Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex

Science

Volumn 284, Issue 5415, 1999, Pages 812-815

  Hillier, Brian J ^a   Christopherson, Karen S ^a   Prehoda, Kenneth E ^a   Bredt, David S ^a   Lim, Wendell A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NITRIC OXIDE SYNTHASE; PDZ PROTEIN; PEPTIDE; POSTSYNAPTIC DENSITY PROTEIN 95; RECEPTOR PROTEIN; SYNTROPHIN; UNCLASSIFIED DRUG;

ARTICLE; CARBOXY TERMINAL SEQUENCE; DROSOPHILA; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; DYSTROPHIN-ASSOCIATED PROTEINS; LIGANDS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MUSCLE PROTEINS; NITRIC OXIDE SYNTHASE; NITRIC OXIDE SYNTHASE TYPE I; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SIGNAL TRANSDUCTION;

EID: 0033617473     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.284.5415.812     Document Type: Article

References (45)

1. The name PDZ is derived from the first three proteins in which these domains were identified: PSD-95, the Drosophila septate junction protein Discs-Large (Dlg), and the epithelial tight juction protein ZO-1.
2. E. Kim et al., Nature 378, 85 (1995); H. C. Kornau et al., Science 269, 1737 (1995); T. Sato et al., ibid. 268, 411 (1995).
3. E. Kim et al., Nature 378, 85 (1995); H. C. Kornau et al., Science 269, 1737 (1995); T. Sato et al., ibid. 268, 411 (1995).
4. E. Kim et al., Nature 378, 85 (1995); H. C. Kornau et al., Science 269, 1737 (1995); T. Sato et al., ibid. 268, 411 (1995).
5. J. S. Simske et al., Cell 85, 195 (1996); H. Dong et al., Nature 386, 279 (1997).
6. J. S. Simske et al., Cell 85, 195 (1996); H. Dong et al., Nature 386, 279 (1997).
7. A. S. Fanning and J. M. Anderson, Curr. Biol. 6, 1365 (1996); S. K. Kim, Curr. Opin. Cell Biol. 9, 853 (1997); R. Ranganathan and E. M. Ross, Curr. Biol. 7, R770 (1997); S. E. Craven and D. S. Bredt, Cell 93, 495 (1998).
8. A. S. Fanning and J. M. Anderson, Curr. Biol. 6, 1365 (1996); S. K. Kim, Curr. Opin. Cell Biol. 9, 853 (1997); R. Ranganathan and E. M. Ross, Curr. Biol. 7, R770 (1997); S. E. Craven and D. S. Bredt, Cell 93, 495 (1998).
9. A. S. Fanning and J. M. Anderson, Curr. Biol. 6, 1365 (1996); S. K. Kim, Curr. Opin. Cell Biol. 9, 853 (1997); R. Ranganathan and E. M. Ross, Curr. Biol. 7, R770 (1997); S. E. Craven and D. S. Bredt, Cell 93, 495 (1998).
10. A. S. Fanning and J. M. Anderson, Curr. Biol. 6, 1365 (1996); S. K. Kim, Curr. Opin. Cell Biol. 9, 853 (1997); R. Ranganathan and E. M. Ross, Curr. Biol. 7, R770 (1997); S. E. Craven and D. S. Bredt, Cell 93, 495 (1998).
11. J. E. Brenman et al., Cell 84, 757 (1996); J. E. Brenman et al, J. Neurosci. 16, 7407 (1996).
12. J. E. Brenman et al., Cell 84, 757 (1996); J. E. Brenman et al, J. Neurosci. 16, 7407 (1996).
13. S. Tsunoda et al., Nature 388, 243 (1997); J. Chevesich, A. J. Kreuz, C. Montell, Neuron 18, 95 (1997).
14. S. Tsunoda et al., Nature 388, 243 (1997); J. Chevesich, A. J. Kreuz, C. Montell, Neuron 18, 95 (1997).
15. X. Z. Xu et al., J. Cell Biol. 142, 545 (1998).
16. Z. Songyang et al., Science 275, 73 (1997).
17. D. A. Doyle et al., Cell 85, 1067 (1996); J. H. Cabral et al., Nature 382, 649 (1996); D. L. Daniels et al., Nature Struct. Biol. 5, 317 (1998).
18. D. A. Doyle et al., Cell 85, 1067 (1996); J. H. Cabral et al., Nature 382, 649 (1996); D. L. Daniels et al., Nature Struct. Biol. 5, 317 (1998).
19. D. A. Doyle et al., Cell 85, 1067 (1996); J. H. Cabral et al., Nature 382, 649 (1996); D. L. Daniels et al., Nature Struct. Biol. 5, 317 (1998).
20. J. Schultz et al., Nature Struct. Biol. 5, 19 (1998).
21. Disrupting the nNOS/PSD-95 interaction is a major pharmacological goal, because overstimulation of NMDA receptors during cerebral ischemia produces neurotoxic amounts of NO that cause brain Injury [T. M. Dawson, V. L. Dawson, S. H. Snyder, Ann. Neurol. 32, 297 (1992); Z. Huang et al., Science 265, 1883 (1994)].
22. Disrupting the nNOS/PSD-95 interaction is a major pharmacological goal, because overstimulation of NMDA receptors during cerebral ischemia produces neurotoxic amounts of NO that cause brain Injury [T. M. Dawson, V. L. Dawson, S. H. Snyder, Ann. Neurol. 32, 297 (1992); Z. Huang et al., Science 265, 1883 (1994)].
23. J. E. Brenman et al., Cell 82, 743 (1995).
24. C. D. Thomas et al., Proc. Natl. Acad. Sci. U.S.A. 95, 15090 (1998); K. S. Lau et al., FEBS Lett. 431, 71 (1998).
25. C. D. Thomas et al., Proc. Natl. Acad. Sci. U.S.A. 95, 15090 (1998); K. S. Lau et al., FEBS Lett. 431, 71 (1998).
26. E. Cuppen et al., Mol. Biol. Cell 9, 671 (1998); R. van Huizen et al., EMBO J. 17, 2285 (1998).
27. E. Cuppen et al., Mol. Biol. Cell 9, 671 (1998); R. van Huizen et al., EMBO J. 17, 2285 (1998).
28. 60 (A60C)] to obtain mercury derivatives. Initial mercury atom positions were found with the use of the program SOLVE [T. C Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], and positions were refined with the program SHARP [E. de la Fortelle and G. Bricogne, Methods Enzymol. 276, 472 (1997)]. The resulting electron density map was subjected to solvent flattening with the program SOLOMON [CCP4: A Suite of Programs for Protein Crystallography (SERC Daresbury Laboratory, Warrington, UK, 1979)]. Map interpretation and model building were done with the program O [T. A. Jones et al., Acta Crystallogr. D52, 30 (1996)]. The structures were subjected to cycles of positional and restrained individual B-factor refinement and to a bulk solvent correction with the program CNS [A. T. Brünger et al., ibid. D54, 905 (1998)].
29. 60 (A60C)] to obtain mercury derivatives. Initial mercury atom positions were found with the use of the program SOLVE [T. C Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], and positions were refined with the program SHARP [E. de la Fortelle and G. Bricogne, Methods Enzymol. 276, 472 (1997)]. The resulting electron density map was subjected to solvent flattening with the program SOLOMON [CCP4: A Suite of Programs for Protein Crystallography (SERC Daresbury Laboratory, Warrington, UK, 1979)]. Map interpretation and model building were done with the program O [T. A. Jones et al., Acta Crystallogr. D52, 30 (1996)]. The structures were subjected to cycles of positional and restrained individual B-factor refinement and to a bulk solvent correction with the program CNS [A. T. Brünger et al., ibid. D54, 905 (1998)].
30. 60 (A60C)] to obtain mercury derivatives. Initial mercury atom positions were found with the use of the program SOLVE [T. C Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], and positions were refined with the program SHARP [E. de la Fortelle and G. Bricogne, Methods Enzymol. 276, 472 (1997)]. The resulting electron density map was subjected to solvent flattening with the program SOLOMON [CCP4: A Suite of Programs for Protein Crystallography (SERC Daresbury Laboratory, Warrington, UK, 1979)]. Map interpretation and model building were done with the program O [T. A. Jones et al., Acta Crystallogr. D52, 30 (1996)]. The structures were subjected to cycles of positional and restrained individual B-factor refinement and to a bulk solvent correction with the program CNS [A. T. Brünger et al., ibid. D54, 905 (1998)].
31. 60 (A60C)] to obtain mercury derivatives. Initial mercury atom positions were found with the use of the program SOLVE [T. C Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], and positions were refined with the program SHARP [E. de la Fortelle and G. Bricogne, Methods Enzymol. 276, 472 (1997)]. The resulting electron density map was subjected to solvent flattening with the program SOLOMON [CCP4: A Suite of Programs for Protein Crystallography (SERC Daresbury Laboratory, Warrington, UK, 1979)]. Map interpretation and model building were done with the program O [T. A. Jones et al., Acta Crystallogr. D52, 30 (1996)]. The structures were subjected to cycles of positional and restrained individual B-factor refinement and to a bulk solvent correction with the program CNS [A. T. Brünger et al., ibid. D54, 905 (1998)].
32. 60 (A60C)] to obtain mercury derivatives. Initial mercury atom positions were found with the use of the program SOLVE [T. C Terwilliger and J. Berendzen, Acta Crystallogr. D52, 749 (1996)], and positions were refined with the program SHARP [E. de la Fortelle and G. Bricogne, Methods Enzymol. 276, 472 (1997)]. The resulting electron density map was subjected to solvent flattening with the program SOLOMON [CCP4: A Suite of Programs for Protein Crystallography (SERC Daresbury Laboratory, Warrington, UK, 1979)]. Map interpretation and model building were done with the program O [T. A. Jones et al., Acta Crystallogr. D52, 30 (1996)]. The structures were subjected to cycles of positional and restrained individual B-factor refinement and to a bulk solvent correction with the program CNS [A. T. Brünger et al., ibid. D54, 905 (1998)].
33. This mechanism of association, referred to as β-strand invasion or β-strand augmentation [S. C. Harrison, Cell 86, 341 (1996)], is commonly observed in the interactions of viral capsid assembly proteins.
34. 19 in strand A of the nNOS PDZ domain (Fig. 2, B and C). Thus the site -4 interaction in a peptide complex is replaced by a tertiary interaction in the heterodimer complex.
35. Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.
36. 2-terminal to the GLGF loop. The nNOS β finger can only participate In two of these four hydrogen bonds. Given that both ligand types are similar in affinity (B. Hillier, unpublished data), either the energetic contribution of these hydrogen bonds is small or the tertiary interactions observed in the heterodimer compensate for their loss. In PDZ-peptide complexes, no direct charge-charge interactions are made with the terminal carboxylate (the interaction with the conserved basic residue is mediated by a water molecule). This property, which sets the PDZ domain apart from most examples of carboxylate recognition proteins, may explain why a molecule like the nNOS β finger, which lacks a formal negative charge at its tip, still functions as a ligand.
37. S. H. Gee et al., J. Biol. Chem. 273, 21980 (1998).
38. A PDZ domain from the protein tyrosine phosphatase BL binds an internal motif in the RIL (reversion-induced LIM gene) protein, and a PDZ domain from InaD binds an internal motif from the protein phospholipase C-β (PLC-β) (14). The RIL protein contains the sequence GLNLKQRGY, and PLC-β contains the sequence QICVKQGR. Both are consistent with class II PDZ motifs, followed by turn-preferring residues. For turn preferences, see B. L. Sibanda and J. M. Thornton, Methods Enzymol. 202, 59 (1991).
39. The nNOS PDZ domain can also interact with the second PDZ domain from PSD-93. However, PSD-93 is an isoform of PSD-95 that is nearly identical in sequence (5).
40. M. Niethammer et al., Neuron 20, 693 (1998).
41. J. Schepens et al., FEBS Lett. 409, 53 (1997); N. L. Stricker et al., Nature Biotechnol. 15, 336 (1997).
42. J. Schepens et al., FEBS Lett. 409, 53 (1997); N. L. Stricker et al., Nature Biotechnol. 15, 336 (1997).
43. P. J. Kraulis, J. Appl. Crystallogr. 24, 946 (1991).
44. WebLab ViewerLite 3.1 for Power Macintosh, Molecular Simulations Inc.
45. Supported by grants from NIH (W.A.L. and D.S.B.); by awards to WAL from the Howard Hughes Medical Institute Research Resources Program, the Burroughs Wellcome Fund, the Searle Scholars Program, and the Packard Foundation; and by awards to D.S.B. from the National Association for Research on Schizophrenia and Depression and the EJLB and Culpeper Foundations. K.E.P. is a Cancer Research Institute postdoctoral fellow. We thank T. Earnest and the staff of the Macromolecular Crystallography Facility at the Advanced Light Source (Department of Energy, Lawrence Livermore National Laboratory), P. Foster, T. Gonzalez, E. Ruttenberg, K. Thorn, and members of the University of California San Francisco Macromolecular Structure Group for assistance; and H. Bourne, D. Julius, R. Nicoll, J. Weissman, and members of the Lim laboratory for comments. Coordinates have been deposited in the Protein Data Bank (ID codes IQAU and IQAV).