1 Takai, Y., Sasaki, T. & Matozaki, T. Small GTP-binding proteins. Physiological reviews 81, 153-208 (2001).
2 Goitre, L., Trapani, E., Trabalzini, L. & Retta, S. F. in Ras Signaling 1-18 (Springer, 2014).
3 Colicelli, J. Human RAS superfamily proteins and related GTPases. Sci. STKE 2004, re13-re13 (2004).
4 Kumar, S., Stecher, G. & Tamura, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology and evolution 33, 1870-1874 (2016).
5 Valencia, A., Chardin, P., Wittinghofer, A. & Sander, C. The ras protein family: evolutionary tree and role of conserved amino acids. Biochemistry 30, 4637-4648 (1991).
6 Wright, L. P. & Philips, M. R. Thematic review series: lipid posttranslational modifications CAAX modification and membrane targeting of Ras. Journal of lipid research 47, 883-891 (2006).
7 Rossman, K. L., Der, C. J. & Sondek, J. GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors. Nature reviews Molecular cell biology 6, 167-180 (2005).
8 Yang, J., Zhang, Z., Roe, S. M., Marshall, C. J. & Barford, D. Activation of Rho GTPases by DOCK exchange factors is mediated by a nucleotide sensor. Science 325, 1398-1402 (2009).
9 Kulkarni, K., Yang, J., Zhang, Z. & Barford, D. Multiple factors confer specific Cdc42 and Rac protein activation by dedicator of cytokinesis (DOCK) nucleotide exchange factors. Journal of Biological Chemistry 286, 25341-25351 (2011).
10 Mizuno, T. et al. A stimulatory GDP/GTP exchange protein for smg p21 is active on the post-translationally processed form of c-Ki-ras p21 and rhoA p21. Proceedings of the National Academy of Sciences 88, 6442-6446 (1991).
11 Yamamoto, T. et al. Purification and characterization from bovine brain cytosol of proteins that regulate the GDP/GTP exchange reaction of smg p21s, ras p21-like GTP-binding proteins. Journal of Biological Chemistry 265, 16626-16634 (1990).
12 Williams, C. L. The polybasic region of Ras and Rho family small GTPases: a regulator of protein interactions and membrane association and a site of nuclear localization signal sequences. Cellular signalling 15, 1071-1080 (2003).
13 Bergom, C. et al. The Tumor-suppressive Small GTPase DiRas1 Binds the Noncanonical Guanine Nucleotide Exchange Factor SmgGDS and Antagonizes SmgGDS Interactions with Oncogenic Small GTPases. Journal of Biological Chemistry 291, 6534-6545 (2016).
14 Ogita, Y. et al. Di-Ras2 Protein Forms a Complex with SmgGDS Protein in Brain Cytosol in Order to Be in a Low Affinity State for Guanine Nucleotides. Journal of Biological Chemistry 290, 20245-20256 (2015).
15 Hamel, B. et al. SmgGDS is a guanine nucleotide exchange factor that specifically activates RhoA and RhoC. Journal of Biological Chemistry 286, 12141-12148 (2011).
16 Schuld, N. J. et al. The chaperone protein SmgGDS interacts with small GTPases entering the prenylation pathway by recognizing the last amino acid in the CAAX motif. Journal of Biological Chemistry 289, 6862-6876 (2014).
17 Berg, T. J. et al. Splice variants of SmgGDS control small GTPase prenylation and membrane localization. Journal of Biological Chemistry 285, 35255-35266 (2010).
18 Williams, C. Vol. 12 2933-2934 (Cell Cycle., 2013).
19 Tew, G. W. et al. SmgGDS regulates cell proliferation, migration, and NF-κB transcriptional activity in non-small cell lung carcinoma. Journal of Biological Chemistry 283, 963-976 (2008).
20 Zhi, H. et al. SmgGDS is up‐regulated in prostate carcinoma and promotes tumour phenotypes in prostate cancer cells. The Journal of pathology 217, 389-397 (2009).
21 Hauser, A. D. et al. The SmgGDS splice variant SmgGDS-558 is a key promoter of tumor growth and RhoA signaling in breast cancer. Molecular Cancer Research 12, 130-142 (2014).
22 Schuld, N. et al. SmgGDS-558 regulates the cell cycle in pancreatic, non-small cell lung, and breast cancers. Cell Cycle 13, 941-952 (2014).
23 Tanaka, S.-i. et al. Statins Exert the Pleiotropic Effects Through Small GTP-Binding Protein Dissociation Stimulator Upregulation With a Resultant Rac1 DegradationSignificance. Arteriosclerosis, thrombosis, and vascular biology 33, 1591-1600 (2013).
24 Kudo, S. et al. (Am Heart Assoc, 2015).
25 Minami, T. et al. Statins up-regulate SmgGDS through β1-integrin/Akt1 pathway in endothelial cells. Cardiovascular research 109, 151-161 (2016).
26 Nogi, M. et al. SmgGDS Prevents Thoracic Aortic Aneurysm Formation and Rupture by Phenotypic Preservation of Aortic Smooth Muscle Cells. Circulation, CIRCULATIONAHA. 118.035648 (2018).
27 Shimizu, H. et al. Structure-based analysis of the guanine nucleotide exchange factor SmgGDS reveals armadillo-repeat motifs and key regions for activity and GTPase binding. Journal of Biological Chemistry 292, 13441-13448 (2017).
28 Shimizu, H., Toma-Fukai, S., Kontani, K., Katada, T. & Shimizu, T. GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism. Proceedings of the National Academy of Sciences 115, 9563-9568 (2018).
29 Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods in enzymology 276, 307-326 (1997).
30 Kabsch, W. Xds. Acta Crystallographica Section D: Biological Crystallography 66, 125-132 (2010).
31 Vonrhein, C., Blanc, E., Roversi, P. & Bricogne, G. Automated structure solution with autoSHARP. Macromolecular Crystallography Protocols: Volume 2: Structure Determination, 215-230 (2007).
32 Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallographica Section D: Biological Crystallography 62, 1002-1011 (2006).
33 Cowtan, K. Fitting molecular fragments into electron density. Acta Crystallographica Section D: Biological Crystallography 64, 83-89 (2008).
34 Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. Journal of applied crystallography 30, 1022-1025 (1997).
35 Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica Section D: Biological Crystallography 53, 240-255 (1997).
36 Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallographica Section D: Biological Crystallography 60, 2126-2132 (2004).
37 Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of applied crystallography 26, 283-291 (1993).
38 Fiser, A. & Do, R. K. G. Modeling of loops in protein structures. Protein science 9, 1753-1773 (2000).
39 Martí-Renom, M. A. et al. Comparative protein structure modeling of genes and genomes. Annual review of biophysics and biomolecular structure 29, 291-325 (2000).
40 Šali, A. & Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints. Journal of molecular biology 234, 779-815 (1993).
41 Webb, B. & Sali, A. Protein structure modeling with MODELLER. Protein Structure Prediction, 1-15 (2014).
42 Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. Journal of molecular biology 215, 403-410 (1990).
43 Blaszczyk, M. et al. Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking. Methods 93, 72-83 (2016).
44 Kurcinski, M., Jamroz, M., Blaszczyk, M., Kolinski, A. & Kmiecik, S. CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site. Nucleic acids research 43, W419-W424 (2015).
45 Omer, C. A., Diehl, R. E. & Kral, A. M. in Methods in enzymology Vol. 250 3-12 (Elsevier, 1995).
46 Kuhlmann, N. et al. Structural and mechanistic insights into the regulation of the fundamental Rho regulator RhoGDIα by lysine acetylation. Journal of Biological Chemistry 291, 5484-5499 (2016).
47 Shimizu, N. et al. in AIP Conference Proceedings. 050017 (AIP Publishing).
48 Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. & Svergun, D. I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. Journal of applied crystallography 36, 1277-1282 (2003).
49 Svergun, D. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. Journal of applied crystallography 25, 495-503 (1992).
50 Svergun, D. I. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophysical journal 76, 2879-2886 (1999).
51 Volkov, V. V. & Svergun, D. I. Uniqueness of ab initio shape determination in small-angle scattering. Journal of applied crystallography 36, 860-864 (2003).
52 Yamashita, K., Hirata, K. & Yamamoto, M. KAMO: towards automated data processing for microcrystals. Acta Crystallographica Section D: Structural Biology 74, 441-449 (2018).
53 Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D: Biological Crystallography 66, 213-221 (2010).
54 Laskowski, R. A. & Swindells, M. B. (ACS Publications, 2011).
55 Morris, G. M. et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of computational chemistry 19, 1639-1662 (1998).
56 Morris, G. M. et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry 30, 2785-2791 (2009).
57 Wilson, J. M., Prokop, J. W., Lorimer, E., Ntantie, E. & Williams, C. L. Differences in the Phosphorylation-Dependent Regulation of Prenylation of Rap1A and Rap1B. Journal of Molecular Biology 428, 4929-4945 (2016).
58 Krissinel, E. & Henrick, K. Protein interfaces, surfaces and assemblies service PISA at European Bioinformatics Institute. J Mol Biol 372, 774-797 (2007).
59 Bos, J. L., Rehmann, H. & Wittinghofer, A. GEFs and GAPs: critical elements in the control of small G proteins. Cell 129, 865-877 (2007).
60 Hoffman, G. R., Nassar, N. & Cerione, R. A. Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI. Cell 100, 345-356 (2000).
61 Dharmaiah, S. et al. Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ. Proceedings of the National Academy of Sciences 113, E6766-E6775 (2016).
62 Garcia-Mata, R., Boulter, E. & Burridge, K. The invisible hand: regulation of RHO GTPases by RHOGDIs. Nature reviews. Molecular cell biology 12, 493 (2011).
63 Gasper, R., Sot, B. & Wittinghofer, A. GTPase activity of Di-Ras proteins is stimulated by Rap1GAP proteins. Small GTPases 1, 133-141 (2010).
64 Sievers, F. et al. Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Molecular systems biology 7, 539 (2011).
65 Holm, L. & Sander, C. Dali: a network tool for protein structure comparison. Trends in biochemical sciences 20, 478-480 (1995).
66 Tewari, R., Bailes, E., Bunting, K. A. & Coates, J. C. Armadillo-repeat protein functions: questions for little creatures. Trends in cell biology 20, 470-481 (2010).
67 Noren, N. K., Liu, B. P., Burridge, K. & Kreft, B. p120 catenin regulates the actin cytoskeleton via Rho family GTPases. The Journal of cell biology 150, 567-580 (2000).
68 Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Crystallographica Section A: Crystal Physics, Diffraction, Theoretical and General Crystallography 32, 922-923 (1976).
69 Gillette, W. K. et al. Farnesylated and methylated KRAS4b: high yield production of protein suitable for biophysical studies of prenylated protein-lipid interactions. Scientific reports 5, 15916 (2015).
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