The structure of a D-lyxose isomerase from the σB regulon of Bacillus subtilis
Jon Marles-Wright
Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH
Search for more papers by this authorCorresponding Author
Richard J. Lewis
Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH
Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH===Search for more papers by this authorJon Marles-Wright
Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH
Search for more papers by this authorCorresponding Author
Richard J. Lewis
Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH
Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH===Search for more papers by this author
Supporting Information
Additional Supporting Information may be found in the online version of this article.
Filename | Description |
---|---|
PROT_23028_sm_suppinfo.doc5.3 MB | Supporting Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1 Storz G,Hengge-Aronis R. Bacterial stress responses. Washington DC: ASM Press; 2000.
- 2 Marles-Wright J,Lewis RJ. Stress responses of bacteria. Curr Opin Struct Biol 2007; 17: 755–760.
- 3 Petersohn A,Brigulla M,Haas S,Hoheisel JD,Volker U,Hecker M. Global analysis of the general stress response of Bacillus subtilis. J Bacteriol 2001; 183: 5617–5631.
- 4 Price CW,Fawcett P,Ceremonie H,Su N,Murphy CK,Youngman P. Genome-wide analysis of the general stress response in Bacillus subtilis. Mol Microbiol 2001; 41: 757–774.
- 5 Hecker M,Volker U. General stress response of Bacillus subtilis and other bacteria. Adv Microb Physiol 2001; 44: 35–91.
- 6 Kim TJ,Gaidenko TA,Price CW. A multicomponent protein complex mediates environmental stress signaling in Bacillus subtilis. J Mol Biol 2004; 341: 135–150.
- 7 Zhang S,Haldenwang WG. Contributions of ATP, GTP, and redox state to nutritional stress activation of the Bacillus subtilis sigmaB transcription factor. J Bacteriol 2005; 187: 7554–7560.
- 8 Marles-Wright J,Grant T,Delumeau O,van Duinen G,Firbank SJ,Lewis PJ,Murray JW,Newman JA,Quin MB,Race PR,Rohou A,Tichelaar W,van Heel M,Lewis RJ. Molecular architecture of the “stressosome,” a signal integration and transduction hub. Science 2008; 322: 92–96.
- 9 Chen CC,Lewis RJ,Harris R,Yudkin MD,Delumeau O. A supramolecular complex in the environmental stress signalling pathway of Bacillus subtilis. Mol Microbiol 2003; 49: 1657–1669.
- 10 Avila-Perez M,van der Steen JB,Kort R,Hellingwerf KJ. Red light activates the sigmab-mediated general stress response of Bacillus subtilis via the energy branch of the upstream signaling cascade. J Bacteriol 2010; 192: 755–762.
- 11 Delumeau O,Lewis RJ,Yudkin MD. Protein-protein interactions that regulate the energy stress activation of sigma (b) in Bacillus subtilis. J Bacteriol 2002; 184: 5583–5589.
- 12 Hecker M,Volker U. Non-specific, general and multiple stress resistance of growth-restricted Bacillus subtilis cells by the expression of the sigmaB regulon. Mol Microbiol 1998; 29: 1129–1136.
- 13 Hecker M,Schumann W,Volker U. Heat-shock and general stress response in Bacillus subtilis. Mol Microbiol 1996; 19: 417–428.
- 14 Derre I,Rapoport G,Msadek T. Ctsr, a novel regulator of stress and heat shock response, controls clp and molecular chaperone gene expression in gram-positive bacteria. Mol Microbiol 1999; 31: 117–131.
- 15 Gerth U,Kruger E,Derre I,Msadek T,Hecker M. Stress induction of the Bacillus subtilis clpp gene encoding a homologue of the proteolytic component of the clp protease and the involvement of clpp and clpx in stress tolerance. Mol Microbiol 1998; 28: 787–802.
- 16 Kruger E,Msadek T,Ohlmeier S,Hecker M. The Bacillus subtilis clpc operon encodes DNA repair and competence proteins. Microbiology 1997; 143 (Part 4): 1309–1316.
- 17 Petersohn A,Antelmann H,Gerth U,Hecker M. Identification and transcriptional analysis of new members of the sigmaB regulon in Bacillus subtilis. Microbiology 1999; 145 (Part 4): 869–880.
- 18 Scharf C,Riethdorf S,Ernst H,Engelmann S,Volker U,Hecker M. Thioredoxin is an essential protein induced by multiple stresses in Bacillus subtilis. J Bacteriol 1998; 180: 1869–1877.
- 19 Hoper D,Volker U,Hecker M. Comprehensive characterization of the contribution of individual sigb-dependent general stress genes to stress resistance of Bacillus subtilis. J Bacteriol 2005; 187: 2810–2826.
- 20 Quin M,Newman J,Firbank S,Lewis RJ,Marles-Wright J. Crystallization and preliminary X-ray analysis of rsbs from Moorella thermoacetica at 2.5 a resolution. Acta Crystallogr 2008; 64: 196–199.
- 21 Evans G,Pettifer RF. Chooch: a program for deriving anomalous-scattering factors from X-ray fluorescence spectra. J Appl Crystallogr 2001; 34: 82–86.
- 22 Leslie AG. The integration of macromolecular diffraction data. Acta Crystallogr D Biol Crystallogr 2006; 62: 48–57.
- 23 Evans P. Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 2006; 62: 72–82.
- 24 Wang JW,Chen JR,Gu YX,Zheng CD,Jiang F,Fan HF,Terwilliger TC,Hao Q. Sad phasing by combination of direct methods with the solve/resolve procedure. Acta Crystallogr D Biol Crystallogr 2004; 60: 1244–1253.
- 25 Langer G,Cohen SX,Lamzin VS,Perrakis A. Automated macromolecular model building for X-ray crystallography using arp/warp version 7. Nat Protoc 2008; 3: 1171–1179.
- 26 Adams PD,Afonine PV,Bunkoczi G,Chen VB,Davis IW,Echols N,Headd JJ,Hung LW,Kapral GJ,Grosse-Kunstleve RW,McCoy AJ,Moriarty NW,Oeffner R,Read RJ,Richardson DC,Richardson JS,Terwilliger TC,Zwart PH. Phenix: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 2010; 66: 213–221.
- 27 Emsley P,Lohkamp B,Scott WG,Cowtan K. Features and development of coot. Acta Crystallogr D Biol Crystallogr 2010; 66: 486–501.
- 28 De Lano WL. The pymol molecular graphics system. De Lano Scientific; 2002. Available at: www.pymol.org.
- 29 van Staalduinen LM,Park CS,Yeom SJ,Adams-Cioaba MA,Oh DK,Jia Z. Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli o157:H7. J Mol Biol 2010; 401: 866–881.
- 30 Krissinel E,Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007; 372: 774–797.
- 31 Harding MM. Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr D Biol Crystallogr 2006; 62: 678–682.
- 32 Waldron KJ,Robinson NJ. How do bacterial cells ensure that metalloproteins get the correct metal? Nat Rev Microbiol 2009; 7: 25–35.
- 33 Andreini C,Bertini I,Cavallaro G,Holliday GL,Thornton JM. Metal ions in biological catalysis: from enzyme databases to general principles. J Biol Inorg Chem 2008; 13: 1205–1218.