Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation (original) (raw)

Abstract

The amphiphysins are brain-enriched proteins, implicated in clathrin-mediated endocytosis, that interact with dynamin through their SH3 domains. To elucidate the nature of this interaction, we have solved the crystal structure of the amphiphysin-2 (Amph2) SH3 domain to 2.2 A. The structure possesses several notable features, including an extensive patch of negative electrostatic potential covering a large portion of its dynamin binding site. This patch accounts for the specific requirement of amphiphysin for two arginines in the proline-rich binding motif to which it binds on dynamin. We demonstrate that the interaction of dynamin with amphiphysin SH3 domains, unlike that with SH3 domains of Grb2 or spectrin, prevents dynamin self-assembly into rings. Deletion of a unique insert in the n-Src loop of Amph2 SH3, a loop adjacent to the dynamin binding site, significantly reduces this effect. Conversely, replacing the n-Src loop of the N-terminal SH3 domain of Grb2 with that of Amph2 causes it to favour dynamin ring disassembly. Transferrin uptake assays show that shortening the n-Src loop of Amph2 SH3 reduces the ability of this domain to inhibit endocytosis in vivo. Our data suggest that amphiphysin SH3 domains are important regulators of the multimerization cycle of dynamin in endocytosis.

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Selected References

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  1. Abrahams J. P., Leslie A. G. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):30–42. doi: 10.1107/S0907444995008754. [DOI] [PubMed] [Google Scholar]
  2. Barylko B., Binns D., Lin K. M., Atkinson M. A., Jameson D. M., Yin H. L., Albanesi J. P. Synergistic activation of dynamin GTPase by Grb2 and phosphoinositides. J Biol Chem. 1998 Feb 6;273(6):3791–3797. doi: 10.1074/jbc.273.6.3791. [DOI] [PubMed] [Google Scholar]
  3. Bauerfeind R., Takei K., De Camilli P. Amphiphysin I is associated with coated endocytic intermediates and undergoes stimulation-dependent dephosphorylation in nerve terminals. J Biol Chem. 1997 Dec 5;272(49):30984–30992. doi: 10.1074/jbc.272.49.30984. [DOI] [PubMed] [Google Scholar]
  4. Butler M. H., David C., Ochoa G. C., Freyberg Z., Daniell L., Grabs D., Cremona O., De Camilli P. Amphiphysin II (SH3P9; BIN1), a member of the amphiphysin/Rvs family, is concentrated in the cortical cytomatrix of axon initial segments and nodes of ranvier in brain and around T tubules in skeletal muscle. J Cell Biol. 1997 Jun 16;137(6):1355–1367. doi: 10.1083/jcb.137.6.1355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carr J. F., Hinshaw J. E. Dynamin assembles into spirals under physiological salt conditions upon the addition of GDP and gamma-phosphate analogues. J Biol Chem. 1997 Oct 31;272(44):28030–28035. doi: 10.1074/jbc.272.44.28030. [DOI] [PubMed] [Google Scholar]
  6. Damke H., Baba T., Warnock D. E., Schmid S. L. Induction of mutant dynamin specifically blocks endocytic coated vesicle formation. J Cell Biol. 1994 Nov;127(4):915–934. doi: 10.1083/jcb.127.4.915. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. David C., McPherson P. S., Mundigl O., de Camilli P. A role of amphiphysin in synaptic vesicle endocytosis suggested by its binding to dynamin in nerve terminals. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):331–335. doi: 10.1073/pnas.93.1.331. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. David C., Solimena M., De Camilli P. Autoimmunity in stiff-Man syndrome with breast cancer is targeted to the C-terminal region of human amphiphysin, a protein similar to the yeast proteins, Rvs167 and Rvs161. FEBS Lett. 1994 Aug 29;351(1):73–79. doi: 10.1016/0014-5793(94)00826-4. [DOI] [PubMed] [Google Scholar]
  9. De Camilli P., Takei K., McPherson P. S. The function of dynamin in endocytosis. Curr Opin Neurobiol. 1995 Oct;5(5):559–565. doi: 10.1016/0959-4388(95)80059-x. [DOI] [PubMed] [Google Scholar]
  10. Diederichs K., Karplus P. A. Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol. 1997 Apr;4(4):269–275. doi: 10.1038/nsb0497-269. [DOI] [PubMed] [Google Scholar]
  11. Feng S., Chen J. K., Yu H., Simon J. A., Schreiber S. L. Two binding orientations for peptides to the Src SH3 domain: development of a general model for SH3-ligand interactions. Science. 1994 Nov 18;266(5188):1241–1247. doi: 10.1126/science.7526465. [DOI] [PubMed] [Google Scholar]
  12. Folli F., Solimena M., Cofiell R., Austoni M., Tallini G., Fassetta G., Bates D., Cartlidge N., Bottazzo G. F., Piccolo G. Autoantibodies to a 128-kd synaptic protein in three women with the stiff-man syndrome and breast cancer. N Engl J Med. 1993 Feb 25;328(8):546–551. doi: 10.1056/NEJM199302253280805. [DOI] [PubMed] [Google Scholar]
  13. González-Gaitán M., Jäckle H. Role of Drosophila alpha-adaptin in presynaptic vesicle recycling. Cell. 1997 Mar 21;88(6):767–776. doi: 10.1016/s0092-8674(00)81923-6. [DOI] [PubMed] [Google Scholar]
  14. Gout I., Dhand R., Hiles I. D., Fry M. J., Panayotou G., Das P., Truong O., Totty N. F., Hsuan J., Booker G. W. The GTPase dynamin binds to and is activated by a subset of SH3 domains. Cell. 1993 Oct 8;75(1):25–36. [PubMed] [Google Scholar]
  15. Grabs D., Slepnev V. I., Songyang Z., David C., Lynch M., Cantley L. C., De Camilli P. The SH3 domain of amphiphysin binds the proline-rich domain of dynamin at a single site that defines a new SH3 binding consensus sequence. J Biol Chem. 1997 May 16;272(20):13419–13425. doi: 10.1074/jbc.272.20.13419. [DOI] [PubMed] [Google Scholar]
  16. Herskovits J. S., Burgess C. C., Obar R. A., Vallee R. B. Effects of mutant rat dynamin on endocytosis. J Cell Biol. 1993 Aug;122(3):565–578. doi: 10.1083/jcb.122.3.565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hinshaw J. E., Schmid S. L. Dynamin self-assembles into rings suggesting a mechanism for coated vesicle budding. Nature. 1995 Mar 9;374(6518):190–192. doi: 10.1038/374190a0. [DOI] [PubMed] [Google Scholar]
  18. Jones T. A., Zou J. Y., Cowan S. W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. doi: 10.1107/s0108767390010224. [DOI] [PubMed] [Google Scholar]
  19. Kosaka T., Ikeda K. Possible temperature-dependent blockage of synaptic vesicle recycling induced by a single gene mutation in Drosophila. J Neurobiol. 1983 May;14(3):207–225. doi: 10.1002/neu.480140305. [DOI] [PubMed] [Google Scholar]
  20. Leprince C., Romero F., Cussac D., Vayssiere B., Berger R., Tavitian A., Camonis J. H. A new member of the amphiphysin family connecting endocytosis and signal transduction pathways. J Biol Chem. 1997 Jun 13;272(24):15101–15105. doi: 10.1074/jbc.272.24.15101. [DOI] [PubMed] [Google Scholar]
  21. Lichte B., Veh R. W., Meyer H. E., Kilimann M. W. Amphiphysin, a novel protein associated with synaptic vesicles. EMBO J. 1992 Jul;11(7):2521–2530. doi: 10.1002/j.1460-2075.1992.tb05317.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lim W. A., Richards F. M., Fox R. O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature. 1994 Nov 24;372(6504):375–379. doi: 10.1038/372375a0. [DOI] [PubMed] [Google Scholar]
  23. Maignan S., Guilloteau J. P., Fromage N., Arnoux B., Becquart J., Ducruix A. Crystal structure of the mammalian Grb2 adaptor. Science. 1995 Apr 14;268(5208):291–293. doi: 10.1126/science.7716522. [DOI] [PubMed] [Google Scholar]
  24. Marks B., McMahon H. T. Calcium triggers calcineurin-dependent synaptic vesicle recycling in mammalian nerve terminals. Curr Biol. 1998 Jun 18;8(13):740–749. doi: 10.1016/s0960-9822(98)70297-0. [DOI] [PubMed] [Google Scholar]
  25. Maycox P. R., Link E., Reetz A., Morris S. A., Jahn R. Clathrin-coated vesicles in nervous tissue are involved primarily in synaptic vesicle recycling. J Cell Biol. 1992 Sep;118(6):1379–1388. doi: 10.1083/jcb.118.6.1379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. McClure S. J., Robinson P. J. Dynamin, endocytosis and intracellular signalling (review). Mol Membr Biol. 1996 Oct-Dec;13(4):189–215. doi: 10.3109/09687689609160598. [DOI] [PubMed] [Google Scholar]
  27. McMahon H. T., Wigge P., Smith C. Clathrin interacts specifically with amphiphysin and is displaced by dynamin. FEBS Lett. 1997 Aug 18;413(2):319–322. doi: 10.1016/s0014-5793(97)00928-9. [DOI] [PubMed] [Google Scholar]
  28. McPherson P. S., Garcia E. P., Slepnev V. I., David C., Zhang X., Grabs D., Sossin W. S., Bauerfeind R., Nemoto Y., De Camilli P. A presynaptic inositol-5-phosphatase. Nature. 1996 Jan 25;379(6563):353–357. doi: 10.1038/379353a0. [DOI] [PubMed] [Google Scholar]
  29. Micheva K. D., Ramjaun A. R., Kay B. K., McPherson P. S. SH3 domain-dependent interactions of endophilin with amphiphysin. FEBS Lett. 1997 Sep 8;414(2):308–312. doi: 10.1016/s0014-5793(97)01016-8. [DOI] [PubMed] [Google Scholar]
  30. Morris S. A., Schmid S. L. Synaptic vesicle recycling. The Ferrari of endocytosis? Curr Biol. 1995 Feb 1;5(2):113–115. doi: 10.1016/s0960-9822(95)00028-5. [DOI] [PubMed] [Google Scholar]
  31. Muhlberg A. B., Warnock D. E., Schmid S. L. Domain structure and intramolecular regulation of dynamin GTPase. EMBO J. 1997 Nov 17;16(22):6676–6683. doi: 10.1093/emboj/16.22.6676. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Murshudov G. N., Vagin A. A., Dodson E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240–255. doi: 10.1107/S0907444996012255. [DOI] [PubMed] [Google Scholar]
  33. Musacchio A., Noble M., Pauptit R., Wierenga R., Saraste M. Crystal structure of a Src-homology 3 (SH3) domain. Nature. 1992 Oct 29;359(6398):851–855. doi: 10.1038/359851a0. [DOI] [PubMed] [Google Scholar]
  34. Musacchio A., Saraste M., Wilmanns M. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nat Struct Biol. 1994 Aug;1(8):546–551. doi: 10.1038/nsb0894-546. [DOI] [PubMed] [Google Scholar]
  35. Nachshen D. A., Drapeau P. The regulation of cytosolic pH in isolated presynaptic nerve terminals from rat brain. J Gen Physiol. 1988 Feb;91(2):289–303. doi: 10.1085/jgp.91.2.289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Noble M. E., Musacchio A., Saraste M., Courtneidge S. A., Wierenga R. K. Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin. EMBO J. 1993 Jul;12(7):2617–2624. doi: 10.2210/pdb1shf/pdb. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Okamoto P. M., Herskovits J. S., Vallee R. B. Role of the basic, proline-rich region of dynamin in Src homology 3 domain binding and endocytosis. J Biol Chem. 1997 Apr 25;272(17):11629–11635. doi: 10.1074/jbc.272.17.11629. [DOI] [PubMed] [Google Scholar]
  38. Pawson T., Schlessingert J. SH2 and SH3 domains. Curr Biol. 1993 Jul 1;3(7):434–442. doi: 10.1016/0960-9822(93)90350-w. [DOI] [PubMed] [Google Scholar]
  39. Pearse B. M., Robinson M. S. Clathrin, adaptors, and sorting. Annu Rev Cell Biol. 1990;6:151–171. doi: 10.1146/annurev.cb.06.110190.001055. [DOI] [PubMed] [Google Scholar]
  40. Poodry C. A., Edgar L. Reversible alteration in the neuromuscular junctions of Drosophila melanogaster bearing a temperature-sensitive mutation, shibire. J Cell Biol. 1979 Jun;81(3):520–527. doi: 10.1083/jcb.81.3.520. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Ramjaun A. R., Micheva K. D., Bouchelet I., McPherson P. S. Identification and characterization of a nerve terminal-enriched amphiphysin isoform. J Biol Chem. 1997 Jun 27;272(26):16700–16706. doi: 10.1074/jbc.272.26.16700. [DOI] [PubMed] [Google Scholar]
  42. Ringstad N., Nemoto Y., De Camilli P. The SH3p4/Sh3p8/SH3p13 protein family: binding partners for synaptojanin and dynamin via a Grb2-like Src homology 3 domain. Proc Natl Acad Sci U S A. 1997 Aug 5;94(16):8569–8574. doi: 10.1073/pnas.94.16.8569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Sakamuro D., Elliott K. J., Wechsler-Reya R., Prendergast G. C. BIN1 is a novel MYC-interacting protein with features of a tumour suppressor. Nat Genet. 1996 Sep;14(1):69–77. doi: 10.1038/ng0996-69. [DOI] [PubMed] [Google Scholar]
  44. Salim K., Bottomley M. J., Querfurth E., Zvelebil M. J., Gout I., Scaife R., Margolis R. L., Gigg R., Smith C. I., Driscoll P. C. Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase. EMBO J. 1996 Nov 15;15(22):6241–6250. [PMC free article] [PubMed] [Google Scholar]
  45. Scaife R., Gout I., Waterfield M. D., Margolis R. L. Growth factor-induced binding of dynamin to signal transduction proteins involves sorting to distinct and separate proline-rich dynamin sequences. EMBO J. 1994 Jun 1;13(11):2574–2582. doi: 10.1002/j.1460-2075.1994.tb06547.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Seedorf K., Kostka G., Lammers R., Bashkin P., Daly R., Burgess W. H., van der Bliek A. M., Schlessinger J., Ullrich A. Dynamin binds to SH3 domains of phospholipase C gamma and GRB-2. J Biol Chem. 1994 Jun 10;269(23):16009–16014. [PubMed] [Google Scholar]
  47. Shpetner H. S., Herskovits J. S., Vallee R. B. A binding site for SH3 domains targets dynamin to coated pits. J Biol Chem. 1996 Jan 5;271(1):13–16. doi: 10.1074/jbc.271.1.13. [DOI] [PubMed] [Google Scholar]
  48. Shupliakov O., Löw P., Grabs D., Gad H., Chen H., David C., Takei K., De Camilli P., Brodin L. Synaptic vesicle endocytosis impaired by disruption of dynamin-SH3 domain interactions. Science. 1997 Apr 11;276(5310):259–263. doi: 10.1126/science.276.5310.259. [DOI] [PubMed] [Google Scholar]
  49. Sparks A. B., Hoffman N. G., McConnell S. J., Fowlkes D. M., Kay B. K. Cloning of ligand targets: systematic isolation of SH3 domain-containing proteins. Nat Biotechnol. 1996 Jun;14(6):741–744. doi: 10.1038/nbt0696-741. [DOI] [PubMed] [Google Scholar]
  50. Takei K., McPherson P. S., Schmid S. L., De Camilli P. Tubular membrane invaginations coated by dynamin rings are induced by GTP-gamma S in nerve terminals. Nature. 1995 Mar 9;374(6518):186–190. doi: 10.1038/374186a0. [DOI] [PubMed] [Google Scholar]
  51. Theriot J. A., Mitchison T. J. The three faces of profilin. Cell. 1993 Dec 3;75(5):835–838. doi: 10.1016/0092-8674(93)90527-w. [DOI] [PubMed] [Google Scholar]
  52. Tsutsui K., Maeda Y., Tsutsui K., Seki S., Tokunaga A. cDNA cloning of a novel amphiphysin isoform and tissue-specific expression of its multiple splice variants. Biochem Biophys Res Commun. 1997 Jul 9;236(1):178–183. doi: 10.1006/bbrc.1997.6927. [DOI] [PubMed] [Google Scholar]
  53. Tuma P. L., Collins C. A. Dynamin forms polymeric complexes in the presence of lipid vesicles. Characterization of chemically cross-linked dynamin molecules. J Biol Chem. 1995 Nov 3;270(44):26707–26714. doi: 10.1074/jbc.270.44.26707. [DOI] [PubMed] [Google Scholar]
  54. Volchuk A., Narine S., Foster L. J., Grabs D., De Camilli P., Klip A. Perturbation of dynamin II with an amphiphysin SH3 domain increases GLUT4 glucose transporters at the plasma membrane in 3T3-L1 adipocytes. Dynamin II participates in GLUT4 endocytosis. J Biol Chem. 1998 Apr 3;273(14):8169–8176. doi: 10.1074/jbc.273.14.8169. [DOI] [PubMed] [Google Scholar]
  55. Wang L. H., Südhof T. C., Anderson R. G. The appendage domain of alpha-adaptin is a high affinity binding site for dynamin. J Biol Chem. 1995 Apr 28;270(17):10079–10083. doi: 10.1074/jbc.270.17.10079. [DOI] [PubMed] [Google Scholar]
  56. Warnock D. E., Baba T., Schmid S. L. Ubiquitously expressed dynamin-II has a higher intrinsic GTPase activity and a greater propensity for self-assembly than neuronal dynamin-I. Mol Biol Cell. 1997 Dec;8(12):2553–2562. doi: 10.1091/mbc.8.12.2553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Wigge P., Köhler K., Vallis Y., Doyle C. A., Owen D., Hunt S. P., McMahon H. T. Amphiphysin heterodimers: potential role in clathrin-mediated endocytosis. Mol Biol Cell. 1997 Oct;8(10):2003–2015. doi: 10.1091/mbc.8.10.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wigge P., McMahon H. T. The amphiphysin family of proteins and their role in endocytosis at the synapse. Trends Neurosci. 1998 Aug;21(8):339–344. doi: 10.1016/s0166-2236(98)01264-8. [DOI] [PubMed] [Google Scholar]
  59. Wigge P., Vallis Y., McMahon H. T. Inhibition of receptor-mediated endocytosis by the amphiphysin SH3 domain. Curr Biol. 1997 Aug 1;7(8):554–560. doi: 10.1016/s0960-9822(06)00254-5. [DOI] [PubMed] [Google Scholar]
  60. Wu X., Knudsen B., Feller S. M., Zheng J., Sali A., Cowburn D., Hanafusa H., Kuriyan J. Structural basis for the specific interaction of lysine-containing proline-rich peptides with the N-terminal SH3 domain of c-Crk. Structure. 1995 Feb 15;3(2):215–226. doi: 10.1016/s0969-2126(01)00151-4. [DOI] [PubMed] [Google Scholar]
  61. van der Bliek A. M., Redelmeier T. E., Damke H., Tisdale E. J., Meyerowitz E. M., Schmid S. L. Mutations in human dynamin block an intermediate stage in coated vesicle formation. J Cell Biol. 1993 Aug;122(3):553–563. doi: 10.1083/jcb.122.3.553. [DOI] [PMC free article] [PubMed] [Google Scholar]