The structure of the TrmE GTP-binding protein and its implications for tRNA modification

EMBO Journal

Volumn 24, Issue 1, 2005, Pages 23-33

  Scrima, Andrea ^a   Vetter, Ingrid R ^a   Armengod, M Eugenia ^b   Wittinghofer, Alfred ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^b Insituto de Investigationes Citol   (Spain)

Author keywords

GTP binding; Tetrahydrofolate; TrmE; tRNA modification

Indexed keywords

CYSTEINE; DIMETHYLGLYCINE; DIMETHYLGLYCINE OXIDASE; ENZYME; FOLINIC ACID; GUANINE NUCLEOTIDE BINDING PROTEIN; GUANOSINE TRIPHOSPHATE; OXIDOREDUCTASE; PROTEIN TRME; SCHIFF BASE; TETRAHYDROFOLIC ACID; TRANSFER RNA; UNCLASSIFIED DRUG; URIDINE;

ALPHA HELIX; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ANTICODON; ARTICLE; CHEMICAL MODIFICATION; CHEMICAL REACTION; CRYSTAL STRUCTURE; DIMERIZATION; DNA MODIFICATION; FORMYLATION; HYDROGENATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN HYDROLYSIS; PROTEIN STRUCTURE; RNA STRUCTURE; SEQUENCE HOMOLOGY; THERMOTOGA MARITIMA; TRANSFER RNA MODIFICATION; X RAY ANALYSIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; GTP-BINDING PROTEINS; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATE; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RNA, TRANSFER; SEQUENCE ALIGNMENT; TETRAHYDROFOLATES; URIDINE;

EID: 13244284641     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.emboj.7600507     Document Type: Article

References (43)

1. 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
2. Bourne HR, Sanders DA, McCormick F (1990) The GTPase superfamily: a conserved switch for diverse cell functions. Nature 348: 125-132
3. Bourne HR, Sanders DA, McCormick F (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature 349: 117-127
4. Brégeon D, Colot V, Radman M, Taddei F (2001) Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 15: 2295-2306
5. 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
6. Brünger 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
7. 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
8. 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
9. 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
10. 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
11. 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
12. Finer-Moore JS, Santi DV, Stroud RM. (2003) Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure. Biochemistry 42: 248-256
13. Hagervall TG, Edmonds CG, McCloskey JA, Björk GR (1987) Transfer RNA (5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. J Biol Chem 262: 8488-8495
14. 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
15. Herrmann C, Nassar N (1996) Ras and its effectors. Prog Biophys Mol Biol 66: 1-41
16. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637
17. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Crystallogr 26: 795-800
18. Kambampati R, Lauhon CT (2003) MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 42: 1109-1117
19. Kraulis PJ (1991) MolScript - a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946-950
20. Lauhon CT (2002) Requirement for IscS in biosynthesis of all thionucleosides in Escherichia coli. J Bacteriol 184: 6820-6829
21. Lenzen C, Cool RH, Prinz H, Kuhlmann J, Wittinghofer A (1998) Kinetic analysis by fluorescence of the interaction between Ras and the catalytic domain of the guanine nucleotide exchange factor Cdc25Mm. Biochemistry 19: 7420-7430
22. Leys D, Basran J, Scrutton NS (2003) Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase. EMBO J 22: 4038-4048
23. 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
24. 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 12S rRNA A1555G mutation. J Biol Chem 277: 27256-27264
25. Merrit EA, Murphy MEP (1994) Raster3D version 20 - a program for photorealistic molecular graphics. Acta Crystallogr D 50: 869-873
26. Nicholls A, Sharp KA, Honig B (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281-296
27. Saraste M, Sibbald PR, Wittinghofer A (1990) The P-loop - a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 15: 430-434
28. Stone RL, Dixon JE (1994) Protein-tyrosine phosphatases. J Biol Chem 269: 31323-31326
29. Sullivan MA, Cannon JF, Webb FH, Bock RM (1985) Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2- thiouridine. J Bacteriol 161: 368-376
30. Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K (2002) Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO J 21: 6581-6589
31. 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
32. Usón I, Sheldrick GM (1999) Advances in direct methods for protein crystallography. Curr Opin Struct Biol 9: 643-648
33. Vetter IR, Wittinghofer A (2001) The guanine nucleotide-binding switch in three dimensions. Science 294: 1299-1304
34. Vilkaitis G, Merkienè E, Serva S, Weinhold E, Klimasauskas S (2001) The mechanism of DNA cytosine-5 methylation. J Biol Chem 276: 20924-20934
35. White DJ, Merod R, Thomasson B, Hartzell PL (2001) GidA is an FAD-binding protein involved in development of Myxococcus xanthus. Mol Microbiol 42: 503-517
36. 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
37. Yasukawa T, Suzuki T, Ishii N, Ohta S, Watanabe K (2001) Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J 20: 4794-4802
38. Yasukawa T, Suzuki T, Ishii N, Ueda T, Ohta S, Watanabe K (2000a) Defect in modification at the anticodon wobble nucleotide of mitochondrial tRNA(Lys) with the MERRF encephalomyopathy pathogenic mutation. FEBS Lett 467: 175-178
39. Yasukawa T, Suzuki T, Ueda T, Ohta S, Watanabe K (2000b) Modification defect at anticodon wobble nucleotide of mitochondrial tRNAs(Leu)(UUR) with pathogenic mutations of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes. J Biol Chem 275: 4251-4257
40. 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
41. Yokoyama S, Nishimura S (1995) Modified nucleotides and codon recognition. In tRNA: Structure, Biosynthesis and Function, Söll D, RajBhandary UL (eds) pp 207-223. Washington, DC: American Society for Microbiology
42. 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
43. 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