Functional study on GTP hydrolysis by the GTP-binding protein from Sulfolobus solfataricus, a member of the HflX family

Journal of Biochemistry

Volumn 148, Issue 1, 2010, Pages 103-113

  Huang, Bo ^a   Wu, Hao ^b   Hao, Ning ^a   Blombach, Fabian ^c   Van Der Oost, John ^c   Li, Xuemei ^a   Zhang, Xuejun C ^a,b   Rao, Zihe ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^c WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

crystal structure; GTPase; HflX; mutation; SsGBP

Indexed keywords

GUANOSINE TRIPHOSPHATE; RAS PROTEIN; BACTERIAL PROTEIN; ESCHERICHIA COLI PROTEIN; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANOSINE DIPHOSPHATE; HFLX PROTEIN, E COLI; MAGNESIUM; MUTANT PROTEIN;

ARTICLE; MUTAGENESIS; NONHUMAN; NUCLEOPHILICITY; POINT MUTATION; PROTEIN BINDING; PROTEIN HYDROLYSIS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; SULFOLOBUS SOLFATARICUS; THERMOSTABILITY; WILD TYPE; AMINO ACID SUBSTITUTION; CHEMISTRY; DRUG EFFECTS; ENZYME ACTIVE SITE; GENETICS; HYDROLYSIS; KINETICS; METABOLISM; PROTEIN TERTIARY STRUCTURE; TIME; X RAY CRYSTALLOGRAPHY;

ARCHAEA; SULFOLOBUS SOLFATARICUS;

AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI PROTEINS; GTP-BINDING PROTEINS; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATE; HYDROLYSIS; KINETICS; MAGNESIUM; MUTANT PROTEINS; POINT MUTATION; PROTEIN STRUCTURE, TERTIARY; SULFOLOBUS SOLFATARICUS; TIME FACTORS;

EID: 77954391276     PISSN: 0021924X     EISSN: 17562651     Source Type: Journal    
DOI: 10.1093/jb/mvq039     Document Type: Article

References (32)

1. Wu, H., Sun, L., Blombach, F., Brouns, S.J., Snijders, A.P., Lorenzen, K., van den Heuvel, R.H., Heck, A.J., Fu, S., Li, X., Zhang, X.C., Rao, Z., and van der Oost, J. (2009) Structure of the ribosome associating GTPase HflX. Proteins 78, 705-713
2. Leipe, D.D., Wolf, Y.I., Koonin, E.V., and Aravind, L. (2002) Classification and evolution of P-loop GTPases and related ATPases. J. Mol. Biol. 317, 41-72
3. Vetter, I.R. and Wittinghofer, A. (2001) The guanine nucleotide-binding switch in three dimensions. Science 294, 1299-1304
4. Jain, N., Dhimole, N., Khan, A.R., De, D., Tomar, S.K., Sajish, M., Dutta, D., Parrack, P., and Prakash, B. (2009) E. coli HflX interacts with 50S ribosomal subunits in presence of nucleotides. Biochem. Biophys. Res. Commun. 379, 201-205
5. Polkinghorne, A., Ziegler, U., Gonzalez-Hernandez, Y., Pospischil, A., Timms, P., and Vaughan, L. (2008) Chlamydophila pneumoniae HflX belongs to an unchar-acterized family of conserved GTPases and associates with the Escherichia coli 50S large ribosomal subunit. Microbiology 154, 3537-3546
6. Shields, M.J., Fischer, J.J., and Wieden, H.J. (2009) Toward understanding the function of the universally conserved GTPase HflX from Escherichia coli: a kinetic approach. Biochemistry 48, 10793-10802
7. Zhu, G., Liu, J., Terzyan, S., Zhai, P., Li, G., and Zhang, X.C. (2003) High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalyt-ically important phosphate-binding loop. J. Biol. Chem. 278, 2452-2460
8. Jurnak, F., Heffron, S., and Bergmann, E. (1990) Conformational changes involved in the activation of ras p21: implications for related proteins. Cell 60, 525-528
9. Der, C.J., Finkel, T., and Cooper, G.M. (1986) Biological and biochemical properties of human rasH genes mutated at codon 61. Cell 44, 167-176
10. Pai, E.F., Krengel, U., Petsko, G.A., Goody, R.S., Kabsch, W., and Wittinghofer, A. (1990) Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 9, 2351-2359
11. Barbieri, M.A., Li, G., Mayorga, L.S., and Stahl, P.D. (1996) Characterization of Rab5:Q79L-stimulated endo-some fusion. Arch. Biochem. Biophys. 326, 64-72
12. Ericsson, U.B., Hallberg, B.M., Detitta, G.T., Dekker, N., and Nordlund, P. (2006) Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal. Biochem. 357, 289-298
13. Wu, H., Sun, L., Brouns, S.J., Fu, S., Akerboom, J., Li, X., and van der Oost, J. (2007) Purification, crystallization and preliminary crystallographic analysis of a GTP-binding protein from the hyperthermophilic archaeon Sulfolobus solfataricus. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 63, 239-241
14. Scheffzek, K., Ahmadian, M.R., Kabsch, W., Wiesmuller, L., Lautwein, A., Schmitz, F., and Wittinghofer, A. (1997) The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277, 333-338
15. Li, G. and Liang, Z. (2001) Phosphate-binding loop and Rab GTPase function: mutations at Ser29 and Ala30 of Rab5 lead to loss-of-function as well as gain-of-function phenotype. Biochem. J. 355, 681-689
16. Li, G., Barbieri, M.A., Colombo, M.I., and Stahl, P.D. (1994) Structural features of the GTP-binding defective Rab5 mutants required for their inhibitory activity on endocytosis. J. Biol. Chem. 269, 14631-14635
17. Geladopoulos, T.P., Sotiroudis, T.G., and Evangelopoulos, A.E. (1991) A malachite green colori-metric assay for protein phosphatase activity. Anal Biochem 192, 112-116
18. Chang, M.H., Chae, K.S., Han, D.M., and Jahng, K.Y. (2004) The GanB Galpha-protein negatively regulates asexual sporulation and plays a positive role in conidial germination in Aspergillus nidulans. Genetics 167, 1305-1315
19. Ford, B., Hornak, V., Kleinman, H, and Nassar, N. (2006) Structure of a transient intermediate for GTP hydrolysis by ras. Structure 14, 427-436
20. Brownbridge, G.G., Lowe, P.N., Moore, K.J., Skinner, R.H., and Webb, M.R. (1993) Interaction of GTPase activating proteins (GAPs) with p21ras measured by a novel fluorescence anisotropy method. Essential role of Arg-903 of GAP in activation of GTP hydrolysis on p21ras. J. Biol. Chem. 268, 10914-10919
21. Gille, A. and Seifert, R. (2003) 20(30)-O-(N-methylanthraniloyl)- substituted GTP analogs: a novel class of potent competitive adenylyl cyclase inhibitors. J. Biol. Chem. 278, 12672-12679
22. Tesmer, V.M., Kawano, T., Shankaranarayanan, A., Kozasa, T., and Tesmer, J.J. (2005) Snapshot of activated G proteins at the membrane: the Galphaq-GRK2-Gbetagamma complex. Science 310, 1686-1690
23. Sprang, S.R. (1997) G protein mechanisms: insights from structural analysis. Annu. Rev. Biochem. 66, 639-678
24. Sasaki, T., Kikuchi, A., Araki, S., Hata, Y., Isomura, M., Kuroda, S., and Takai, Y. (1990) Purification and characterization from bovine brain cytosol of a protein that inhibits the dissociation of GDP from and the subsequent binding of GTP to smg p25A, a ras p21-like GTP-binding protein. J. Biol. Chem. 265, 2333-2337
25. Mishra, R., Gara, S.K., Mishra, S., and Prakash, B. (2005) Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: implications for GTP hydrolysis. Proteins 59, 332-338
26. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326
27. McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., and Read, R.J. (2007) Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674
28. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
29. Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., and Terwilliger, T.C. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948-1954
30. French, G.S. and Wilson, K.S. (1978) Acta. Cryst. A34, 517
31. Bailey, S. (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallographica D 50, 760-763
32. Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291