Dimerisation-dependent GTPase reaction of MnmE: How potassium acts as GTPase-activating element

EMBO Journal

Volumn 25, Issue 12, 2006, Pages 2940-2951

  Scrima, Andrea ^a   Wittinghofer, Alfred ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

Author keywords

GAP; GTP binding; GTPase; MnmE; Potassium

Indexed keywords

GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATASE; GUANOSINE TRIPHOSPHATE; NUCLEOTIDE BINDING PROTEIN; POTASSIUM;

ARTICLE; CATALYST; CONFORMATIONAL TRANSITION; DIMERIZATION; ENZYME ACTIVATION; ENZYME ACTIVE SITE; GENE MUTATION; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STABILITY; REACTION ANALYSIS; STRUCTURE ANALYSIS;

EID: 33745520400     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/sj.emboj.7601171     Document Type: Article

References (51)

1. Berezin C, Glaser F, Rosenberg Y, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N (2004) ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 20: 1322-1324
2. Bjork GR, Durand JM, Hagervall TG, Leipuviene R, Lundgren HK, Nilsson K, Chen P, Qian Q, Urbonavicius J (1999) Transfer RNA modification: influence on translational frameshifting and metabolism. FEBS Lett 452: 47-51
3. Bourne HR, Sanders DA, McCormick F (1990) The GTPase superfamily: a conserved switch for diverse cell functions. Nature 348: 125-132
4. Bourne HR, Sanders DA, McCormick F (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature 349: 117-127
5. Brégeon D, Colot V, Radman M, Taddei F (2001) Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 15: 2295-2306
6. Brierley I, Meredith MR, Bloys AJ, Hagervall TG (1997) Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: influence of tRNA anticodon modification on frameshifting. J Mol Biol 270: 360-373
7. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54: 905-921
8. Cabedo H, Macian F, Villarroya M, Escudero JC, Martinez-Vicente M, Knecht E, Armengod ME (1999) The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties. EMBO J 18: 7063-7076
9. Caldon CE, Yoong P, March PE (2001) Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function. Mol Microbiol 41: 289-297
10. Chaudhry C, Farr GW, Todd MJ, Rye HS, Brunger AT, Adams PD, Horwich AL, Sigler PB (2003) Role of the gamma-phosphate of ATP in triggering protein folding by GroEL-GroES: function, structure and energetics. EMBO J 22: 4877-4887
11. Colby G, Wu M, Tzagoloff A (1998) MTO1 codes for a mitochondrial protein required for respiration in paromomycin-resistant mutants of Saccharomyces cerevisiae. J Biol Chem 273: 27945-27952
12. Daumke O, Weyand M, Chakrabarti PP, Vetter IR, Wittinghofer A (2004) The GTPase-activating protein Rap1GAP uses a catalytic asparagine. Nature 429: 197-201
13. Decoster E, Vassal A, Faye G (1993) MSS1, a nuclear-encoded mitochondrial GTPase involved in the expression of COX1 subunit of cytochrome c oxidase. J Mol Biol 232: 79-88
14. de La Fortelle E, Bricogne G (1997) Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol 276: 472-494
15. Dittrich M, Hayashi S, Schulten K (2004) ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase. Biophys J 87: 2954-2967
16. Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM (2004) Substrate twinning activates the signal recognition particle and its receptor. Nature 427: 215-221
17. Elseviers D, Petrullo LA, Gallagher P (1984) Novel E. coli mutants deficient in biosynthesis of 5-methylaminomethyl-2-thiouridine. Nucleic Acids Res 12: 3521-3534
18. Focia PJ, Shepotinovskaya IV, Seidler JA, Freymann DM (2004) Heterodimeric GTPase core of the SRP targeting complex. Science 303: 373-377
19. Ghosh A, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C (2006) How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Nature 440: 101-104
20. Gibbs CS, Zoller MJ (1991) Rational scanning mutagenesis of a protein kinase identifies functional regions involved in catalysis and substrate interactions. J Biol Chem 266: 8923-8931
21. Hagervall TG, Pomerantz SC, McCloskey JA (1998) Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position. J Mol Biol 284: 33-42
22. Johnson LN, Noble ME, Owen DJ (1996) Active and inactive protein kinases: structural basis for regulation. Cell 85: 149-158
23. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallogr 26: 795-800
24. Kraulis PJ (1991) MolScript - a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946-950
25. Li X, Guan MX (2002) A human mitochondrial GTP binding protein related to tRNA modification may modulate phenotypic expression of the deafness-associated mitochondrial 12S rRNA mutation. Mol Cell Biol 22: 7701-7711
26. Li X, Li R, Lin X, Guan MX (2002) Isolation and characterization of the putative nuclear modifier gene MTO1 involved in the pathogenesis of deafness-associated mitochondrial 12 S rRNA A1555G mutation. J Biol Chem 277: 27256-27264
27. Martinez-Vicente M, Yim L, Villarroya M, Mellado M, Perez-Paya E, Bjork GR, Armengod ME (2005) 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 280: 30660-30670
28. McRee DE (1999) XtalView/Xfit - a versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125: 156-165
29. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst D 53: 240-255
30. Praefcke GJ, McMahon HT (2004) The dynamin superfamily: universal membrane tubulation and fission molecules? Nat Rev Mol Cell Biol 5: 133-147
31. Rehmann H, Bos JL (2004) Signal transduction: thumbs up for inactivation. Nature 429: 138-139
32. Saraste M, Sibbald PR, Wittinghofer A (1990) The P-Loop - a common motif in ATP- and GTP-binding proteins. TIBS 15: 430-434
33. Scheffzek K, Ahmadian MR, Kabsch W, Wiesmüller L, Lautwein A, Schmitz F, Wittinghofer A (1997) The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic ras mutants. Science 277: 333-338
34. Scrima A, Vetter IR, Armengod ME, Wittinghofer A (2005) The structure of the TrmE GTP-binding protein and its implications for tRNA modification. EMBO J 24: 23-33
35. Seewald MJ, Körner C, Wittinghofer A, Vetter IR (2002) RanGAP mediates GTP hydrolysis without an arginine finger. Nature 415: 662-666
36. Sousa MC, McKay DB (1998) The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change. Biochemistry 37: 15392-15399
37. Suelter CH (1970) Enzymes activated by monovalent cations. Science 168: 789-795
38. Sun Y-J, Forouhar F, Li H-M, Tu S-L, Kao S, Shr H-L, Chou C-C, Hsiao C-D (2002) Crystal structure of pea Toc34 - a novel GTPase of the chloroplast protein translocon. Nat Struct Biol 9: 95-100
39. Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K (2001) Novel taurine-containing uridine derivatives and mitochondrial human diseases. Nucleic Acids Res Suppl 1: 257-258
40. Urbonavicius J, Qian Q, Durand JMB, Hagervall TG, Björk GR (2001) Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J 20: 4863-4873
41. Usón I, Sheldrick GM (1999) Advances in direct methods for protein crystallography. Curr Opin Struct Biol 9: 643-648
42. Vetter IR, Wittinghofer A (2001) The guanine nucleotide-binding switch in three dimensions. Science 294: 1299-1304
43. Wang J, Boisvert DC (2003) Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP) 14 at 2.0 A resolution. J Mol Biol 327: 843-855
44. Wilbanks SM, McKay DB (1995) How potassium affects the activity of the molecular chaperone Hsc70. II. Potassium binds specifically in the ATPase active site. J Biol Chem 270: 2251-2257
45. Wittinghofer A (1997) Signaling mechanistics: aluminum fluoride for molecule of the year. Curr Biol 7: R682-R685
46. Wittinghofer A (2006) Phosphoryl transfer in Ras proteins, conclusive or elusive? TIBS 31: 20-23
47. Yamanaka K, Hwang J, Inouye M (2000) Characterization of GTPase activity of TrmE, a member of a novel GTPase superfamily, from Thermotoga maritima. J Bacteriol 182: 7078-7082
48. Yim L, Martinez-Vicente M, Villarroya M, Aguado C, Knecht E, Armengod ME (2003) The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function. J Biol Chem 278: 28378-28387
49. Yokoyama S, Nishimura S (1995) Modified nucleosides and codon recognition. In tRNA: Structure, Biosynthesis and Function, Söll D, RajBhandary UL (eds) pp 207-223. Washington, DC: American Society for Microbiology
50. Yokoyama S, Watanabe T, Murao K, Ishikura H, Yamaizumi Z, Nishimura S, Miyazawa T (1985) Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc Natl Acad Sci USA 82: 4905-4909
51. Yokoyama S, Yamaizumi Z, Nishimura S, Miyazawa T (1979) 1H NMR studies on the conformational characteristics of 2-thiopyrimidine nucleotides found in transfer RNAs. Nucleic Acids Res 6: 2611-2626