Crystal structure of an Escherichia coli tRNAGly microhelix at 2.0 Å resolution

Biochemical and Biophysical Research Communications

Volumn 363, Issue 3, 2007, Pages 621-625

  Forster C ^a   Brauer, A B E ^a   Perbandt, M ^b   Lehmann, D ^a   Furste J P ^a   Betzel, Ch ^b   Erdmann, V A ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Glycyl tRNA synthetase (GlyRS) system; Magnesium binding sites; tRNA identity elements; tRNAGly acceptor stem microhelix

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; MAGNESIUM; TRANSFER RNA;

AMINOACYLATION; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; CRYSTALLIZATION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL;

BASE SEQUENCE; CRYSTALLIZATION; ESCHERICHIA COLI; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, TRANSFER, GLY; X-RAY DIFFRACTION;

ESCHERICHIA COLI;

EID: 34848926827     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.09.008     Document Type: Article

References (29)

1. M. Ibba, C. Franclyn, S. Cusack (Eds.), The Aminoacyl-tRNA Synthetases, Landess Bioscience, Georgetown, Texas, USA, 2005.
2. Eriani G., Delarue M., Poch O., Gangloff J., and Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347 (1990) 203-206
3. Shiba K., Schimmel P., Motegi H., and Noda T. Human Glycyl-tRNA Synthetase. J. Biol. Chem. 269 (1994) 30049-30055
4. Ostrem D.L., and Berg P. Glycyl transfer ribonucleic acid synthetase from Escherichia coli. Purification, properties, and substrate binding. Biochemistry 13 (1974) 1338-1348
5. Webster T.A., Gibson B.W., Keng T., Biemann K., and Schimmel P. Primary structures of both subunits of Escherichia coli glycyl-tRNA synthetase. J. Biol. Chem. 258 (1983) 10637-10641
6. Toth M.J., and Schimmel P. Deletions in the large (beta) subunit of a hetero-oligomeric aminoacyl-tRNA synthetase. J. Biol. Chem. 265 (1990) 1000-1004
7. Toth M.J., and Schimmel P. A mutation in the small (alpha) subunit of glycyl-tRNA synthetase affects amino acid activation and subunit association parameters. J. Biol. Chem. 265 (1990) 1005-1009
8. Nagel G.M., Cumberledge S., Johnson M.S., Petrella E., and Weber B. The β subunit of E. coli glycyl-tRNA synthetase plays a major role in tRNA recognition. Nucl. Acids Res. 12 (1984) 4377-4384
9. Gly acceptor identity. Proc. Natl. Acad. Sci. USA 88 (1991) 6147-6151
10. Kern D., Giegé R., and Ebel J.P. Glycyl-tRNA synthetase from Baker's yeast. Interconversion between active and inactive forms of the enzyme. Biochemistry 20 (1981) 122-131
11. Nada S., Chang P.K., and Dignam J.D. Primary structure of the gene for glycyl-tRNA synthetase from Bombyx mori. J. Biol. Chem. 268 (1993) 7660-7667
12. K. Shiba, Glycyl-tRNA synthetases, in: M. Ibba, C. Franclyn, S. Cusack (Eds.), The Aminoacyl-tRNA Synthetases, Landess Bioscience, Georgetown, Texas, USA, 2005, pp. 125-134 (Chapter 13).
13. Logan D.T., Mazauric M.H., Kern D., and Moras D. Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. EMBO J. 14 (1995) 4156-4167
14. Sprinzl M., and Vassilenko K.S. Compilation of tRNA sequences and sequences of tRNA genes. Nucl. Acids Res. 33 (2005) D139-D140
15. Gly acceptor-stem microhelix. Acta Crystallogr. F63 (2007) 46-48
16. Shi H., and Moore P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited. RNA 6 (2000) 1091-1105
17. Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D60 (2004) 2126-2132
18. Navaza J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. A50 (1994) 157-163
19. McCoy A.J., Grosse-Kunstleve R.W., Storoni L.C., and Read R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D61 (2005) 458-464
20. Collaborative Computational Project, Number 4, The CCP 4 Suite: Programs for Protein Crystallography, Acta Crystallogr. D50 (1994), 760-763.
21. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53 (1997) 240-255
22. Read R.J., and Schierbeek A.J. A phased translation function. J. Appl. Cryst. 21 (1988) 490-495
23. W.L. DeLano, The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA, USA.
24. Lu X.-J., and Olson E.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucl. Acids Res. 17 (2003) 5108-5121
25. Ser acceptor stem: conformation and hydration of a microhelix in a crystal structure at 1.8 Å resolution (unpublished results).
26. Ala from Escherichia coli shows unique GU wobble base pair at 1.16 Å resolution. RNA 5 (1999) 670-677
27. Teeter M.M., Quigley G.J., and Rich A. In: Spiro T.G. (Ed). Nucleic Acids-Metal Ion Interaction (1980), Wiley, New York 145-177
28. Quigley G.J., Teeter M.M., and Rich A. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc. Natl. Acad. Sci. USA 75 (1978) 64-68
29. Limmer S., Hofmann H.-P., Ott G., and Sprinzl M. The 3′-terminal end (NCCA) of tRNA determines the structure and stability of the aminoacyl acceptor stem. Proc. Natl. Acad. Sci. USA 90 (1993) 6199-6202