfB from M. tuberculosis(598 views) Ruggiero A, Tizzano B, Pedone E, Pedone C, Wilmanns M, Berisio R
Instituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy
European Molecular Biology Laboratory, Hamburg, DESY, Notkestrasse 85, 22603 Hamburg, Germany
Dipartimento delle Scienze Biologiche, Sezione di Biostrutture, Università degli Studi di Napoli Federico II, I-80134 Naples, Italy
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Yeremeev, V. V., Kondratieva, T. K., Rubakova, E. I., Petrovskaya, S. N., Kazarian, K. A., Telkov, M. V., Proteins of the Rpf family: immune cell reactivity and vaccination efficacy against tuberculosis in mice (2003) Infect. Immun., 71, pp. 4789-4794
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Keep, N. H., Ward, J. M., Cohen-Gonsaud, M., Henderson, B., Wake up! Peptidoglycan lysis and bacterial non-growth states (2006) Trends Microbiol., 14, pp. 271-276
Tufariello, J. M., Jacobs Jr., W. R., Chan, J., Individual Mycobacterium tuberculosis resuscitation-promoting factor homologues are dispensable for growth in vitro and in vivo (2004) Infect. Immun., 72, pp. 515-526
Downing, K. J., Mischenko, V. V., Shleeva, M. O., Young, D. I., Young, M., Kaprelyants, A. S., Mutants of Mycobacterium tuberculosis lacking three of the five rpf-like genes are defective for growth in vivo and for resuscitation in vitro (2005) Infect. Immun., 73, pp. 3038-3043
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Finn, R. D., Tate, J., Mistry, J., Coggill, P. C., Sammut, S. J., Hotz, H. R., The Pfam protein families database (2008) Nucleic Acids Res., 36, pp. D281-288
Thunnissen, A. M., Rozeboom, H. J., Kalk, K. H., Dijkstra, B. W., Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism (1995) Biochemistry, 34, pp. 12729-12737
Weaver, L. H., Grutter, M. G., Matthews, B. W., The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue (1995) J. Mol. Biol., 245, pp. 54-68
Leung, A. K., Duewel, H. S., Honek, J. F., Berghuis, A. M., Crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-N-acetylchitohexaose (2001) Biochemistry, 40, pp. 5665-5673
Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M., PROCHECK: a program to check the stereochemical quality of protein structures (1993) J. Appl. Crystallogr., 26, pp. 283-291
Hutchinson, E. G., Thornton, J. M., PROMOTIF-a program to identify and analyze structural motifs in proteins (1996) Protein Sci., 5, pp. 212-220
Lobo, L. A., Adhesive properties of the purified plasminogen activator Pla of Yersinia pestis (2006) FEMS Microbiol. Lett., 262, pp. 158-162
Richardson, J. S., Richardson, D. C., Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation (2002) Proc. Natl Acad. Sci. USA, 99, pp. 2754-2759
Siepen, J. A., Radford, S. E., Westhead, D. R., Beta edge strands in protein structure prediction and aggregation (2003) Protein Sci., 12, pp. 2348-2359
Meroueh, S. O., Bencze, K. Z., Hesek, D., Lee, M., Fisher, J. F., Stemmler, T. L., Mobashery, S., Three-dimensional structure of the bacterial cell wall peptidoglycan (2006) Proc. Natl Acad. Sci. USA, 103, pp. 4404-4409
Finn, R. D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Pfam: clans, Web tools and services (2006) Nucleic Acids Res., 34, pp. D247-251
Terwilliger, T. C., SOLVE and RESOLVE: automated structure solution and density modification (2003) Methods Enzymol., 374, pp. 22-37
Jones, T. A., Interactive electron-density map interpretation: from INTER to O (2004) Acta Crystallogr., Sect. D: Biol. Crystallogr., 60, pp. 2115-2125
McCoy, A. J., Solving structures of protein complexes by molecular replacement with Phaser (2007) Acta Crystallogr., Sect. D: Biol. Crystallogr., 63, pp. 32-41
Winn, M. D., Murshudov, G. N., Papiz, M. Z., Macromolecular TLS refinement in REFMAC at moderate resolutions (2003) Methods Enzymol., 374, pp. 300-321
Crystal Structure of the Resuscitation-Promoting Factor (Delta DUF)RpfB from M. tuberculosis
Mycobacterium tuberculosis is able to establish a non-replicating state and survive in an intracellular habitat for years. Resuscitation of dormant M. tuberculosis bacteria is promoted by resuscitation-promoting factors (Rpfs), which are secreted from slowly replicating bacteria close to dormant bacteria. Here we report the crystal structure of a truncated form of RpfB (residues 194-362), the sole indispensable Rpf of the five Rpfs encoded in this bacterium genome. The structure, denoted as (Delta DUF) RpfB, exhibits a comma-like shape formed by a lysozyme-like globular catalytic domain and an elongated G5 domain, which is widespread among cell surface binding proteins. The G5 domain, whose structure was previously uncharacterised, presents some peculiar features. The basic structural motif of this domain, which represents the tail of the comma-like structure, is a novel super-secondary-structure element, made of two P-sheets interconnected by a pseudo-triple helix. This intricate organisation leads to the exposure of several backbone hydrogen-bond donors/acceptors. Mutagenesis analyses and solution studies indicate that this protein construct as wen as the full-length form are elongated monomeric proteins. Although (Delta DUF) RpfB does not self-associate, the exposure of structural elements (backbone H-bond donors/acceptors and hydrophobic side chains) that are usually buried in globular proteins is typically associated with adhesive properties. This suggests that the RpfB G5 domain has a cell-wall adhesive function, which allows the catalytic domain to be properly oriented for the cleavage reaction. Interestingly, sequence comparisons indicate that these structural features are also shared by G5 domains involved in biofilm formation. (C) 2008 Elsevier Ltd. All rights reserved
Crystal Structure of the Resuscitation-Promoting Factor (Delta DUF)RpfB from M. tuberculosis