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. 2011 Apr 14;2(4):308–319. doi: 10.1007/s13238-011-1036-z

Structural study of the Cdc25 domain from Ral-specific guanine-nucleotide exchange factor RalGPS1a

Wei Peng 1, Jiwei Xu 1, Xiaotao Guan 1, Yao Sun 1, Xuejun C Zhang 1, Xuemei Li 1, Zihe Rao 1,
PMCID: PMC4875206  PMID: 21494904

Abstract

The guanine-nucleotide exchange factor (GEF) RalGPS1a activates small GTPase Ral proteins such as RalA and RalB by stimulating the exchange of Ral bound GDP to GTP, thus regulating various downstream cellular processes. RalGPS1a is composed of an Nterminal Cdc25-like catalytic domain, followed by a PXXP motif and a C-terminal pleckstrin homology (PH) domain. The Cdc25 domain of RalGPS1a, which shares about 30% sequence identity with other Cdc25-domain proteins, is thought to be directly engaged in binding and activating the substrate Ral protein. Here we report the crystal structure of the Cdc25 domain of RalGPS1a. The bowl shaped structure is homologous to the Cdc25 domains of SOS and RasGRF1. The most remarkable difference between these three Cdc25 domains lies in their active sites, referred to as the helical hairpin region. Consistent with previous enzymological studies, the helical hairpin of RalGPS1a adopts a conformation favorable for substrate binding. A modeled RalGPS1a-RalA complex structure reveals an extensive binding surface similar to that of the SOS-Ras complex. However, analysis of the electrostatic surface potential suggests an interaction mode between the RalGPS1a active site helical hairpin and the switch 1 region of substrate RalA distinct from that of the SOS-Ras complex.

Keywords: RalGPS1a, RalA, cdc25 domain, crystal structure

Footnotes

These authors contributed equally to this work.

References

  1. Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.W., Kapral G.J., Grosse-Kunstleve R.W., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010;66:213–221. doi: 10.1107/S0907444909052925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Albright C.F., Giddings B.W., Liu J., Vito M., Weinberg R.A. Characterization of a guanine nucleotide dissociation stimulator for a ras-related GTPase. EMBO J. 1993;12:339–347. doi: 10.1002/j.1460-2075.1993.tb05662.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics. 2006;22:195–201. doi: 10.1093/bioinformatics/bti770. [DOI] [PubMed] [Google Scholar]
  4. Bodemann B.O., White M.A. Ral GTPases and cancer: linchpin support of the tumorigenic platform. Nat Rev Cancer. 2008;8:133–140. doi: 10.1038/nrc2296. [DOI] [PubMed] [Google Scholar]
  5. Boguski M.S., McCormick F. Proteins regulating Ras and its relatives. Nature. 1993;366:643–654. doi: 10.1038/366643a0. [DOI] [PubMed] [Google Scholar]
  6. Boriack-Sjodin P.A., Margarit S.M., Bar-Sagi D., Kuriyan J. The structural basis of the activation of Ras by Sos. Nature. 1998;394:337–343. doi: 10.1038/28548. [DOI] [PubMed] [Google Scholar]
  7. Broek D., Toda T., Michaeli T., Levin L., Birchmeier C., Zoller M., Powers S., Wigler M. The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell. 1987;48:789–799. doi: 10.1016/0092-8674(87)90076-6. [DOI] [PubMed] [Google Scholar]
  8. Cascone I., Selimoglu R., Ozdemir C., Del Nery E., Yeaman C., White M., Camonis J. Distinct roles of RalA and RalB in the progression of cytokinesis are supported by distinct RalGEFs. EMBO J. 2008;27:2375–2387. doi: 10.1038/emboj.2008.166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ceriani M., Scandiuzzi C., Amigoni L., Tisi R., Berruti G., Martegani E. Functional analysis of RalGPS2, a murine guanine nucleotide exchange factor for RalA GTPase. Exp Cell Res. 2007;313:2293–2307. doi: 10.1016/j.yexcr.2007.03.016. [DOI] [PubMed] [Google Scholar]
  10. Chardin P., Tavitian A. The ral gene: a new ras related gene isolated by the use of a synthetic probe. EMBO J. 1986;5:2203–2208. doi: 10.1002/j.1460-2075.1986.tb04485.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chien Y., White M.A. RAL GTPases are linchpin modulators of human tumour-cell proliferation and survival. EMBO Rep. 2003;4:800–806. doi: 10.1038/sj.embor.embor899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Colicelli J. Human RAS superfamily proteins and related GTPases. Sci STKE. 2004;2004:RE13. doi: 10.1126/stke.2502004re13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. de Bruyn K.M., de Rooij J., Wolthuis R.M., Rehmann H., Wesenbeek J., Cool R.H., Wittinghofer A.H., Bos J.L. RalGEF2, a pleckstrin homology domain containing guanine nucleotide exchange factor for Ral. J Biol Chem. 2000;275:29761–29766. doi: 10.1074/jbc.M001160200. [DOI] [PubMed] [Google Scholar]
  14. de Rooij J., Rehmann H., van Triest M., Cool R.H., Wittinghofer A., Bos J.L. Mechanism of regulation of the Epac family of cAMP-dependent RapGEFs. J Biol Chem. 2000;275:20829–20836. doi: 10.1074/jbc.M001113200. [DOI] [PubMed] [Google Scholar]
  15. DeLano W.L. The PyMOL Molecular Graphics System. San Carlos, CA: Delano Scientific; 2002. [Google Scholar]
  16. Emanuelsson O., Brunak S., von Heijne G., Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007;2:953–971. doi: 10.1038/nprot.2007.131. [DOI] [PubMed] [Google Scholar]
  17. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
  18. Freedman T.S., Sondermann H., Friedland G.D., Kortemme T., Bar-Sagi D., Marqusee S., Kuriyan J. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A. 2006;103:16692–16697. doi: 10.1073/pnas.0608127103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gouet P., Courcelle E., Stuart D.I., Métoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 1999;15:305–308. doi: 10.1093/bioinformatics/15.4.305. [DOI] [PubMed] [Google Scholar]
  20. Hall B.E., Yang S.S., Boriack-Sjodin P.A., Kuriyan J., Bar-Sagi D. Structure-based mutagenesis reveals distinct functions for Ras switch 1 and switch 2 in Sos-catalyzed guanine nucleotide exchange. J Biol Chem. 2001;276:27629–27637. doi: 10.1074/jbc.M101727200. [DOI] [PubMed] [Google Scholar]
  21. Laskowski R.A., Macarthur M.W., Moss D.S., Thornton J.M. Procheck-a Program to Check the Stereochemical Quality of Protein Structures. J Appl Cryst. 1993;26:283–291. doi: 10.1107/S0021889892009944. [DOI] [Google Scholar]
  22. Lim K.H., Baines A.T., Fiordalisi J.J., Shipitsin M., Feig L.A., Cox A.D., Der C.J., Counter C.M. Activation of RalA is critical for Ras-induced tumorigenesis of human cells. Cancer Cell. 2005;7:533–545. doi: 10.1016/j.ccr.2005.04.030. [DOI] [PubMed] [Google Scholar]
  23. Lo Conte L., Chothia C., Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol. 1999;285:2177–2198. doi: 10.1006/jmbi.1998.2439. [DOI] [PubMed] [Google Scholar]
  24. Lyskov S., Gray J.J. The RosettaDock server for local protein-protein docking. Nucleic Acids Res. 2008;36:W233–238. doi: 10.1093/nar/gkn216. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Margarit S.M., Sondermann H., Hall B.E., Nagar B., Hoelz A., Pirruccello M., Bar-Sagi D., Kuriyan J. Structural evidence for feedback activation by Ras. of the Ras-specific nucleotide exchange factor SOS. Cell. 2003;112:685–695. doi: 10.1016/s0092-8674(03)00149-1. [DOI] [PubMed] [Google Scholar]
  26. Matthews B.W. Solvent content of protein crystals. J Mol Biol. 1968;33:491–497. doi: 10.1016/0022-2836(68)90205-2. [DOI] [PubMed] [Google Scholar]
  27. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J Appl Crystallogr. 2007;40:658–674. doi: 10.1107/S0021889807021206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Moskalenko S., Henry D.O., Rosse C., Mirey G., Camonis J.H., White M.A. The exocyst is a Ral effector complex. Nat Cell Biol. 2002;4:66–72. doi: 10.1038/ncb728. [DOI] [PubMed] [Google Scholar]
  29. Murai H., Ikeda M., Kishida S., Ishida O., Okazaki-Kishida M., Matsuura Y., Kikuchi A. Characterization of Ral GDP dissociation stimulator-like (RGL) activities to regulate c-fos promoter and the GDP/GTP exchange of Ral. J Biol Chem. 1997;272:10483–10490. doi: 10.1074/jbc.272.16.10483. [DOI] [PubMed] [Google Scholar]
  30. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Macromolecular Crystallography, Pt A. 1997;276:307–326. doi: 10.1016/S0076-6879(97)76066-X. [DOI] [PubMed] [Google Scholar]
  31. Quilliam L.A. Specificity and expression of RalGPS as RalGEFs. Methods Enzymol. 2006;407:108–114. doi: 10.1016/S0076-6879(05)07010-2. [DOI] [PubMed] [Google Scholar]
  32. Rameh L.E., Arvidsson A., Carraway K.L., 3rd, Couvillon A.D., Rathbun G., Crompton A., VanRenterghem B., Czech M.P., Ravichandran K.S., Burakoff S.J., et al. A comparative analysis of the phosphoinositide binding specificity of pleckstrin homology domains. J Biol Chem. 1997;272:22059–22066. doi: 10.1074/jbc.272.35.22059. [DOI] [PubMed] [Google Scholar]
  33. Rangarajan A., Hong S.J., Gifford A., Weinberg R.A. Species- and cell type-specific requirements for cellular transformation. Cancer Cell. 2004;6:171–183. doi: 10.1016/j.ccr.2004.07.009. [DOI] [PubMed] [Google Scholar]
  34. Rebhun J.F., Chen H., Quilliam L.A. Identification and characterization of a new family of guanine nucleotide exchange factors for the ras-related GTPase Ral. J Biol Chem. 2000;275:13406–13410. doi: 10.1074/jbc.C000085200. [DOI] [PubMed] [Google Scholar]
  35. Rehmann H., Das J., Knipscheer P., Wittinghofer A., Bos J.L. Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state. Nature. 2006;439:625–628. doi: 10.1038/nature04468. [DOI] [PubMed] [Google Scholar]
  36. Terwilliger T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr. 2003;59:38–44. doi: 10.1107/S0907444902018036. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Wilbur W.J., Lipman D.J. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983;80:726–730. doi: 10.1073/pnas.80.3.726. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Wolthuis R.M., de Ruiter N.D., Cool R.H., Bos J.L. Stimulation of gene induction and cell growth by the Ras effector Rlf. EMBO J. 1997;16:6748–6761. doi: 10.1093/emboj/16.22.6748. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Zhang X.J., Matthews B.W. Edpdb — a Multifunctional Tool for Protein-Structure Analysis. J Appl Cryst. 1995;28:624–630. doi: 10.1107/S0021889895001063. [DOI] [Google Scholar]

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