Functional diversity of PH domains: An exhaustive modelling study

Folding and Design

Volumn 2, Issue 6, 1997, Pages 343-355

  Blomberg, Niklas ^a   Nilges, D Michael ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Electrostatics; Homology modelling; Phospholipid binding; Signal transduction

Indexed keywords

AGAMMAGLOBULINAEMIA TYROSINE KINASE; AMINO ACID; DYNAMIN; GUANOSINE TRIPHOSPHATASE; ISOENZYME; PHOSPHOLIPASE C; PHOSPHOLIPASE C DELTA; PHOSPHOPROTEIN; PLASMA PROTEIN; PLATELET PROTEIN P47; PROTEIN TYROSINE KINASE; SPECTRIN;

ANIMAL; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; ENZYMOLOGY; GENETICS; MICROTUBULE; MOLECULAR GENETICS; MOUSE; MULTIGENE FAMILY; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; THROMBOCYTE;

AMINO ACIDS; ANIMALS; BLOOD PLATELETS; BLOOD PROTEINS; COMPUTER SIMULATION; DYNAMINS; ELECTROSTATICS; GTP PHOSPHOHYDROLASES; ISOENZYMES; MICE; MICROTUBULES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHOSPHOLIPASE C; PHOSPHOPROTEINS; PROTEIN STRUCTURE, TERTIARY; PROTEIN-TYROSINE KINASES; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECTRIN;

EID: 0031302711     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(97)00048-5     Document Type: Article

References (40)

1. Sander, C. & Schneider, R. (1991). Database of homology derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
2. Haslam, R., Kolde, H.B. & Hemmings, B.A. (1993). Pleckstrin domain homology. Nature 363, 309-310.
3. Mayer, BJ., Ren, R., Clark, K.L & Baltimore, D. (1993). A putative modular domain present in diverse signalling proteins. Cell 73, 629-630.
4. Musacchio, A., Gibson, T., Rice, P., Thompson, J. & Saraste, M. (1993). The PH domain: a common piece in the structural patchwork of signalling proteins. Trends Biochem. Sci. 18, 343-348.
5. Saraste, M. &. Hyvönen, M. (1995). Pleckstrin homology domains: a fact file. Curr. Opin. Struct. Biol. 5, 403-408.
6. Downing, A.K., Driscoll, P.C., Gout, I., Salim, K., Zvelebil, M.J. & Waterfield, M.D. (1994). Three-dimensional solution structure of the pleckstrin homology domain from dynamin. Curr. Biol. 4, 884-891.
7. Ferguson, K.M., Lemmon, M.A., Schlessinger, J. & Sigler, P.B. (1994). Crystal structure at 2.2 A resolution of the pleckstrin homology domain from human dynamin. Cell 79, 199-209.
8. Fushman, D., Cahill, S., Lemmon, M.A., Schlessinger, J. & Cowburn, D. (1995). Solution structure of pleckstrin homology domain of dynamin by heteronuclear NMR spectroscopy. Proc. Natl Acad. Sci. USA 92, 816-820.
9. Macias, MJ., Musacchio, A., Ponstingl, H., Nilges, M., Saraste, M. & Oschkinat, H. (1994). Structure of the pleckstrin homology domain from β-spectrin. Nature 369, 675-677.
10. Timm, D., Salim, K., Gout, I., Guruprasad, L, Waterfield, M. & Blundell, T. (1994). Crystal structure of the pleckstrin homology domain from dynamin. Nat. Struct. Biol. 1, 782-788.
11. Yoon, H.S., Hajduk, PJ., Petros, A.M., Olejniczak, E.T., Meadows, R.P. & Fesik, S.W. (1994). Solution structure of a pleckstrin-homology domain. Nature 369, 672-675.
12. Zhang, P., Talluri, S., Deng, H., Branton, D. & Wagner, G. (1995). Solution structure of the pleckstrin homology domain of Drosophila β-spectrin. Structure 3, 1185-1195.
13. Ferguson, K.M., Lemmon, M.A., Sigler, P.B. & Schlessinger, J. (1995). Scratching the surface with the PH domain. Nat. Struct. Biol. 9, 715-718.
14. Harlan, J.E., Hajduk, PJ., Yoon, H.S. & Fesik, S.W. (1994). Pleckstrin homology domains bind to phosphatidylinositol-4,5-bisphosphate. Nature 371, 168-170.
15. Hyvönen, M., Macias, M.J., Nilges, M., Oschkinat, H., Saraste, M. & Wilmanns, M. (1995). Structure of the binding site for inositol phosphates in a PH domain. EMBO J. 14, 4676-4685.
16. Ferguson, K.M., Lemmon, MA, Schlessinger, J. & Sigler, P.B. (1995). Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain. Cell 83, 1037-1046.
17. Zheng, J., Cahill, S., Lemmon, M., Fushman, D., Schlessinger, J. & Cowburn, D. (1996). Identification of the binding site for acidic phospholipids on the PH domain of dynamin: implications for stimulation of GTPase activity. J. Mol. Biol. 255, 14-21.
18. Salim, K., et al., & Panayotou, G. (1996). Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase. EMBO J. 15, 6241-6250.
19. Touhara, K., Inglese, J., Pitcher, J.A., Shaw, G. & Lefkowitz, R.J. (1994). Binding of G protein beta gamma-subunits to pleckstrin homology domains. J. Biol. Chem. 269, 10217-10220.
20. Konishi, H., et al., & Kikkawa, U. (1995). Molecular cloning and characterization of a new member of the rac protein kinase family. Biochem. Biophys. Res. Commun. 216, 526-534.
21. Gibson, T.J., Hyvo¨nen, M., Musacchio, A. & Saraste, M. (1994). PH domain: the first anniversary. Trends Biochem. Sci. 19, 349-353.
22. Eck, M.J., Dhe-Pagnanon, S., Trüb, T., Nolle, R.T. & Shoelson, S.E. (1996). Structure of the IRS-1 PTB domain bound to the juxtamembrane region of the insulin receptor. Cell 85, 584-592.
23. Zhou, M.-M., et al., & Fesik, S.W. (1996). Structure and ligand recognition of the phosphotyrosine binding domain of She. Nature 378, 584-592.
24. Lemmon, M.A., Ferguson, K.M. & Schlessinger, J. (1996). PH domains: diverse sequence with a common fold recruit signaling molecules to the cell surface. Cell 85, 621-624.
25. Sali, A. & Blundell, T. (1993). Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815.
26. Br̈nger, A.T. (1992). X-PLOR. A System for X-ray Crystallography and NMR. Yale University Press, New Haven, USA.
27. Morris, A.L., MacArthur, M.W., Hutchinson, E.G. & Thornton, J. (1992). Stereochemical quality of protein structure co-ordinates. Proteins 12, 345-364.
28. Sippl, MJ. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins 17, 355-362.
29. Hyvo¨nen, M. & Saraste, M. (1997). Structure of the PH domain and Btk motif from Bruton's tyrosine kinase: molecular explanations for X-linked agammaglobulinaemia. EMBO J. 16, 3396-3404.
30. Sali, A., Potterton, L, Yuan, F., van Vlijmen, H. & Karplus, M. (1995). Evaluation of comparative protein modeling by MODELLER. Proteins 23,318-326.
31. Vriend, G. & Sander, C. (1993). Quality control of protein models: directional atomic contact analysis. J. Appl. Crystallogr. A 26, 47-60.
32. Nicholls, A., Sharp, K. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
33. Shaw, G. (1996). The pleckstrin homology domain: an intriguing multifunctional protein module. Bioessays 18, 35-46.
34. Casari, G., Sander, C. & Valencia, A. (1995). A method to predict functional residues in proteins. Nat. Struct. Biol. 2, 171-178.
35. Koshiba, S., Kigawa, T., Kim, J.-H., Shirouzu, M., Bowtell, D. & Yokoyama, S. (1997). The solution structure of the Pleckstrin homology domain of mouse Son-of-sevenless 1 (mSosI). J. Mol. Biol. 269,579-591.
36. Vihinen, M., et al., & Smith, C.I. (1995). Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry 34, 1475-1481.
37. Harlan, J.E., Yoon, H.S., Hajduk, PJ. & Fesik, S.W. (1995). Structural characterization of the interaction between a pleckstrin homology domain and phosphatidylinositol-4,5-bisphosphate. Biochemistry 34, 9859-9864.
38. Zheng, Y., Zangrilli, D., Cerione, R. & Eva, A. (1996). The pleckstrin homology domain mediates transformation by oncogenic Ddbl through specific intracellular targeting. J. Biol. Chem. 271, 19017-19020.
39. Nilges, M., Clore, G.M. & Gronenborn, A.M. (1987). A simple method for delineating well-defined and variable regions in protein structures determined from interproton distance data. FEBS Lett 219, 17-21.
40. Kraulis, P. (1991). Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. A 24, 946-950.