Model of the Ran-RCC1 interaction using biochemical and docking experiments

Journal of Molecular Biology

Volumn 289, Issue 4, 1999, Pages 1119-1130

  Azuma, Yoshiaki ^a   Renault, Louis ^b   García Ranea, Juan A ^c   Valencia, Alfonso ^c   Nishimoto, Takeharu ^a   Wittinghofer, Alfred ^b  

^a KYUSHU UNIVERSITY   (Japan)

^b MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^c CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

Docking model; Guanine nucleotide exchange; Ran; RCC1

Indexed keywords

ALANINE; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANINE NUCLEOTIDE EXCHANGE FACTOR;

ARTICLE; CONTROLLED STUDY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; STEADY STATE; X RAY CRYSTALLOGRAPHY;

FELIS CATUS;

EID: 0033021182     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2820     Document Type: Article

References (56)

1. Aghazadeh B., Zhu K., Kubiseski T. J., Liu G. A., Pawson T., Zheng Y., Rosen M. K. Structure and mutagenesis of the Dbl homology domain. Nature Struct. Biol. 5:1998;1098-1107.
2. Ahmadian M. R., Stege P., Scheffzek K., Wittinghofer A. Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras. Nature Struct. Biol. 4:1997;686-689.
3. Atrian S., Sanchez-Pulido L., Gonzàlez-Duarte R., Valencia A. Shaping of Drosophila alcohol dehydrogenase through evolution. Relationshop with enzyme functionality. J. Mol. Evol. 47:1997;211-221.
4. Azuma Y., Seino H., Seki T., Uzawa S., Klebe C., Ohba T., Wittinghofer A., Hayashi N., Nishimoto T. Conserved histidine residues of RCC1 are essential for nucleotide exchange on Ran. J. Biochem. 120:1996;82-91.
5. 2+and the β-phosphate to destabilize GDP on ARF1. EMBO J. 17:1998;3651-3659.
6. Boriack-Sjodin P. A., Margarit S. M., Bar-Sagi D., Kuriyan J. The structural basis of the activation of Ras by Sos. Nature. 394:1998;337-343.
7. Carrera V., Moroni A., Martegani E., Volponi C., Cool R. H., Alberghina L., Vanoni M. Mutations at position 1122 in the catalytic domain of the mouse ras-specific guanine nucleotide exchange factor DCD25 Mm originate both loss-of-function and gain-of-function proteins. FEBS Letters. 440:1998;291-296.
8. Casari G., Sander C., Valencia A. A method to predict functional residues in proteins. Nature Struct. Biol. 2:1995a;171-178.
9. Casari G., Sander C., Valencia A. Sequencespace. Bohr S. B. M. Protein Fold: A Distance Based Approach. 1995b;124-131 CRC Press, Boca Raton, New York, London, Tokyo.
10. Cherfils J., Menetrey J., Mathieu M., Labras G., Robineau S., Beraud-Dufour S., Antonny B., Chardin P. Structure of the SEC7 domain of the Arf exchange factor ARNO. Nature. 392:1998;101-105.
11. Dasso M. RCC1 in the cell cycle: the regulation of chomosome condensation takes on new roles. Trends Biochem. Sci. 18:1993;96-101.
12. Dasso M., Seki T., Azuma Y., Ohba T., Nishimoto T. A mutant form of Ran protein disrupts nuclear function in Xenopus laevis egg extracts by inhibiting the RCC1 protein, a regulator of chromosome condensation. EMBO J. 13:1994;5732-5744.
13. Goldberg J. Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching. Cell. 95:1998;237-248.
14. Goldberg J. Structural and functional analysis of the ARF1-ARFGAP complex reveals a role for coatamer in GTP hydrolysis. Cell. 96:1999;893-902.
15. Hiratsuka T. New ribose-modified fluorescent analogs of adenine and guanine nucleotides available as substrates for various enzymes. Biochim. Biophys. Acta. 742:1983;496-508.
16. Ji D. D., Sultan A. A. K., Chakrabarti D., Horrocks P., Doerig C., Arnot D. E. An RCC1-type guanidine exchange factor for the Ran G-protein is found in the plasmodium falciparum nucleus. Mol. Biochem. Parasitol. 95:1998;165-170.
17. Kabsch W., Sander C. Dictionary of proteins secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
18. Katchalski-Katzir E., Shariv I., Eisenstein M., Friesem A. A., Aflalo C., Vakser I. A. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl Acad. Sci. USA. 89:1992;2195-2199.
19. Kawashima T., Berthet-Colominas C., Wulff M., Cusack S., Leberman R. The structure of the Escherichia coli EF-Tu-EF-Ts complex at 2.5 Å resolution. Nature. 379:1996;511-518.
20. RCC1and fluorescence measurements of their interaction. Biochemistry. 32:1993;11923-11928.
21. Klebe C., Prinz H., Wittinghofer A., Goody R. S. The kinetic mechanism of Ran-nucleotide exchange catalyzed by RCC1. Biochemistry. 34:1995;12543-12552.
22. Kuhlmann J., Macara I., Wittinghofer A. Dynamic and equilibrium studies on the interaction of Ran with its effector RanBP1. Biochemistry. 36:1997;12027-12035.
23. Lambright D. G., Sondek J., Bohm A., Skiba N. P., Hamm H. E., Sigler P. B. The 2.0 Å crystal structure of a heterotrimeric G protein. Nature. 379:1996;311-319.
24. Lengauer T., Rarey M. Computational methods for biomolecular docking. Curr. Opin. Struct. Biol. 6:1996;402-406.
25. Mm. Biochemistry. 37:1998;7420-7430.
26. Liu X., Wang H., Eberstadt M., Schnuchel A., Olejniczak E. T., Meadows R. P., Schkeryants J. M., Janowick D. A., Harlan J. E., Harris E. A. S., Staunton D. W., Fesik S. W. NMR structure and mutagenesis of the N-terminal Dbl homology domain of the nucleotide exchange factor trio. Cell. 95:1998;269-277.
27. Lounsbury K. M., Richards S. A., Carey K. L., Macara I. G. Mutations within the Ran/TC4 GTPase. Effects on regulatory factor interactions and subcellular localization. J. Biol. Chem. 271:1996;32834-32841.
28. Meindl A., Dry K., Herrmann K., Manson F., Ciccodicola A., Edgar A., Carvalho M. R. S., Achatz H., Hellebrand H., Lennon A., Migliaccio C., Porter K., Zrenner E., Bird A., Jay M. et al. A gene (RPGR) with homology to the RCC1 guanine nucleotide exchange factor is mutated in X-linked retinitis pigmentosa (RP3). Nature Genet. 13:1996;35-42.
29. Mossessova E., Gulbis J. M., Goldberg J. Structure of the guanine nucleotide exchange factor Sec7 domain of human ARNO and analysis of the interaction with ARF GTPase. Cell. 92:1998;415-423.
30. Neer E. J., Schmidt C. J., Nambudripad R., Smith T. F. The ancient regulatory-protein family of WD-repeat proteins. Nature. 371:1994;297-300.
31. Noguchi E., Hayashi N., Azuma Y., Seki T., Nakasima M., Yanagida M., He X., Mueller U., Sazer S., Nishimoto T. Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1. EMBO J. 15:1996;5595-5605.
32. Nomura N., Miyajima N., Sazuka T., Tanaka A., Kawarabayasi Y., Sato S., Nagase T., Seki N., Ishikawa K., Tabata S. Prediction of the coding sequences of unidentified human genes. DNA Res. 1:1994;27-35.
33. Ohtsubo M., Ozaki H., Nishimoto T. The RCC1 protein, a regulator for the onset of chromosome condensation locates in the nucleus and binds to DNA. J. Cell Biol. 109:1989;1389-1397.
34. Pazos F., Sanchez-Pulido L., García-Ranea J. A., Andrade M. A., Atrian S., Valencia A. Comparative analysis of different methods for the detection of specificity regions in protein families. Lundh D., Olsson B., Narayanan A. Biocomputing and Emergent Computation. 1997;132-145 World Scientific, Singapore, New Jersey, London.
35. Renault L., Nassar N., Vetter I., Becker J., Roth M., Wittinghofer A. The 1.7 Å crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller. Nature. 392:1998;97-101.
36. Rensland H., John J., Linke R., Simon I., Schlichting I., Wittinghofer A., Goody R. S. Substrate and product structural requirements for binding of nucleotides to H-ras p21: the mechanism of discrimination between guanosine and adenosine nucleotides. Biochemistry. 34:1995;593-599.
37. Rittinger K., Walker P. A., Eccleston J. F., Smerdon S. J., Gamblin S. J. Structure at 1.65 Å of RHOA and its GTPase-activating protein in complex with a transition-state analogue. Nature. 389:1997;758-762.
38. Roepmann R., Vanduijnhoven G., Rosenberg T., Pinckers A. J. L. G., Bleekerwagemakers L. M., Bergen A. A. B., Post J., Beck A., Reinhardt R., Ropers H. H., Cremers F. P. M., Berger W. Positional cloning of the gene for X-linked retinitis pigmentosa 3-homology with the guanine-nucleotide-exchange factor RCC1. Human Mol. Genet. 5:1996;1035-1041.
39. Rosa J. L., Barbacid M. Agiant protein that stimulates guanine nucleotide exchange on ARF1 and Rab proteins forms a cytosolic ternary complex with clathrin and Hsp70. Oncogene. 15:1997;1-6.
40. Rosa J. L., Casarolimarano R. P., Buckler A. J., Vilaro S., Barbacid M. p619, a giant protein related to the chromosome condensation regulator RCC1, stimulates guanine nucleotide exchange on ARF1 and Rab proteins. EMBO J. 15:1996;4262-4273.
41. Rudolph M. G., Bayer P., Abo A., Kuhlmann J., Vetter I., Wittinghofer A. The Cdc42/rac interactive binding region motif of the Wiskott Aldrich syndrome protein (WASP) is necessary but not sufficient for tight binding to Cdc42 and structure formation. J. Biol. Chem. 273:1998;18067-18076.
42. Scheffzek K., Klebe C., Fritz-Wolf K., Kabsch W., Wittinghofer A. Crystal structure of the nuclear Ras-related protein Ran in its GDP-bound form. Nature. 374:1995;378-381.
43. Scheffzek K., Ahmadian M. R., Kabsch W., Wiesmüller L., Lautwein A., Schmitz F., Wittinghofer A. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science. 277:1997;333-338.
44. Scheffzek K., Ahmadian M. R., Wittinghofer A. GTPase activating proteins: helping hands to complement an active site. Trends Biochem. Sci. 23:1998;257-262.
45. Seki T., Hayashi N., Nishimoto T. RCC1 in the Ran pathway. J. Biochem. 120:1996;207-214.
46. Soisson A. M., Nimnual A. S., Uy M., Bar-Sagi D., Kuriyan J. Crystal structure of the Dbl and pleckstrin homology domains from the human son of sevenless rotein. Cell. 95:1998;259-268.
47. Stewart M., Kent H. M., McCoy A. J. The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2). J. Mol. Biol. 284:1998;1517-1527.
48. Strynadka N. C. J., Eisenstein M., Katchalski-Katzir E., Shoichet B. K., Kuntz I. D., Abagyan R., Totrov M., Janin J., Cherfils J., Zimmerman F., Olson A., Duncan B., Rao M., Jackson R., Sternberg M., James M. N. G. Molecular docking programs successfully predict the binding of a B-lactamase inhibitory protein to TEM-1 B-lactamase. Nature Struct. Biol. 3:1996;233-239.
49. Thompson J. D., Higgins D. G., Gibson T. J. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
50. Vakser I. A. Protein docking for low-resolution structures. Protein Eng. 8:1995;371-377.
51. Valencia A., Sander C. The ras superfamily. Zerial M., Huber L. A., Tooze J. Guidebook to the Small GTPases. 1995;12-19 Oxford University Press, Oxford, New York, Tokyo.
52. van den Berghe N., Cool R. H., Wittinghofer A. Discriminatory residues in Ras and Rap for guanine nucleotide exchange factor recognition. J. Biol. Chem. 274:1999;11078-11085.
53. Vetter I., Novak C., Nishimoto T., Kuhlmann J., Wittinghofer A. Structure of a Ran-binding domain with Ran bound to a GTP analogue: implications for nuclear transport. Nature. 398:1999;39-46.
54. 1γ2. Cell. 83:1995;1047-1058.
55. Wang Y., Jiang Y., Meyering-Voss M., Sprinzl M., Sigler P. B. Crystal structure of the EF-Tu. EF-Ts complex form Thermus thermophilus. Nature Struct. Biol. 4:1997;650-656.
56. Wittinghofer F. Ras signaling: caught in the act of the switch-on. Nature. 394:1998;317-320.