Solution structure of a low-molecular-weight protein tyrosine phosphatase from Bacillus subtilis

Journal of Bacteriology

Volumn 188, Issue 4, 2006, Pages 1509-1517

  Xu, Huimin ^a   Xia, Bin ^a,b   Jin, Changwen ^a,b  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; ASPARTIC ACID; PHENYLALANINE; PHOSPHATE; PHOSPHOTYROSINE; PROTEIN TYROSINE PHOSPHATASE; PROTEIN YWLE; THREONINE; TYROSINE; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BACILLUS SUBTILIS; BETA SHEET; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; EUKARYOTE; GRAM POSITIVE BACTERIUM; HYDROGEN BOND; HYDROLYSIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ASSEMBLY; SURFACE PROPERTY; UBIQUITINATION;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; GENES, BACTERIAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PROTEIN STRUCTURE, TERTIARY; PROTEIN-TYROSINE-PHOSPHATASE; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); EUKARYOTA; POSIBACTERIA; PROKARYOTA;

EID: 32444448489     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.188.4.1509-1517.2006     Document Type: Article

References (55)

1. Berti, A., S. Rigacci, G. Raugei, D. Degl'Innocenti, and G. Ramponi. 1994. Inhibition of cellular response to platelet-derived growth factor by low M(r) phosphotyrosine protein phosphatase overexpression. FEBS Lett. 349:7-12.
2. Case, D. A., D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, J. Wang, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Merz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crowley, V. Tsui, H. Gohlke, R. J. Radmer, Y. Duan, J. Pitera, I. Massova, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollman. 2002. AMBER 7, p. 130-131. University of California, San Francisco, Calif.
3. Chiarugi, P., M. L. Taddei, P. Cirri, D. Talini, F. Buricchi, G. Camici, G. Manao, G. Raugei, and G. Ramponi. 2000. Low molecular weight protein-tyrosine phosphatase controls the rate and the strength of NIH-3T3 cells adhesion through its phosphorylation on tyrosine 131 or 132. J. Biol. Chem. 275:37619-37627.
4. r phosphotyrosine protein phosphatase. FEBS Lett. 372:49-53.
5. Chiarugi, P., P. Cirri, M. L. Taddei, E. Giannoni, G. Camici, G. Manao, G. Raugei, and G. Ramponi. 2000. The low M(r) protein-tyrosine phosphatase is involved in Rho-mediated cytoskeleton rearrangement after integrin and platelet-derived growth factor stimulation. J. Biol. Chem. 275:4640-4646.
6. Cirri, P., T. Fiaschi, P. Chiarugi, G. Camici, G. Manao, G. Raugei, and G. Ramponi. 1996. The molecular basis of the differing kinetic behavior of the two low molecular mass phosphotyrosine protein phosphatase isoforms. J. Biol. Chem. 271:2604-2607.
7. Cornilescu, G., F. Delaglio, and A. Bax. 1999. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13:289-302.
8. Cozzone, A. J., C. Grangeasse, P. Doublet, and B. Duclos. 2004. Protein phosphorylation on tyrosine in bacteria. Arch. Microbiol. 181:171-181.
9. Davis, J. P., M. M. Zhou, and R. L. Van Etten. 1994. Kinetic and site-directed mutagenesis studies of the cysteine residues of bovine low molecular weight phosphotyrosyl protein phosphatase. J. Biol. Chem. 269:8734-8740.
10. Delaglio, F., S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, and A. Bax. 1995. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6:277-293.
11. Denu, J. M., G. Zhou, Y. Guo, and J. E. Dixon. 1995. The catalytic role of aspartic acid-92 in a human dual-specific protein-tyrosine-phosphatase. Biochemistry 34:3396-3403.
12. DeVinney, R., O. Steele-Mortimer, and B. B. Finlay. 2000. Phosphatases and kinases delivered to the host cell by bacterial pathogens. Trends Microbiol. 8:29-33.
13. Dosset, P., J.-C. Hus, M. Blackledge, and D. Marion. 2000. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16:23-28.
14. Duggan, B. M., G. B. Legge, H. J. Dyson, and P. E. Wright. 2001. SANE (Structure Assisted NOE Evaluation): an automated model-based approach for NOE assignment. J. Biomol. NMR 19:321-329.
15. 15N relaxation data exclusively. J. Biomol. NMR 6:153-162.
16. 15N NMR relaxation. Biochemistry 33:5984-6003.
17. 15N relaxation with monomer/dimer equilibration. J. Mol. Biol. 266:173-194.
18. Grangeasse, C., B. Obadia, I. Myakovic, J. Deutscher, A. J. Cozzone, and P. Doublet. 2003. Autophosphorylation of the Escherichia coli protein kinase Wzc regulates tyrosine phosphorylation of Ugd, a UDP-glucose dehydrogenase. J. Biol. Chem. 278:39323-39329.
19. Grangeasse, C., P. Doublet, C. Vincent, E. Vaganay, M. Riberty, B. Duclos, and A. J. Cozzone. 1998. Functional characterization of the low-molecular mass phosphotyrosine-protein phosphatase of Acinetobacter johnsonii. J. Mol. Biol. 278:339-347.
20. Güntert, P., C. Mumenthaler, and K. Wüthrich. 1997. Torsion angle dynamics for NMR structure calculation with the new program DYANA, J. Mol. Biol. 273:283-298.
21. Herrmann, T., P. Güntert, and K. Wüthrich. 2002. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319:209-227.
22. Higgins, D., J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
23. Hunter, T. 1995. Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell 80:225-236.
24. Hunter, T. 2000. Signaling-2000 and beyond. Cell 100:113-127.
25. Johnson, B. A., and R. A. Blevins. 1994. NMR View: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4:603-614.
26. Kay, L. E. 1998. Protein dynamics from NMR. Nat. Struct. Biol. 5(Suppl.):513-517.
27. Koul, A., A. Choidas, M. Treder, A. K. Tyagi, K. Drlica, Y. Singh, and A. Ullrich. 2000. Cloning and characterization of secretory tyrosine phosphatases of Mycobacterium tuberculosis. J. Bacteriol. 182:5425-5432.
28. Laskowski, R. A., J. A. C. Rullmann, M. W. MacArthur, R. Kaptein, and J. M. Thornton. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8:477-486.
29. Logan, T. M., M. M. Zhou, D. G. Nettesheim, R. P. Meadows, R. L. Van Etten, and S. W. Fesik, 1994. Solution structure of a low molecular weight protein tyrosine phosphatase. Biochemistry 33:11087-11096.
30. Madhurantakam, C., E. Rajakumara, P. A. Mazumdar, B. Sana, D. Mitra, H. G. Wiker, R. Sankaranarayanan, and A. K. Das. 2005. Crystal dtructure of low-molecular-weight protein tyrosine phosphatase from Mycobacterium tuberculosis at 1.9-Å resolutions. J. Bacteriol. 187:2175-2181.
31. Marchetta, M., T. Gamberi, S. Sarno, F. Magherini, G. Raugei, G. Camici, L. A. Pinna, and A. Modesti. 2004. Expression of the Stp1 LMW-PTP and inhibition of protein CK2 display a cooperative effect on immunophilin Fpr3 tyrosine phosphorylation and Saccharomyces cerevisiae growth. Cell. Mol. Life Sci. 61:1176-1184.
32. Myakovic, I., S. Poncet, G. Boël, A. Mazé, S. Gillet, E. Jamet, P. Decottignies, C. Grangeasse, P. Doublet, P. Le Maréchal, and J. Deutscher. 2003. Transmembrane modulator-dependent bacterial tyrosine kinase activates UDP-glucose dehydrogenases. EMBO J. 22:4709-4718.
33. Mijakovic, I., L. Musumeci, L. Tautz, D. Petranovic, R. A. Edwards, P. R. Jensen, T. Mustelin, J. Deutscher, and N. Bottini. 2005. In vitro characterization of the Bacillus subtilis protein tyrosine phosphatase YwqE. J. Bacteriol. 187:3384-3390.
34. Mulder, F. A. A., D. Schipper, R. Bott, and R. Boelens. 1999. Altered flexibility in the substrate-binding site of related native and engineered high-alkaline Bacillus subtilisins. J. Mol. Biol. 292:111-123.
35. Mustelin, T., T. Vang, and N. Bottini. 2005. Protein tyrosine phosphatases and the immune response. Nat. Rev. Immunol. 5:43-57.
36. Musumeci, L., C. Bongiorni, L. Tautz, R. A. Edwards, A. Osterman, M. Perego, T. Mustelin, and N. Bottini. 2005. Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis. J. Bacteriol. 187:4945-4956.
37. Neel, B. G., and N. K. Tonks. 1997. Protein tyrosine phosphatases in signal transduction. Curr. Opin. Cell Biol. 9:193-204.
38. Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham III, S. DeBolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91:1-41.
39. Preneta, R., S. Jarraud, C. Vincent, P. Doublet, B. Duclos, J. Etienne, and A. J. Cozzone. 2002. Isolation and characterization of a protein-tyrosine kinase and a phosphotyrosine-protein phosphatase from Klebsiella pneumoniae. Comp. Biochem. Physiol. B 131:103-112.
40. r phosphotyrosine protein phosphatases. Biochim. Biophys. Acta 1341:137-156.
41. Reid, D. G., L. K. MacLachlan, A. J. Edwards, J. A. Hubbard, and P. J. Sweeney. 1997. Introduction to the NMR of proteins, p. 13-16. In D. G. Reid (ed.), Protein NMR techniques. Humana Press, Totowa, NJ.
42. Schnell, J. R., H. J. Dyson, and P. E. Wright. 2004. Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu. Rev. Biophys. Biomol. Struct. 33:119-140.
43. Soulat, D., E. Vaganay, B. Duclos, A. L. Genestier, J. Etienne, and A. J. Cozzone. 2002. Staphylococcus aureus contains two low-molecular-mass phosphotyrosine protein phosphatases. J. Bacteriol. 184:5194-5199.
44. Su, X. D., N. Taddei, M. Stefani, G. Ramponi, and P. Nordlumd. 1994. The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase. Nature 370:575-578.
45. Vincent, C., B. Duclos, C. Grangeasse, E. Vaganay, M. Riberty, A. J. Cozzone, and P. Doublet. 2000. Relationship between exopolysaccharide production and protein-tyrosine phosphorylation in gram-negative bacteria. J. Mol. Biol. 304:311-321.
46. Vincent, C., P. Doublet, C. Grangeasse, E. Vaganay, A. J. Cozzone, and B. Duclos. 1999. Cells of Escherichia coli contain a protein-tyrosine kinase, Wzc, and a phosphotyrosine-protein phosphatase, Wzb. J. Bacteriol. 181:3472-3477.
47. Volkman, B. F., D. Lipson, D. E. Wemmer, and D. Kern. 2001. Two-state allosteric behavior in a single-domain signaling protein. Science 291:2429-2433.
48. Wang, S., L. Tabernero, M. Zhang, E. Harms, R. L. Van Etten, and C. V. Stauffacher. 2000. Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate. Biochemistry 39:1903-1914.
49. Xu, H., P. Zhang, and C. Jin. 2005. NMR assignments of a low molecular weight protein tyrosine phosphatase (PTPase) from Bacillus subtilis. J. Biomol. NMR 31:363.
50. Yuvaniyama, J., J. M. Denu, J. E. Dixon, and M. A. Saper. 1996. Crystal structure of the dual specificity protein phosphatase VHR. Science 272:1328-1331.
51. Zhang, M., C. V. Stauffacher, and R. L. Van Etten. 1995. The three dimensional structure, chemical mechanism and function of the low molecular weight protein tyrosine phosphatases, p. 1-23. In W. Merlevede (ed.), Advances in protein phosphatases, vol. 9. Leuven University Press, Leuven, Belgium.
52. Zhang, M., C. V. Stauffacher, D. Lin, and R. L. Van Etten. 1998. Crystal structure of a human low molecular weight phosphotyrosyl phosphatase. J. Biol. Chem. 273:21714-21720.
53. Zhang, M., R. L. Van Etten, and C. V. Stauffacher. 1994. Crystal structure of bovine heart phosphotyrosyl phosphatase at 2.2-Å resolution. Biochemistry 33:11097-11105.
54. 129 of low molecular weight protein tyrosine phosphatase is involved in leaving group protonation. J. Biol. Chem. 269:25947-25950.
55. Zhang, Z. Y. 2001. Protein tyrosine phosphatases: prospects for therapeutics. Curr. Opin. Chem. Biol. 5:416-423.