Diversity in protein recognition by PTB domains

Current Opinion in Structural Biology

Volumn 9, Issue 6, 1999, Pages 690-695

  Forman Kay, Julie D ^a   Pawson, Tony ^b  

^a HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOTYROSINE; PROTEIN;

AMINO ACID SEQUENCE; BINDING SITE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; REVIEW;

EID: 0032776320     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)00031-7     Document Type: Review

References (54)

1. Koch C.A., Anderson D., Moran M.F., Ellis C., Pawson T. SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins. Science. 252:1991;668-674.
2. Pawson T. Protein modules and signaling networks. Nature. 373:1995;573-580.
3. Sudol M. From Src homology domains to other signaling modules: proposal of the 'protein recognition code'. Oncogene. 17:1998;1469-1474. This paper contains a clear presentation of the simple hypothesis of modular binding domains recognizing sequence motifs.
4. van der Geer P., Wiley S., Lai V.K., Olivier J.P., Gish G.D., Stephens R., Kaplan D., Shoelson S., Pawson T. A conserved amino-terminal Shc domain binds to phosphotyrosine motifs in activated receptors and phosphopeptides. Curr Biol. 5:1995;404-412.
5. Blaikie P., Immanuel D., Wu J., Li N., Yajnik V., Margolis B. A region in Shc distinct from the SH2 domain can bind tyrosine-phosphorylated growth factor receptors. J Biol Chem. 269:1994;32031-32034.
6. Kavanaugh W.M., Williams L.T. An alternative to SH2 domains for binding tyrosine-phosphorylated proteins. Science. 266:1994;1862-1865.
7. Cowburn D. Adaptors and integrators. Structure. 4:1996;1005-1008.
8. Cowburn D. Peptide recognition by PTB and PDZ domains. Curr Opin Struct Biol. 7:1997;835-838.
9. Zhou M.M., Fesik S.W. Structure and function of the phosphotyrosine binding (PTB) domain. Prog Biophys Mol Biol. 64:1995;221-235.
10. Zhou Y., Abagyan R. How why phosphotyrosine-containing peptides bind to the SH2 and PTB domains. Fold Des. 3:1998;513-522.
11. van der Geer P., Pawson T. The PTB domain: a new protein module implicated in signal transduction. Trends Biochem Sci. 20:1995;277-280.
12. Kuriyan J., Cowburn D. Modular peptide recognition domains in eukaryotic signaling. Annu Rev Biophys Biomol Struct. 26:1997;259-288.
13. Shoelson S.E. SH2 and PTB domain interactions in tyrosine kinase signal transduction. Curr Opin Chem Biol. 1:1997;227-234.
14. Sudol M. Structure and function of the WW domain. Prog Biophys Mol Biol. 65:1996;113-132.
15. Fedorov A.A., Fedorov E., Gertler F., Almo S.C. Structure of EVH1, a novel proline-rich ligand-binding module involved in cytoskeletal dynamics and neural function. Nat Struct Biol. 6:1999;661-665. This paper describing the structure of the EVH1 domain complexed with a proline-rich ligand presents a nice comparison of the topologies of pleckstrin homology, EVH1, ran-binding and PTB domains, as well as a discussion of the multiple domains binding proline-rich ligands.
16. Mahoney N.M., Rozwarski D.A., Fedorov E., Fedorov A.A., Almo S.C. Profilin binds proline-rich ligands in two distinct amide backbone orientations. Nat Struct Biol. 6:1999;666-671.
17. Freund C., Dotsch V., Nishizawa K., Reinherz E.L., Wagner G. The GYF domain is a novel structural fold that is involved in lymphoid signaling through proline-rich sequences. Nat Struct Biol. 6:1999;656-660.
18. Zhou M.M., Ravichandran K.S., Olejniczak E.F., Petros A.M., Meadows R.P., Sattler M., Harlan J.E., Wade W.S., Burakoff S.J., Fesik S.W. Structure and ligand recognition of the phosphotyrosine binding domain of Shc. Nature. 378:1995;584-592.
19. Songyang Z., Margolis B., Chaudhuri M., Shoelson S.E., Cantley L.C. The phosphotyrosine interaction domain of SHC recognizes tyrosine-phosphorylated NPXY and motif. J Biol Chem. 270:1995;14863-14866.
20. Wolf G., Trub T., Ottinger E., Groninga L., Lynch A., White M.F., Miyazaki M., Lee J., Shoelson S.E. PTB domains of IRS1 and Shc have distinct but overlapping binding specificities. J Biol Chem. 270:1995;27407-27410.
21. Bonita D.P., Miyake S., Lupher M.L. Jr., Langdon W.Y., Band H. Phosphotyrosine binding domain-dependent upregulation of the platelet-derived growth factor receptor alpha signaling cascade by transforming mutants of Cbl: implications for Cbl's function and oncogenicity. Mol Cell Biol. 17:1997;4597-4610.
22. Lupher M.L. Jr., Songyang Z., Shoelson S.E., Cantley L.C., Band H. The Cbl phosphotyrosine-binding domain selects a D(N/D)XpY motif and binds to the Tyr292 negative regulatory phosphorylation site of ZAP-70. J Biol Chem. 272:1997;33140-33144.
23. Meng W., Sawasdikosol S., Burakoff S.J., Eck M.J. Structure of the amino-terminal domain of Cbl complexed to its binding site on ZAP-70 kinase. Nature. 398:1999;84-90. The authors describe the structure of the Cbl binding domain, which was originally identified as a PTB domain, and reveal its Src homology 2 domain fold.
24. Eck M.J., Dhe-Paganon S., Trub T., Nolte R.T., Shoelson S.E. Structure of the IRS1 PTB domain bound to the juxtamembrane region of the insulin receptor. Cell. 85:1996;695-705.
25. Zhou M.M., Huang B., Olejniczak E.T., Meadows R.P., Shuker S.B., Miyazaki M., Trub T., Shoelson S.E., Fesik S.W. Structural basis for IL4 receptor phosphopeptide recognition by the IRS-1 PTB domain. Nat Struct Biol. 3:1996;388-393.
26. Yoon H.S., Hajduk P.J., Petros A.M., Olejniczak E.T., Meadows R.P., Fesik S.W. Solution structure of a pleckstrin-homology domain. Nature. 369:1994;672-675.
27. Ogura K., Tsuchiya S., Terasawa H., Yuzawa S., Hatanaka H., Mandiyan V., Schlessinger J., Inagaki F. Solution structure of the SH2 domain of Grb2 complexed with the Shc-derived phosphotyrosine-containing peptide. J Mol Biol. 289:1999;439-445.
28. Li S.C., Zwahlen C., Vincent S.J., McGlade C.J., Kay L.E., Pawson T., Forman-Kay J.D. Structure of a Numb PTB domain-peptide complex suggests a basis for diverse binding specificity. Nat Struct Biol. 5:1998;1075-1083. The structure of the Numb phosphotyrosine-binding (PTB) domain-GPpY peptide complex exhibits a significantly different binding mode compared to previously determined PTB domain-peptide complexes. In particular, the peptide has a helical conformation, rather than forming an extended chain with hydrogen-bond interactions with strand β5 of the PTB domain.
29. Borg J.P., Ooi J., Levy E., Margolis B. The phosphotyrosine interaction domains of X11 and FE65 bind to distinct sites on the YENPTY motif of amyloid precursor protein. Mol Cell Biol. 16:1996;6229-6241.
30. Howell B.W., Lanier L.M., Frank R., Gertler F.B., Cooper J.A. The disabled 1 phosphotyrosine-binding domain binds to the internalization signals of transmembrane glycoproteins and to phospholipids. Mol Cell Biol. 19:1999;5179-5188. The binding of the mammalian Dab (Disabled) PTB domain to both non-phosphorylated protein and lipid targets in a noncompetitive manner is described. Of significant interest is that phosphorylation of the target protein abolishes binding, providing strong evidence that the specificity of each PTB domain is unique.
31. Zambrano N., Buxbaum J.D., Minopoli G., Fiore F., De Candia P., De Renzis S., Faraonio R., Sabo S., Cheetham J., Sudol M., Russo T. Interaction of the phosphotyrosine interaction/phosphotyrosine binding-related domains of Fe65 with wild-type and mutant Alzheimer's beta-amyloid precursor proteins. J Biol Chem. 272:1997;6399-6405.
32. Zhang Z., Lee C.H., Mandiyan V., Borg J.P., Margolis B., Schlessinger J., Kuriyan J. Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain. EMBO J. 16:1997;6141-6150.
33. Prehoda K.E., Lee D.J., Lim W.A. Structure of the enabled/VASP homology 1 domain-peptide complex: a key component in the spatial control of actin assembly. Cell. 97:1999;471-480.
34. Callebaut I., Cossart P., Dehoux P. EVH1/WH1 domains of VASP and WASP proteins belong to a large family including Ran-binding domains of the RanBP1 family. FEBS Lett. 441:1998;181-185.
35. Vetter I.R., Nowak C., Nishimoto T., Kuhlmann J., Wittinghofer A. Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport. Nature. 398:1999;39-46.
36. Ravichandran K.S., Zhou M.M., Pratt J.C., Harlan J.E., Walk S.F., Fesik S.W., Burakoff S.J. Evidence for a requirement for both phospholipid and phosphotyrosine binding via the Shc phosphotyrosine-binding domain in vivo. Mol Cell Biol. 17:1997;5540-5549.
37. •].
38. •], provides the first description of non-pTyr-dependent Src homology 2 (SH2) domain interactions, the first involving SAP SH2 and its SLAM target and the second involving Grb10 SH2 and its target in the C2 domain of Nedd4.
39. Li S.C., Songyang Z., Vincent S.J., Zwahlen C., Wiley S., Cantley L., Kay L.E., Forman-Kay J., Pawson T. High-affinity binding of the Drosophila Numb phosphotyrosine-binding domain to peptides containing a Gly-Pro-(p)Tyr motif. Proc Natl Acad Sci USA. 94:1997;7204-7209.
40. Juven-Gershon T., Shifman O., Unger T., Elkeles A., Haupt Y., Oren M. The Mdm2 oncoprotein interacts with the cell fate regulator Numb. Mol Cell Biol. 18:1998;3974-3982. A sequence of the mdm2 protein shares significant sequence similarity with the GPpY peptide (identified from library screening). This suggests that the Numb PTB domain mediates a specific interaction with mdm2 via this sequence.
41. Chien C.T., Wang S., Rothenberg M., Jan L.Y., Jan Y.N. Numb-associated kinase interacts with the phosphotyrosine binding domain of Numb and antagonizes the function of Numb in vivo. Mol Cell Biol. 18:1998;598-607.
42. Dho S.E., Jacob S., Wolting C.D., French M.B., Rohrschneider L.R., McGlade C.J. The mammalian numb phosphotyrosine-binding domain. Characterization of binding specificity and identification of a novel PDZ domain-containing numb binding protein, LNX. J Biol Chem. 273:1998;9179-9187.
43. Sicheri F., Moarefi I., Kuriyan J. Crystal structure of the Src family tyrosine kinase Hck. Nature. 385:1997;602-609.
44. Xu W., Harrison S.C., Eck M.J. Three-dimensional structure of the tyrosine kinase c-Src. Nature. 385:1997;595-602.
45. McGee A.W., Bredt D.S. Identification of an intramolecular interaction between the SH3 and guanylate kinase domains of PSD-95. J Biol Chem. 274:1999;17431-17436.
46. Dho S.E., French M.B., Woods S.A., McGlade C.J. Characterization of four mammalian Numb protein isoforms: identification of cytoplasmic and membrane associated variants of the phosphotyrosine binding domain. J Biol Chem. 274:1999;33097-33104. The identification of differentially localized mammalian Numb isoforms that differ in the presence or absence of an insertion into the PTB domain is suggestive of a second target-binding site in the Numb PTB domain.
47. Dhe-Paganon S., Ottinger E.A., Nolte R.T., Eck M.J., Shoelson S.E. Crystal structure of the pleckstrin homology-phosphotyrosine binding (PH-PTB) targeting region of insulin receptor substrate 1. Proc Natl Acad Sci USA. 96:1999;8378-8383. The interdomain interactions in the structure of a PH and PTB domain-containing fragment of IRS-1 may reveal additional protein recognition surfaces of the two domains.
48. Ferguson K.M., Lemmon M.A., Schlessinger J., Sigler P.B. Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain. Cell. 83:1995;1037-1046.
49. Hyvonen M., Macias M.J., Nilges M., Oschkinat H., Saraste M., Wilmanns M. Structure of the binding site for inositol phosphates in a PH domain. EMBO J. 14:1995;4676-4685.
50. Baraldi E., Carugo K.D., Hyvonen M., Surdo P.L., Riley A.M., Potter B.V., O'Brien R., Ladbury J.E., Saraste M. Structure of the PH domain from Bruton's tyrosine kinase in complex with inositol 1,3,4,5-tetrakisphosphate. Structure. 7:1999;449-460.
51. Hyvonen M., Saraste M. Structure of the PH domain and Btk motif from Bruton's tyrosine kinase: molecular explanations for X-linked agammaglobulinaemia. EMBO J. 16:1997;3396-3404.
52. Pascal S.M., Singer A.U., Gish G., Yamazaki T., Shoelson S.E., Pawson T., Kay L.E., Forman-Kay J.D. Nuclear magnetic resonance structure of an SH2 domain of phospholipase C-gamma 1 complexed with a high affinity binding peptide. Cell. 77:1994;461-472.
53. Alexandrov N.N. SARFing the PDB. Protein Eng. 9:1996;727-732.
54. Kraulis P.J. Molscript: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr. 24:1991;946-950.