Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions

Protein Science

Volumn 16, Issue 4, 2007, Pages 683-694

  Elkins, Jonathan M ^a   Papagrigoriou, Evangelos ^a   Berridge, Georgina ^a   Yang, Xiaowen ^a   Phillips, Claire ^a   Gileadi, Carina ^a   Savitsky, Pavel ^a   Doyle, Declan A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Crystallization; DLG2; DLG3; MPDZ; NHERF 2; PDZ; PDZ domain; PICK1

Indexed keywords

GUANYLATE KINASE; PDZ PROTEIN; PROTEIN DLG2; PROTEIN INTERACTING WITH PROTEIN KINASE C; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTALLIZATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN PURIFICATION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CARRIER PROTEINS; CLONING, MOLECULAR; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 33947712970     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062657507     Document Type: Article

References (50)

1. Appleton, B.A., Zhang, Y., Wu, P., Yin, J.P., Hunziker, W., Skelton, N.J., Sidhu, S.S., and Wiesmann, C. 2006. Comparative structural analysis of the erbin PDZ domain and the first PDZ domain of ZO-1. J. Biol. Chem. 281: 22312-22320.
2. Bellone, C. and Lüscher, C. 2006. Cocaine triggered AMPA receptor redistribution is reversed in vivo by mGluR-dependent long-term depression. Nat. Neurosci. 9: 636-641.
3. Beuming, T., Skrabanek, L., Niv, M.Y., Mukherjee, P., and Weinstein, H. 2005. PDZBase: A protein-protein interaction database for PDZ-domains. Bioinformatics 21: 827-828.
4. Collaborative Computational Project Number 4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D50: 760-763.
5. Coyne, C.B., Voelker, T., Pichla, S.L., and Bergelson, J.M. 2004. The coxsackievirus and adenovirus receptor interacts with the multi-PDZ domain protein-1 (MUPP-1) within the tight junction. J. Biol. Chem. 279: 48079-48084.
6. Dev, K.K. 2004. Making protein interactions druggable: Targeting PDZ domains. Nat. Rev. Drug Discov. 3: 1047-1056.
7. Dev, K.K. and Henley, J.M. 2006. The schizophrenic faces of PICK1. Trends Pharmacol. Sci. 27: 574-579.
8. Dev, K.K., Nakanishi, S., and Henley, J.M. 2004. The PDZ domain of PICK1 differentially accepts protein kinase C-α and GluR2 as interacting ligands. J. Biol. Chem. 279: 41393-41397.
9. Doyle, D.A., Lee, A., Lewis, J., Kim, E., Sheng, M., and MacKinnon, R. 1996. Crystal structures of a complexed and peptide-free membrane protein-binding domain: Molecular basis of peptide recognition by PDZ. Cell 85: 1067-1076.
10. 2+ channel TRPV5 by the NHE regulating factor NHERF2 and the serum and glucocorticoid inducible kinase isoforms SGK1 and SGK3 expressed in Xenopus oocytes. Cell. Physiol. Biochem. 15: 203-212.
11. Emsley, P. and Cowtan, K. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D60: 2126-2132.
12. Fam, S.R., Paquet, M., Castleberry, A.M., Oller, H., Lee, C.J., Traynelis, S.F., Smith, Y., Yun, C.C., and Hall, R.A. 2004. P2Y1 receptor signaling is controlled by interaction with the PDZ scaffold NHERF-2. Proc. Natl. Acad. Sci. 102: 8042-8047.
13. Fujii, K., Maeda, K., Hikida, T., Mustafa, A.K., Balkissoon, R., Xia, J., Yamada, T., Ozeki, Y., Kawahara, R., Okawa, M., et al. 2006. Serine racemanse binds to PICK1: Potential relevance to schizophrenia. Mol. Psychiatry 11: 150-157.
14. Grembecka, J., Cierpicki, T., Devedjiev, Y., Derewenda, U., Kang, B.S., Bushweller, J.H., and Derewenda, Z.S. 2006. The binding of the PDZ tandem of syntenin to target proteins. Biochemistry 45: 3674-3683.
15. Hamazaki, Y., Itoh, M., Sasaki, H., Furuse, M., and Tsukita, S. 2002. Multi-PDZ domain protein 1 (MUPP1) is concentrated at tight junctions through its possible interaction with claudin-1 and junctional adhesion molecule. J. Biol. Chem. 277: 455-461.
16. Harris, B.Z. and Lim, W.A. 2001. Mechanism and role of PDZ domains in signaling complex assembly. J. Cell Sci. 114: 3219-3231.
17. Hillier, B.J., Christopherson, K.S., Prehoda, K.E., Bredt, D.S., and Lim, W.A. 1999. Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex. Science 284: 812-815.
18. Hong, C.-J., Liao, D.-L., Shih, H.-L., and Tsai, S.-J. 2004. Association study of PICK1 rs3952 polymorphism and schizophrenia. Neuroreport 15: 1965-1967.
19. Hung, A.Y. and Sheng, M. 2002. PDZ domains: Structural modules for protein complex assembly. J. Biol. Chem. 277: 5699-5702.
20. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47: 110-119.
21. + exchanger regulatory factor PDZ1 interaction with the carboxyl-terminal region of the cystic fibrosis transmembrane conductance regulator. J. Biol. Chem. 276: 19683-19686.
22. Kim, E. and Sheng, M. 2004. PDZ domain proteins of synapses. Nat. Rev. Neurosci. 5: 771-781.
23. 2 and the multi-PDZ-domain-containing protein MUPP1 in vivo. Biochem. J. 361: 525-536.
24. + exchange. Biochemistry 41: 12336-12342.
25. Lee, S.S., Glaunsinger, B., Mantovani, F., Banks, L., and Javier, R.T. 2000. Multi-PDZ domain protein MUPP1 is a cellular target for both adenovirus E4-ORF1 and high-risk papillomavirus type 18 E6 oncoproteins. J. Virol. 74: 9680-9693.
26. Leslie, A.G.W. 1999. Integration of macromolecular diffraction data. Acta Crystallogr. D55: 1696-1702.
27. Leyland, M.L. and Dart, C. 2004. An alternatively spliced isoform of PSD-93/chapsyn 110 binds to the inwardly rectifying potassium channel, Kir2.1. J. Biol. Chem. 279: 43427-43436.
28. Madsen, K.L., Beuming, T., Niv, M.Y., Chang, C.-W., Dev, K.K., Weinstein, H., and Gether, U. 2005. Molecular determinants for the complex binding specificity of the PDZ domain in PICK1. J. Biol. Chem. 280: 20539-20548.
29. McGuffin, L.J. and Jones, D.T. 2003. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.
30. Morais Cabral, J.H., Petosa, C., Sutcliffe, M.J., Raza, S., Byron, O., Poy, F., Marfatia, S.M., Chishti, A.H., and Liddington, R.C. 1996. Crystal structure of a PDZ domain. Nature 382: 649-652.
31. Murshudov, G.N., Vagin, A.A., Lebedev, A., Wilson, K.S., and Dodson, E.J. 1999. Efficient anisotropic refinement of macromolecular structures using FFT. Acta Crystallogr. D55: 247-255.
32. 2 receptor and defines the specificity and efficiency of receptor-mediated phospholipase C-β3 activation. Mol. Cell. Biol. 24: 5069-5079.
33. Otwinowski, Z. and Minor, W. 1997. Processing of x-ray diffraction data collected in oscillation mode. In Methods in enzymology, (eds. C.W. Carter and R.M. Sweet), pp. 307-326. Academic Press, New York.
34. 2+ channel TRPV5 by the NHE regulating factor NHERF2 and the serum and glucocorticoid inducible kinase SGK1. Cell. Physiol. Biochem. 15: 175-182.
35. Peter, B.J., Kent, H.M., Mills, I.G., Vallis, Y., Butler, P.J.G., Evans, P.R., and McMahon, H.T. 2004. BAR domains as sensors of membrane curvature: The amphiphysin BAR structure. Science 303: 495-499.
36. Schultz, J., Milpetz, F., Bork, P., and Ponting, C.P. 1998. SMART, a simple modular architecture research tool: Identification of signaling domains. Proc. Natl. Acad. Sci. 95: 5857-5864.
37. Sheng, M. and Sala, C. 2001. PDZ domains and the organization of supramolecular complexes. Annu. Rev. Neurosci. 24: 1-29.
38. Songyang, Z., Fanning, A.S., Fu, C., Xu, J., Marfatia, S.M., Chishti, A.H., Crompton, A., Chan, A.C., Anderson, J.M., and Cantley, L.C. 1997. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science 275: 73-77.
39. Staudinger, J., Zhou, J., Burgess, R., Elledge, S.J., and Olson, E.N. 1995. PICK1: A perinuclear binding protein and substrate for protein kinase C isolated by the yeast two-hybrid system. J. Cell Biol. 128: 263-271.
40. Staudinger, J., Lu, J., and Olson, E.N. 1997. Specific interaction of the PDZ domain protein PICK1 with the COOH terminus of protein kinase C-α. J. Biol. Chem. 272: 32019-32024.
41. Steinberg, J.P., Takamiya, K., Shen, Y., Xia, J., Rubio, M.E., Yu, S., Jin, W., Thomas, G.M., Linden, D.J., and Huganir, R.L. 2006. Targeted in vivo mutations of the AMPA receptor subunit GluR2 and its interacting protein PICK1 eliminate cerebellar long-term depression. Neuron 49: 845-860.
42. Storoni, L.C., McCoy, A.J., and Read, R.J. 2004. Likelihood-enhanced fast rotation functions. Acta Crystallogr. D60: 432-438.
43. Stricker, N.L., Christopherson, K.S., Yi, B.A., Schatz, P.J., Raab, R.W., Dawes, G., Bassett, D.E.J., Bredt, D.S., and Li, M. 1997. PDZ domain of neuronal nitric oxide synthase recognizes novel C-terminal peptide sequences. Nat. Biotechnol. 15: 336-342.
44. Sun, F., Hug, M.J., Lewarchik, C.M., Yun, C.-H.C., Bradbury, N.A., and Frizzell, R.A. 2000. E3KARP mediates the association of ezrin and protein kinase A with the cystic fibrosis transmembrane conductance regulator in airway cells. J. Biol. Chem. 275: 29539-29546.
45. Ullmer, C., Schmuck, K., Figge, A., and Lübbert, H. 1998. Cloning and characterization of MUPP1, a novel PDZ domain protein. FEBS Lett. 424: 63-68.
46. van Ham, M. and Hendriks, W. 2003. PDZ domains - Glue and guide. Mol. Biol. Rep. 30: 69-82.
47. Wen, W., Wang, W., and Zhang, M. 2006. Targeting PDZ domain proteins for treating NMDA receptor-mediated excitotoxicity. Curr. Top. Med. Chem. 6: 711-721.
48. Xia, J., Zhang, X., Staudinger, J., and Huganir, R.L. 1999. Clustering of AMPA receptors by the synaptic PDZ domain-containing protein PICK1. Neuron 22: 179-187.
49. Yawata, S., Tsuchida, H., Kengaku, M., and Hirano, T. 2006. Membrane-proximal region of glutamate receptor δ2 subunit is critical for long-term depression and interaction with protein interaction with C kinase 1 in a cerebellar Purkinje neuron. J. Neurosci. 26: 3626-3633.
50. Zhang, Y., Yeh, S., Appleton, B.A., Held, H.A., Kausalya, P.J., Phua, D.C.Y., Wong, W.L., Lasky, L.A., Wiesmann, C., Hunziker, W., et al. 2006. Convergent and divergent ligand specificity among PDZ domains of the LAP and zonula occludens (ZO) families. J. Biol. Chem. 281: 22299-22311.