Structure and Asn-Pro-Phe binding pocket of the Eps15 homology domain

Science

Volumn 281, Issue 5381, 1998, Pages 1357-1360

  De Beer, Tonny ^a   Carter, Royston E ^a   Lobel Rice, Katherine E ^a   Sorkin, Alexander ^a   Overduin, Michael ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; CALCIUM ION; EPS 15 PROTEIN; GROWTH FACTOR; PHENYLALANINE; PROLINE; TRIPEPTIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; EUKARYOTE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; SIGNAL TRANSDUCTION;

EUKARYOTA;

EID: 0032575695     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.281.5381.1357     Document Type: Article

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21. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
22. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
23. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
24. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
25. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
26. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
27. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
28. -1, respectively. No distance and angle restraints were violated by more than 0.35 Å and 2°, respectively. The rmsds from idealized geometry for bonds, angles, and impropers were 0.0028 ± 0.0001 Å, 0.62 ± 0.012°, and 0.47 ± 0.076°. respectively. Ramachandran plot analysis of the 20 structures with Procheck-NMR (20) showed that 85.8, 11.3, 2.5, and 0.5% of the non-Gly and non-Pro residues were in the most favorable, additional allowed, generously allowed, and disallowed regions, respectively.
29. 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.
30. 2 concentration and equilibrium RU, using steady-state affinity analysis (BIAevaluation 2.1).
31. J. Falke, S. K. Drake, A. L. Hazard, O. B. Peersen, Q. Rev. Biophys. 27, 219 (1994); R. Chattopadhyaya, W. E. Meador, A. R. Means, F. A. Quiocho, J. Mol. Biol. 228, 1177 (1992); N. C J. Strydnadka et al., ibid. 273, 238 (1997); J. P. Declerq, B. Tinant, J. Parello, J. Rambaud, ibid. 220, 1017 (1991); L. A. Svensson, E. Thulin, S. Forsen, ibid. 223, 601 (1992).
32. J. Falke, S. K. Drake, A. L. Hazard, O. B. Peersen, Q. Rev. Biophys. 27, 219 (1994); R. Chattopadhyaya, W. E. Meador, A. R. Means, F. A. Quiocho, J. Mol. Biol. 228, 1177 (1992); N. C J. Strydnadka et al., ibid. 273, 238 (1997); J. P. Declerq, B. Tinant, J. Parello, J. Rambaud, ibid. 220, 1017 (1991); L. A. Svensson, E. Thulin, S. Forsen, ibid. 223, 601 (1992).
33. J. Falke, S. K. Drake, A. L. Hazard, O. B. Peersen, Q. Rev. Biophys. 27, 219 (1994); R. Chattopadhyaya, W. E. Meador, A. R. Means, F. A. Quiocho, J. Mol. Biol. 228, 1177 (1992); N. C J. Strydnadka et al., ibid. 273, 238 (1997); J. P. Declerq, B. Tinant, J. Parello, J. Rambaud, ibid. 220, 1017 (1991); L. A. Svensson, E. Thulin, S. Forsen, ibid. 223, 601 (1992).
34. J. Falke, S. K. Drake, A. L. Hazard, O. B. Peersen, Q. Rev. Biophys. 27, 219 (1994); R. Chattopadhyaya, W. E. Meador, A. R. Means, F. A. Quiocho, J. Mol. Biol. 228, 1177 (1992); N. C J. Strydnadka et al., ibid. 273, 238 (1997); J. P. Declerq, B. Tinant, J. Parello, J. Rambaud, ibid. 220, 1017 (1991); L. A. Svensson, E. Thulin, S. Forsen, ibid. 223, 601 (1992).
35. J. Falke, S. K. Drake, A. L. Hazard, O. B. Peersen, Q. Rev. Biophys. 27, 219 (1994); R. Chattopadhyaya, W. E. Meador, A. R. Means, F. A. Quiocho, J. Mol. Biol. 228, 1177 (1992); N. C J. Strydnadka et al., ibid. 273, 238 (1997); J. P. Declerq, B. Tinant, J. Parello, J. Rambaud, ibid. 220, 1017 (1991); L. A. Svensson, E. Thulin, S. Forsen, ibid. 223, 601 (1992).
36. R. A. Laskowski, J. A. C. Rullmann, M. W. MacArthur, R. Kaptein, J. M. Thornton, J. Biomol. NMR 8, 477 (1996).
37. Superposition of residues 121 through 215 yields rmsds of 0.54 ± 0.08 A° and 0.92 ± 0.10 A° for the backbone and all heavy atoms, respectively.
38. 2-terminal residues [DRWGS (17)], which are encoded by the expression vector, and the six COOH-terminal residues, which are derived from the third EH domain (KTW) and expression vector (ELI), are not depicted.
39. A. Nicholls, K. A. Sharp, B. Honig, Proteins 11, 281 (1991).
40. We thank R. Muhandiram and L. E. Kay for NMR pulse sequences, J. Mamay for computational support, S. A. Johnson for assistance with BIAcore experiments, P. P. Di Fiori for cDNA, B. Thimmig and C. McHenry for assistance with sedimentation equilibrium experiments, K. Clay and R. Murphy for MALDI data, and J. Enmon, D. Jones, and F. Tebar for insightful discussions. The NMR Center is supported by the Howard Hughes Medical Institute (HHMI). The University of Colorado Cancer Center Facilities for DNA and Protein Sequencing are supported by NIH. This research is funded by NIH and the HHMI (A.S. and M.O.) and by the American Cancer Society and Pew Scholar's Program (M.O.). T.B. and R.E.C. are recipients of NIH and Cancer League of Colorado postdoctoral fellowships, respectively. The coordinates have been deposited in the Brookhaven Protein Data Bank under accession number 1eh2.