The Yeast YPD1/SLN1 Complex: Insights into Molecular Recognition in Two-Component Signaling Systems

Structure

Volumn 11, Issue 12, 2003, Pages 1569-1581

  Xu, Qingping ^a,b   Porter, Stace W ^a   West, Ann H ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; FUNGAL PROTEIN; HISTIDINE; PHOSPHOTRANSFERASE; PROTEIN HISTIDINE KINASE; PROTEIN SKN1; PROTEIN SLN1; PROTEIN SSK1; PROTEIN YPD1; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DOWN REGULATION; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; YEAST;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0344436666     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2003.10.016     Document Type: Article

References (56)

1. Baikalov I., Schröder I., Kaczor-Grzeskowiak M., Grzeskowiak K., Gunsalus R.P., Dickerson R.E. Structure of the Escherichia coli response regulator NarL. Biochemistry. 35:1996;11053-11061.
2. Birck C., Mourey L., Gouet P., Fabry B., Schumacher J., Rousseau P., Kahn D., Samama J.-P. Conformational changes induced by phosphorylation of the FixJ receiver domain. Structure. 7:1999;1505-1515.
3. Brown J.L., Bussey H., Stewart R.C. Yeast Skn7p functions in a eukaryotic two-component regulatory pathway. EMBO J. 13:1994;5186-5194.
4. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Gross-Kunstleve R.W., Jiang J.-S., Kuzewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR system (CNS). a new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
5. Cho H.S., Lee S.-Y., Yan D., Pan X., Parkinson J.S., Kustu S., Wemmer D.E., Pelton J.G. NMR structure of activated CheY. J. Mol. Biol. 297:2000;543-551.
6. Chooback L., West A.H. Co-crystallization of the yeast phosphorelay protein YPD1 with the SLN1 response regulator domain and preliminary X-ray diffraction analysis. Acta Crystallogr. D Biol. Crystallogr. 59:2003;927-929.
7. Cowtan K.D. "Dm" an automated procedure for phase improvement by density modification Joint CCP. 4(and ESF-EACBM Newsletter on Protein Crystallography 31):1994;34-38.
8. DeLano W.L. The PyMOL molecular graphics system. 2002;DeLano Scientific, San Carlos, CA.
9. Djordjevic S., Goudreau P.N., Xu Q., Stock A.M., West A.H. Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain. Proc. Natl. Acad. Sci. USA. 95:1998;1381-1386.
10. Halkides C.J., McEvoy M.M., Casper E., Matsumura P., Volz K., Dahlquist F.W. The 1.9 Å resolution crystal structure of phosphono-CheY, an analogue of the active form of the response regulator, CheY. Biochemistry. 39:2000;5280-5286.
11. Hoch J.A., Silhavy T.J. Two-Component Signal Transduction. 1995;American Society for Microbiology Press, Washington, DC.
12. Hoch J.A., Varughese K.I. Keeping signals straight in phosphorelay signal transduction. J. Bacteriol. 183:2001;4941-4949.
13. Hutchinson E.G., Thornton J.M. PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5:1996;212-220.
14. Janiak-Spens F., Sparling D.P., West A.H. Novel role for an HPt domain in stabilizing the phosphorylated state of a response regulator domain. J. Bacteriol. 182:2000;6673-6678.
15. Janiak-Spens F., Sparling J.M., Gurfinkel M., West A.H. Differential stabilities of phosphorylated response regulator domains reflect functional roles of the yeast osmoregulatory SLN1 and SSK1 proteins. J. Bacteriol. 181:1999;411-417.
16. Jones S., Marin A., Thornton J.M. Protein domain interfaces. characterization and comparison with oligomeric protein interfaces Protein Eng. 13:2000;77-82.
17. Kato M., Mizuno T., Shimizu T., Hakoshima T. Insights into multistep phosphorelay from the crystal structure of the C-terminal HPt domain of ArcB. Cell. 88:1997;717-723.
18. Kern D., Volkman B.F., Luginbühl P., Nohaile M.J., Kustu S., Wemmer D.E. Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature. 402:1999;894-898.
19. Ketela T., Brown J.L., Stewart R.C., Bussey H. Yeast Skn7p activity is modulated by the Sln1p-Ypd1p osmosensor and contributes to regulation of the HOG1 pathway. Mol. Gen. Genet. 259:1998;372-378.
20. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950.
21. Laskowski R.A. Surfnet. a program for visualizing molecular surfaces, cavities, and intermolecular interactions J. Mol. Graph. 13:1991;323-330.
22. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
23. Lee S.-Y., Cho H.S., Pelton J.G., Yan D., Henderson R.K., King D.S., Huang L.-S., Kustu S., Berry E.A., Wemmer D.E. Crystal structure of an activated response regulator bound to its target. Nat. Struct. Biol. 8:2001;52-56.
24. Lewis R.J., Brannigan J.A., Muchova K., Barak I., Wilkinson A.J. Phosphorylated aspartate in the structure of a response regulator protein. J. Mol. Biol. 294:1999;9-15.
25. Li S., Ault A., Malone C.L., Raitt D., Dean S., Johnston L.H., Deschenes R.J., Fassler J.S. The yeast histidine protein kinase, Sln1p, mediates phosphotransfer to two response regulators, Ssk1p and Skn7p. EMBO J. 17:1998;6952-6962.
26. Madhusudan, Zapf J., Whiteley J.M., Hoch J.A., Xuong N.H., Varughese K.I. Crystal structure of a phosphatase-resistant mutant of sporulation response regulator Spo0F from Bacillus subtilis. Structure. 4:1996;679-690.
27. Matthews B.W. Solvent content of protein crystals. J. Mol. Biol. 33:1968;491-497.
28. McEvoy M.M., Hausrath A.C., Randolph G.B., Remington S.J., Dahlquist F.W. Two binding modes reveal flexibility in kinase/response regulator interactions in the bacterial chemotaxis pathway. Proc. Natl. Acad. Sci. USA. 95:1998;7333-7338.
29. McRee D.E. Practical Protein Crystallography. 1999;Academic Press, San Diego, CA.
30. Merritt E.A., Bacon D.J. Raster3D. photorealistic molecular graphics Methods Enzymol. 277:1997;505-524.
31. Mourey L., Da Re S., Pédelacq J.-D., Tolstykh T., Faurie C., Guillet V., Stock J.B., Samama J.-P. Crystal structure of the CheA histidine phosphotransfer domain that mediates response regulator phosphorylation in bacterial chemotaxis. J. Biol. Chem. 276:2001;31074-31082.
32. Müller-Dieckmann H.-J., Grantz A.A., Kim S.-H. The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1. Structure. 7:1999;1547-1556.
33. Murshudov G.N., Vagin A.A., Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53:1997;240-255.
34. Nooren I.M.A., Thornton J.M. Structural characterisation and functional significance of transient protein-protein interactions. J. Mol. Biol. 325:2003;991-1018.
35. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
36. Pflugrath J.W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D Biol. Crystallogr. 55:1999;1718-1725.
37. Porter S.W., Xu Q., West A.H. Ssk1p response regulator binding surface on histidine-containing phosphotransfer protein Ypd1p. Eukaryot. Cell. 2:2003;27-33.
38. Posas F., Wurgler-Murphy S.M., Maeda T., Witten E.A., Thai T.C., Saito H. Yeast HOG1 MAP kinase cascade is regulated by a multistep phosphorelay mechanism in the SLN1-YPD1-SSK1 "two-component" osmosensor. Cell. 86:1996;865-875.
39. Robinson V.L., Buckler D.R., Stock A.M. A tale of two components. a novel kinase and a regulatory switch Nat. Struct. Biol. 7:2000;626-633.
40. Saito H. Histidine phosphorylation and two-component signaling in eukaryotic cells. Chem. Rev. 101:2001;2497-2509.
41. Song H.K., Lee J.Y., Lee M.G., Min J.M.K., Yang J.K., Suh S.W. Insights into eukaryotic multistep phosphorelay signal transduction revealed by the crystal structure of Ypd1p from Saccharomyces cerevisiae. J. Mol. Biol. 293:1999;753-761.
42. 2+-bound form of CheY and mechanism of phosphoryl transfer in bacterial chemotaxis. Biochemistry. 32:1993;13375-13380.
43. Stock A.M., Robinson V.L., Goudreau P.N. Two-component signal transduction. Annu. Rev. Biochem. 69:2000;183-215.
44. Tomomori C., Tanaka T., Dutta R., Park H., Saha S.K., Zhu Y., Ishima R., Liu D., Tong K.I., Kurokawa H.et al. Solution structure of the homodimeric core domain of Escherichia coli histidine kinase EnvZ. Nat. Struct. Biol. 6:1999;729-734.
45. Urao T., Yamaguchi-Shinozaki K., Shinozaki K. Two-component systems in plant signal transduction. Trends Plant Sci. 5:2000;67-74.
46. Vagin A., Teplyakov A. Molrep. an automated program for molecular replacement J. Appl. Crystallogr. 30:1997;1022-1025.
47. Varughese K.I., Madhusudan, Zhou X.Z., Whiteley J.M., Hoch J.A. Formation of a novel four-helix bundle and molecular recognition sites by dimerization of a response regulator phosphotransferase. Mol. Cell. 2:1998;485-493.
48. Volkman B.F., Nohaile M.J., Amy N.K., Kustu S., Wemmer D.E. Three-dimensional solution structure of the N-terminal receiver domain of NTRC. Biochemistry. 34:1995;1413-1424.
49. Volz K., Matsumura P. Crystal structure of Escherichia coli CheY refined at 1.7-Å resolution. J. Biol. Chem. 266:1991;15511-15519.
50. Wallace A.C., Laskowski R.A., Thornton J.M. Ligplot. a program to generate schematic diagrams of protein-ligand interactions Protein Eng. 8:1995;127-134.
51. Welch M., Chinardet N., Mourey L., Birck C., Samama J.-P. Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nat. Struct. Biol. 5:1998;25-29.
52. West A.H., Stock A.M. Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem. Sci. 26:2001;369-376.
53. Xu Q., West A.H. Conservation of structure and function among histidine-containing phosphotransfer (HPt) domains as revealed by the crystal structure of YPD1. J. Mol. Biol. 292:1999;1039-1050.
54. Zapf J., Sen U., Madhusudan, Hoch J.A., Varughese K.I. A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction. Structure. 8:2000;851-862.
55. Zhao R., Collins E.J., Bourret R.B., Silversmith R.E. Structure and catalytic mechanism of the E. coli chemotaxis phosphatase CheZ. Nat. Struct. Biol. 9:2002;570-575.
56. Zhou H., Dahlquist F.W. Phosphotransfer site of the chemotaxis-specific protein kinase CheA as revealed by NMR. Biochemistry. 36:1997;699-710.