Structure of the periplasmic stress response protein CpxP

Journal of Bacteriology

Volumn 193, Issue 9, 2011, Pages 2149-2157

  Thede, Gina L ^a   Arthur, David C ^a   Edwards, Ross A ^a   Buelow, Daelynn R ^a,b   Wong, Julia L ^a   Raivio, Tracy L ^a   Glover, J N Mark ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CPXP PROTEIN; DIMER; HEAT SHOCK PROTEIN; PERIPLASMIC PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BIOCHEMISTRY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; LOSS OF FUNCTION MUTATION; MOLECULAR INTERACTION; NONHUMAN; PH; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN STRUCTURE;

AMINO ACID MOTIFS; ESCHERICHIA COLI PROTEINS; HYDROGEN-ION CONCENTRATION; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN CONFORMATION; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE; ESCHERICHIA COLI; NEGIBACTERIA;

EID: 79955533578     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01296-10     Document Type: Article

References (69)

1. Adams, P. D., et al. 2002. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58:1948-1954.
2. Ades, S. E., I. L. Grigorova, and C. A. Gross. 2003. Regulation of the alternative sigma factor (E during initiation, adaptation, and shutoff of the extracytoplasmic heat shock response in Escherichia coli. J. Bacteriol. 185: 2512-2519.
3. Andersen, C. A., A. G. Palmer, S. Brunak, and B. Rost. 2002. Continuum secondary structure captures protein flexibility. Structure 10:175-184.
4. Baker, N. A., D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U. S. A. 98:10037-10041.
5. Buelow, D. R., and T. L. Raivio. 2005. Cpx signal transduction is influenced by a conserved N-terminal domain in the novel inhibitor CpxP and the periplasmic protease DegP. J. Bacteriol. 187:6622-6630.
6. Casadaban, M. J. 1976. Transposition and fusion of lac genes to selected promoters in Escherichia coli using bacteriophages lambda and Mu. J. Mol. Biol. 104:541-555.
7. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
8. Danese, P. N., and T. J. Silhavy. 1998. CpxP, a stress-combative member of the Cpx regulon. J. Bacteriol. 180:831-839.
9. E and the Cpx signal transduction systems control the synthesis of periplasmic protein-folding enzymes in Escherichia coli. Genes Dev. 11:1183-1193.
10. Danese, P. N., W. B. Snyder, C. L. Cosma, L. J. Davis, and T. J. Silhavy. 1995. The Cpx two-component signal transduction pathway of Escherichia coli regulates transcription of the gene specifying the stress-inducible periplasmic protease, DegP. Genes Dev. 9:387-398.
11. DiGiuseppe, P. A., and T. J. Silhavy. 2003. Signal detection and target gene induction by the CpxRA two-component system. J. Bacteriol. 185:2432-2440.
12. Dolinsky, T. J., et al. 2007. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35:W522-W525.
13. Dolinsky, T. J., J. E. Nielsen, J. A. McCammon, and N. A. Baker. 2004. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32:W665-W667.
14. Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60:2126-2132.
15. Fleischer, R., R. Heermann, K. Jung, and S. Hunke. 2007. Purification, reconstitution, and characterization of the CpxRAP envelope stress system of Escherichia coli. J. Biol. Chem. 282:8583-8593.
16. Gasteiger, E., et al. 2005. Protein identification and analysis tools on the ExPASy server, p. 571-607. In J. M. Walker (ed.), The proteomics protocols handbook. Humana Press, New York, NY.
17. GE Healthcare UK, Ltd. 2010. GST gene fusion system handbook. GE Healthcare UK, Ltd., Little Chalfont, England.
18. Grass, G., B. Fricke, and D. H. Nies. 2005. Control of expression of a periplasmic nickel efflux pump by periplasmic nickel concentrations. Biometals 18:437-448.
19. Grass, G., C. Grosse, and D. H. Nies. 2000. Regulation of the cnr cobalt and nickel resistance determinant from Ralstonia sp. strain CH34. J. Bacteriol. 182:1390-1398.
20. Holm, L., and P. Rosenstrom. 2010. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38(Suppl.):W545-W549.
21. Holm, L., and C. Sander. 1996. Mapping the protein universe. Science 273:595-603.
22. Humphries, R. M., et al. 2010. N-Acetyllactosamine-induced retraction of bundle-forming pili regulates virulence-associated gene expression in enteropathogenic Escherichia coli. Mol. Microbiol. 76:1111-1126.
23. Isaac, D. D., J. S. Pinkner, S. J. Hultgren, and T. J. Silhavy. 2005. The extracytoplasmic adaptor protein CpxP is degraded with substrate by DegP. Proc. Natl. Acad. Sci. U. S. A. 102:17775-17779.
24. Jones, C. H., P. N. Danese, J. S. Pinkner, T. J. Silhavy, and S. J. Hultgren. 1997. The chaperone-assisted membrane release and folding pathway is sensed by two signal transduction systems. EMBO J. 16:6394-6406.
25. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
26. Kershaw, C. J., N. L. Brown, C. Constantinidou, M. D. Patel, and J. L. Hobman. 2005. The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations. Microbiology 151:1187-1198.
27. Konarev, P. V., V. V. Volkov, A. V. Sokolova, M. H. J. Koch, and D. I. Svergun. 2003. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36:1277-1282.
28. Krissinel, E., and K. Henrick. 2007. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372:774-797.
29. Kwon, E., D. Y. Kim, C. A. Gross, J. D. Gross, and K. K. Kim. 2010. The crystal structure Escherichia coli Spy. Protein Sci. 19:2252-2259.
30. Larsen, R. A., M. G. Thomas, G. E. Wood, and K. Postle. 1994. Partial supression of an Escherichia coli TonB transmembrane domain mutation (DV17) by a missense mutation in ExbB. Mol. Microbiol. 13:627-640.
31. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291.
32. Lee, L. J., J. A. Barrett, and R. K. Poole. 2005. Genome-wide transcriptional response of chemostat-cultured Escherichia coli to zinc. J. Bacteriol. 187: 1124-1134.
33. Leonhartsberger, S., A. Huber, F. Lottspeich, and A. Bock. 2001. The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system. J. Mol. Biol. 307:93-105.
34. Liesegang, H., K. Lemke, R. A. Siddiqui, and H. G. Schlegel. 1993. Characterization of the inducible nickel and cobalt resistance determinant cnr from pMOL28 of Alcaligenes eutrophus CH34. J. Bacteriol. 175:767-778.
35. Lu, J., et al. 2006. Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM. EMBO J. 25:2930-2939.
36. MacRitchie, D. M., D. R. Buelow, N. L. Price, T. L. Raivio. 2007. Twocomponent signaling and gram negative envelope stress response systems. In R. Utsumi (ed.), Bacterial signal transduction: network and drug targets. Landes Bioscience, Austin, TX.
37. McCoy, A. J., et al. 2007. Phaser crystallographic software. J. Appl. Crystallogr. 40:658-674.
38. Monchy, S., et al. 2007. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J. Bacteriol. 189:7417-7425.
39. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:240-255.
40. Nevesinjac, A. Z., and T. L. Raivio. 2005. The Cpx envelope stress response affects expression of the type IV bundle-forming pili of enteropathogenic Escherichia coli. J. Bacteriol. 187:672-686.
41. New England BioLabs. 2007. pMAL protein fusion and purification system instruction manual. New England BioLabs, Ipswich, MA.
42. Noll, M., K. Petrukhin, and S. Lutsenko. 1998. Identification of a novel transcription regulator from Proteus mirabilis, PMTR, revealed a possible role of YJAI protein in balancing zinc in Escherichia coli. J. Biol. Chem. 273:21393-21401.
43. Otwinowski, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326.
44. Pogliano, J. A., S. Lynch, D. Belin, E. C. C. Lin, and J. Beckwith. 1997. Regulation of Escherichia coli cell envelope proteins involved in protein folding and degradation by the Cpx two-component system. Genes Dev. 11:1169-1182.
45. Pompidor, G., et al. 2008. X-ray structure of the metal-sensor CnrX in both the apo- and copper-bound forms. FEBS Lett. 582:3954-3958.
46. Potterton, E., P. Briggs, M. Turkenburg, and E. Dodson. 2003. A graphical user interface to the CCP4 program suite. Acta Crystallogr. D Biol. Crystallogr. 59:1131-1137.
47. Price, N. L., and T. L. Raivio. 2009. Characterization of the Cpx regulon in Escherichia coli strain MC4100. J. Bacteriol. 191:1798-1815.
48. Raivio, T. L., M. W. Laird, J. C. Joly, and T. J. Silhavy. 2000. Tethering of CpxP to the inner membrane prevents spheroplast induction of the Cpx envelope stress response. Mol. Microbiol. 37:1186-1197.
49. Raivio, T. L., D. L. Popkin, and T. J. Silhavy. 1999. The Cpx envelope stress response is controlled by amplification and feedback inhibition. J. Bacteriol. 181:5263-5272.
50. Raivio, T. L., and T. J. Silhavy. 1997. Transduction of envelope stress in Escherichia coli by the Cpx two-component system. J. Bacteriol. 179:7724-7733.
51. Ruiz, N., and T. J. Silhavy. 2005. Sensing external stress: watchdogs of the Escherichia coli cell envelope. Curr. Opin. Microbiol. 8:122-126.
52. Silhavy, T. J., M. L. Berman, and L. W. Enquist. 1984. Experiments in gene fusions. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
53. Svergun, D. I. 1992. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25: 495-503.
54. Svergun, D. I., M. V. Petoukhov, and M. H. Koch. 2001. Determination of domain structure of proteins from X-ray solution scattering. Biophys. J. 80:2946-2953.
55. Svergun, D. I., and V. V. Volkov. 2003. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 36:860-864.
56. Tamames, B., S. F. Sousa, J. Tamames, P. A. Fernandes, and M. J. Ramos. 2007. Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns. Proteins 69:466-475.
57. Terwilliger, T. C. 2003. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D Biol. Crystallogr. 59:38-44.
58. Terwilliger, T. C. 2000. Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56:965-972.
59. Terwilliger, T. C., and J. Berendzen. 1999. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55:849-861.
60. Theobald, D. L., and D. S. Wuttke. 2006. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics 22:2171-2172.
61. Tibazarwa, C., S. Wuertz, M. Mergeay, L. Wyns, and D. van Der Lelie. 2000. Regulation of the cnr cobalt and nickel resistance determinant of Ralstonia eutropha (Alcaligenes eutrophus) CH34. J. Bacteriol. 182:1399-1409.
62. Uni Prot Consortium. 2010. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 38:D142-D148.
63. van Stelten, J., F. Silva, D. Belin, and T. J. Silhavy. 2009. Effects of antibiotics and a proto-oncogene homolog on destruction of protein translocator SecY. Science 325:753-756.
64. Vogt, S. L., et al. 2010. The Cpx envelope stress response both facilitates and inhibits elaboration of the enteropathogenic Escherichia coli bundle-forming pilus. Mol. Microbiol. 76:1095-1110.
65. Winn, M. D., M. N. Isupov, and G. N. Murshudov. 2001. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57:122-133.
66. Wriggers, W. 2010. Using Situs for the integration of multi-resolution structures. Biophys. Rev. 2:21-27.
67. Yamamoto, K., and A. Ishihama. 2006. Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli. Biosci. Biotechnol. Biochem. 70:1688-1695.
68. Yamamoto, K., and A. Ishihama. 2005. Transcriptional response of Escherichia coli to external copper. Mol. Microbiol. 56:215-227.
69. Yamamoto, K., H. Ogasawara, and A. Ishihama. 2008. Involvement of multiple transcription factors for metal-induced spy gene expression in Escherichia coli. J. Biotechnol. 133:196-200.