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Volumn 66, Issue 3, 2007, Pages 726-739

Structural insights into the GTPase domain of Escherichia coli MnmE protein

Author keywords

Aluminium fluoride; Era; GTPase; Homology modeling; MnmE; NMB; Rap2A; Ras; TrmE

Indexed keywords

ALUMINUM FLUORIDE; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANOSINE TRIPHOSPHATASE; PROTEIN MNME; UNCLASSIFIED DRUG;

EID: 33846234741     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21186     Document Type: Conference Paper
Times cited : (7)

References (45)
  • 1
    • 0026026818 scopus 로고
    • The GTPase superfamily: Conserved structure and molecular mechanism
    • Bourne HR, Sanders DA, McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature 1991; 349:117-127.
    • (1991) Nature , vol.349 , pp. 117-127
    • Bourne, H.R.1    Sanders, D.A.2    McCormick, F.3
  • 2
    • 0036295212 scopus 로고    scopus 로고
    • Classification and evolution of P-loop GTPases and related ATPases
    • Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol 2002;317:41-72.
    • (2002) J Mol Biol , vol.317 , pp. 41-72
    • Leipe, D.D.1    Wolf, Y.I.2    Koonin, E.V.3    Aravind, L.4
  • 3
    • 0030722725 scopus 로고    scopus 로고
    • G proteins. The arginine finger strikes again
    • Bourne HR. G proteins. The arginine finger strikes again. Nature 1997;389:673,674.
    • (1997) Nature , vol.389 , pp. 673-674
    • Bourne, H.R.1
  • 5
    • 0031452275 scopus 로고    scopus 로고
    • GDIs and effectors: Taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins
    • Geyer M, Wittinghofer A. GEFs, GAPs, GDIs and effectors: taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins. Curr Opin Struct Biol 1997;7:786-792.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 786-792
    • Geyer, M.1    Wittinghofer, A.2    GEFs, G.3
  • 6
    • 0035834388 scopus 로고    scopus 로고
    • The guanine nucleotide-binding switch in three dimensions
    • Vetter IR, Wittinghofer A. The guanine nucleotide-binding switch in three dimensions. Science 2001;294:1299-1304.
    • (2001) Science , vol.294 , pp. 1299-1304
    • Vetter, I.R.1    Wittinghofer, A.2
  • 7
    • 0033573089 scopus 로고    scopus 로고
    • The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties
    • Cabedo H, Macian F, Villarroya M, Escudero JC, Martinez-Vicente M, Knecht E, Armengod ME. The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties. EMBO J 1999;18:7063-7076.
    • (1999) EMBO J , vol.18 , pp. 7063-7076
    • Cabedo, H.1    Macian, F.2    Villarroya, M.3    Escudero, J.C.4    Martinez-Vicente, M.5    Knecht, E.6    Armengod, M.E.7
  • 8
    • 0043210520 scopus 로고    scopus 로고
    • The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function
    • Yim L, Martinez-Vicente M, Villarroya M, Aguado C, Knecht E, Armengod ME. The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function. J Biol Chem 2003;278:28378-28387.
    • (2003) J Biol Chem , vol.278 , pp. 28378-28387
    • Yim, L.1    Martinez-Vicente, M.2    Villarroya, M.3    Aguado, C.4    Knecht, E.5    Armengod, M.E.6
  • 9
    • 24744470965 scopus 로고    scopus 로고
    • Effects of mutagenesis in the switch I region and conserved arginines of Escherichia coli MnmE protein, a GTPase involved in tRNA modification
    • Martinez-Vicente M, Yim L, Villarroya M, Mellado M, Perez-Paya E, Bjork GR, Armengod ME. Effects of mutagenesis in the switch I region and conserved arginines of Escherichia coli MnmE protein, a GTPase involved in tRNA modification. J Biol Chem 2005;280:30660-30670.
    • (2005) J Biol Chem , vol.280 , pp. 30660-30670
    • Martinez-Vicente, M.1    Yim, L.2    Villarroya, M.3    Mellado, M.4    Perez-Paya, E.5    Bjork, G.R.6    Armengod, M.E.7
  • 10
    • 0032561194 scopus 로고    scopus 로고
    • MTO1 codes for a mitochondrial protein required for respiration in paromomycin-resistant mutants of Saccharomyces cerevisiae
    • Colby G, Wu M, Tzagoloff A. MTO1 codes for a mitochondrial protein required for respiration in paromomycin-resistant mutants of Saccharomyces cerevisiae. J Biol Chem 1998;273: 27945-27952.
    • (1998) J Biol Chem , vol.273 , pp. 27945-27952
    • Colby, G.1    Wu, M.2    Tzagoloff, A.3
  • 11
    • 12544259245 scopus 로고    scopus 로고
    • Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs
    • Umeda N, Suzuki T, Yukawa M, Ohya Y, Shindo H, Watanabe K, Suzuki T. Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. J Biol Chem 2005;280:1613-1624.
    • (2005) J Biol Chem , vol.280 , pp. 1613-1624
    • Umeda, N.1    Suzuki, T.2    Yukawa, M.3    Ohya, Y.4    Shindo, H.5    Watanabe, K.6    Suzuki, T.7
  • 12
    • 0036838879 scopus 로고    scopus 로고
    • Wobble modification defect suppresses translational activity of tRNAs with MERRF and MELAS mutations
    • Yasukawa T, Suzuki T, Ohta S, Watanabe K. Wobble modification defect suppresses translational activity of tRNAs with MERRF and MELAS mutations. Mitochondrion 2002;2:129-141.
    • (2002) Mitochondrion , vol.2 , pp. 129-141
    • Yasukawa, T.1    Suzuki, T.2    Ohta, S.3    Watanabe, K.4
  • 14
    • 6344221310 scopus 로고    scopus 로고
    • Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease
    • Kirino Y, Yasukawa T, Ohta S, Akira S, Ishihara K, Watanabe K, Suzuki T. Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. Proc Natl Acad Sci USA 2004;101:15070-15075.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 15070-15075
    • Kirino, Y.1    Yasukawa, T.2    Ohta, S.3    Akira, S.4    Ishihara, K.5    Watanabe, K.6    Suzuki, T.7
  • 15
    • 18844430007 scopus 로고    scopus 로고
    • Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease
    • Kirino Y, Goto Y, Campos Y, Arenas J, Tsutomu S. Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease. Proc Natl Acad Sci USA 2005;102:7127-7132.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 7127-7132
    • Kirino, Y.1    Goto, Y.2    Campos, Y.3    Arenas, J.4    Tsutomu, S.5
  • 16
    • 13244284641 scopus 로고    scopus 로고
    • The structure of the TrmE GTP-binding protein and its implications for tRNA modification
    • Scrima A, Vetter IR, Armengod ME, Wittinghoffer A. The structure of the TrmE GTP-binding protein and its implications for tRNA modification. EMBO J 2005;24:23-33.
    • (2005) EMBO J , vol.24 , pp. 23-33
    • Scrima, A.1    Vetter, I.R.2    Armengod, M.E.3    Wittinghoffer, A.4
  • 17
    • 0347383758 scopus 로고    scopus 로고
    • Modeller: Generation and refinement of homology-based protein structure models
    • Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003;374: 461-491.
    • (2003) Methods Enzymol , vol.374 , pp. 461-491
    • Fiser, A.1    Sali, A.2
  • 18
    • 0032575355 scopus 로고    scopus 로고
    • Homology model for oncostatin M based on NMR structural data
    • Kitchen D, Hoffman RC, Moy FJ, Powers R. Homology model for oncostatin M based on NMR structural data. Biochemistry 1998;37:10581-10588.
    • (1998) Biochemistry , vol.37 , pp. 10581-10588
    • Kitchen, D.1    Hoffman, R.C.2    Moy, F.J.3    Powers, R.4
  • 20
    • 1242317854 scopus 로고    scopus 로고
    • Backbone 1H, 13C and 15N resonance assignments for the 18.7 kDa GTPase domain of Escherichia coli MnmE protein
    • Monleon D, Yim L, Martinez-Vicente M, Armengod ME, Celda B. Backbone 1H, 13C and 15N resonance assignments for the 18.7 kDa GTPase domain of Escherichia coli MnmE protein. J Biomol NMR 2004;28:307,308.
    • (2004) J Biomol NMR , vol.28 , pp. 307-308
    • Monleon, D.1    Yim, L.2    Martinez-Vicente, M.3    Armengod, M.E.4    Celda, B.5
  • 22
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 23
    • 0030931336 scopus 로고    scopus 로고
    • Seventy-five percent accuracy in protein secondary structure prediction
    • Frishman D, Argos P. Seventy-five percent accuracy in protein secondary structure prediction. Proteins 1997;27:329-335.
    • (1997) Proteins , vol.27 , pp. 329-335
    • Frishman, D.1    Argos, P.2
  • 24
    • 0029889988 scopus 로고    scopus 로고
    • B Rost PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 1996;266:525-539.
    • B Rost PHD: predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol 1996;266:525-539.
  • 25
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 26
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 27
    • 0030956593 scopus 로고    scopus 로고
    • Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three-dimensional structure of murine homeodomain Msx-1
    • Li H, Tejero R, Monleon D, Bassolino-Klimas D, Abate-Shen C, Bruccoleri RE, Montelione GT. Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1. Protein Sci 1997;6:956-970.
    • (1997) Protein Sci , vol.6 , pp. 956-970
    • Li, H.1    Tejero, R.2    Monleon, D.3    Bassolino-Klimas, D.4    Abate-Shen, C.5    Bruccoleri, R.E.6    Montelione, G.T.7
  • 28
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu G, Delaglio F, Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 1999;13:289-302.
    • (1999) J Biomol NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 29
    • 0031576336 scopus 로고    scopus 로고
    • Torsion angle dynamics for NMR structure calculation with the new program DYANA
    • Guntert P, Mumenthaler C, Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997;273:283-298.
    • (1997) J Mol Biol , vol.273 , pp. 283-298
    • Guntert, P.1    Mumenthaler, C.2    Wuthrich, K.3
  • 31
    • 0029249555 scopus 로고
    • Combined use of 13C chemical shift and 1H α-13C a heteronuclear NOE data in monitoring a protein NMR structure refinement
    • Celda B, Biamonti C, Arnau MJ, Tejero R, Montelione GT. Combined use of 13C chemical shift and 1H α-13C a heteronuclear NOE data in monitoring a protein NMR structure refinement. J Biomol NMR 1995;5:161-172.
    • (1995) J Biomol NMR , vol.5 , pp. 161-172
    • Celda, B.1    Biamonti, C.2    Arnau, M.J.3    Tejero, R.4    Montelione, G.T.5
  • 32
    • 0033587699 scopus 로고    scopus 로고
    • Crystal structure of Era: A GTPase-dependent cell cycle regulator containing an RNA binding motif
    • Chen X, Court DL, Ji X. Crystal structure of Era: a GTPase-dependent cell cycle regulator containing an RNA binding motif. Proc Natl Acad Sci USA 1999;96:8396-8401.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 8396-8401
    • Chen, X.1    Court, D.L.2    Ji, X.3
  • 33
    • 0028204451 scopus 로고
    • Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy
    • Kraulis PJ, Domaille PJ, Campbell-Burk SL, Van Aken T, Laue ED. Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry 1994;33:3515-3531.
    • (1994) Biochemistry , vol.33 , pp. 3515-3531
    • Kraulis, P.J.1    Domaille, P.J.2    Campbell-Burk, S.L.3    Van Aken, T.4    Laue, E.D.5
  • 34
  • 35
    • 0035544152 scopus 로고    scopus 로고
    • Automated prediction of 15N, 13Cα, 13Cβ and 13C′ chemical shifts in proteins using a density functional database
    • Xu XP, Case DA. Automated prediction of 15N, 13Cα, 13Cβ and 13C′ chemical shifts in proteins using a density functional database. J Biomol NMR 2001;21:321-333.
    • (2001) J Biomol NMR , vol.21 , pp. 321-333
    • Xu, X.P.1    Case, D.A.2
  • 36
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi R, Billeter M, Wuthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 1996;14:29-32.
    • (1996) J Mol Graph , vol.14 , pp. 29-32
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 37
  • 38
    • 0031231083 scopus 로고    scopus 로고
    • Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras
    • Ahmadian MR, Stege P, Scheffzek K, Wittinghofer A. Confirmation of the arginine-finger hypothesis for the GAP-stimulated GTP-hydrolysis reaction of Ras. Nat Struct Biol 1997;4:686-689.
    • (1997) Nat Struct Biol , vol.4 , pp. 686-689
    • Ahmadian, M.R.1    Stege, P.2    Scheffzek, K.3    Wittinghofer, A.4
  • 39
    • 0033578805 scopus 로고    scopus 로고
    • Nucleotide-binding characteristics of human guanylate-binding protein 1 (hGBP1) and identification of the third GTP-binding motif
    • Praefcke GJ, Geyer M, Schwemmle M, Robert Kalbitzer H, Herrmann C. Nucleotide-binding characteristics of human guanylate-binding protein 1 (hGBP1) and identification of the third GTP-binding motif. J Mol Biol 1999;292:321-332.
    • (1999) J Mol Biol , vol.292 , pp. 321-332
    • Praefcke, G.J.1    Geyer, M.2    Schwemmle, M.3    Robert Kalbitzer, H.4    Herrmann, C.5
  • 40
    • 0033579936 scopus 로고    scopus 로고
    • The conserved arginine in Rho-GTPase-activating protein is essential for efficient catalysis but not for complex formation with Rho-GDP and aluminium fluoride
    • Graham DL, Eccleston JF, Lowe PN. The conserved arginine in Rho-GTPase-activating protein is essential for efficient catalysis but not for complex formation with Rho-GDP and aluminium fluoride. Biochemistry 1999;38: 985-991.
    • (1999) Biochemistry , vol.38 , pp. 985-991
    • Graham, D.L.1    Eccleston, J.F.2    Lowe, P.N.3
  • 41
    • 0032769396 scopus 로고    scopus 로고
    • pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog
    • Schlichting I, Reinstein J. pH influences fluoride coordination number of the AlFx phosphoryl transfer transition state analog. Nat Struct Biol 1999;6:721-723.
    • (1999) Nat Struct Biol , vol.6 , pp. 721-723
    • Schlichting, I.1    Reinstein, J.2
  • 42
    • 0344823672 scopus 로고    scopus 로고
    • NMR structure of an archaeal homologue of ribonuclease P protein Rpp29
    • Sidote DJ, Hoffman DW. NMR structure of an archaeal homologue of ribonuclease P protein Rpp29. Biochemistry 2003;42: 13541-13550.
    • (2003) Biochemistry , vol.42 , pp. 13541-13550
    • Sidote, D.J.1    Hoffman, D.W.2
  • 43
    • 0030729838 scopus 로고    scopus 로고
    • An extensively modified version of MolScript that includes greatly enhanced coloring capabilities
    • Esnouf RM. An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model 1997;15:132-134.
    • (1997) J Mol Graph Model , vol.15 , pp. 132-134
    • Esnouf, R.M.1
  • 44
    • 0034461401 scopus 로고    scopus 로고
    • Characterization of GTPase activity of TrmE, a member of a novel GTPase superfamily, from Thermotoga maritima
    • Yamanaka K, Hwang J, Inouye M. Characterization of GTPase activity of TrmE, a member of a novel GTPase superfamily, from Thermotoga maritima. J Bacteriol 2000;182:7078-7082.
    • (2000) J Bacteriol , vol.182 , pp. 7078-7082
    • Yamanaka, K.1    Hwang, J.2    Inouye, M.3
  • 45
    • 0034043879 scopus 로고    scopus 로고
    • Analysis of guanine nucleotide binding and exchange kinetics of the Escherichia coli GTPase Era
    • Sullivan SM, Mishra R, Neubig RR, Maddock JR. Analysis of guanine nucleotide binding and exchange kinetics of the Escherichia coli GTPase Era. J Bacteriol 2000;182:3460-3466.
    • (2000) J Bacteriol , vol.182 , pp. 3460-3466
    • Sullivan, S.M.1    Mishra, R.2    Neubig, R.R.3    Maddock, J.R.4


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