Structure - Function relationships of the intact aIF2α subunit from the archaeon Pyrococcus abyssi

Biochemistry

Volumn 44, Issue 24, 2005, Pages 8749-8756

  Yatime, Laure ^a   Schmitt, Emmanuelle ^a   Blanquet, Sylvain ^a   Mechulam, Yves ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; CRYSTALLOGRAPHY; MOLECULES; NUCLEAR MAGNETIC RESONANCE; POLYPEPTIDES; RNA; YEAST;

ARCHAEA; EUKARYA; RIBOSOMES; STRUCTURAL MOBILITY;

PROTEINS;

ARCHAEAL INITIATION FACTOR 2ALPHA; ELONGATION FACTOR 1ALPHA; INITIATION FACTOR 2; MESSENGER RNA; METHIONINE TRANSFER RNA; POLYPEPTIDE; PROTEIN SUBUNIT; RIBOSOME RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

ALPHA CHAIN; AMINO TERMINAL SEQUENCE; ARCHAEBACTERIUM; ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; EUKARYOTE; GENETIC CONSERVATION; HUMAN; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; PYROCOCCUS ABYSSI; RIBOSOME SUBUNIT; STRUCTURE ACTIVITY RELATION; YEAST;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; CONSENSUS SEQUENCE; CRYSTALLOGRAPHY, X-RAY; EUKARYOTIC INITIATION FACTOR-2; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; PYROCOCCUS ABYSSI; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP;

ARCHAEA; EUKARYOTA; PYROCOCCUS ABYSSI;

EID: 20544464681     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050373i     Document Type: Article

References (38)

1. Hinnebusch, A. G. (2000) in Translation control of gene expression (Sonenberg, N., Hershey, J. W. B., and Mathews, M. B., Eds.) pp 185-244, Cold Spring Harbor Laboratory Press, Plainview, NY.
2. Kyrpides, N. C., and Woese, C. R. (1998) Archaeal translation initiation revisited: The initiation factor 2 and eukaryotic initiation factor 2B α-β-δ subunit families, Proc. Natl. Acad. Sci. U.S.A. 95, 3726-3730.
3. Schmitt, E., Blanquet, S., and Mechulam, Y. (2002) The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors, EMBO J. 21, 1821-1832.
4. Erickson, F. L., Nika, J., Rippel, S., and Hannig, E. M. (2001) Minimum requirements for the function of eukaryotic translation initiation factor 2. Genetics 158, 123-132.
5. Roll-Mecak, A., Alone, P., Cao, C., Dever, T. E., and Burley, S. K. (2004) X-ray structure of translation initiation factor eIF2γ: Implications for tRNA and eIF2α binding, J. Biol. Chem. 279, 10634-10642.
6. Phe, EF-Tu, and a GTP analog, Science 270, 1464-1472.
7. Yatime, L., Schmitt, E., Blanquet, S., and Mechulam, Y. (2004) Functional molecular mapping of archaeal translation initiation factor 2, J. Biol. Chem. 279, 15984-15993.
8. Nonato, M. C., Widom, J., and Clardy, J. (2002) Crystal structure of the N-terminal segment of human eukaryotic translation initiation factor 2α, J. Biol. Chem. 277, 17057-17061.
9. Dhaliwal, S., and Hoffman, D. W. (2003) The crystal structure of the N-terminal region of the α subunit of translation initiation factor 2 (eIF2α) from Saccharomyces cerevisiae provides a view of the loop containing serine 51, the target of the eIF2α-specific kinases, J. Mol. Biol. 334, 187-195.
10. Ito, T., Marintchev, A., and Wagner, G. (2004) Solution structure of human initiation factor eIF2α reveals homology to the elongation factor eEF1B, Structure 12, 1693-1704.
11. Perez, J. M., Siegal, G., Kriek, J., Hard, K., Dijk, J., Canters, G. W., and Moller, W. (1999) The solution structure of the guanine nucleotide exchange domain of human elongation factor 1β reveals a striking resemblance to that of EF-Ts from Escherichia coli. Structure 7, 217-226.
12. Cousineau, B., Leclerc, F., and Cedergren, R. (1997) On the origin of protein synthesis factors: A gene duplication/fusion model, J. Mol. Evol. 45, 661-670.
13. Lindahl, M., Svensson, L. A., Liljas, A., Sedelnikova, S. E., Eliseikina, I. A., Fomenkova, N. P., Nevskaya, N., Nikonov, S. V., Garber, M. B., Muranova, T. A., et al. (1994) Crystal structure of the ribosomal protein S6 from Thermus thermophilus, EMBO J. 13, 1249-1254.
14. Schenk, P. M., Baumann, S., Mattes, R., and Steinbiss, H. H. (1995) Improved high-level expression system for eukaryotic genes in Escherichia coli using T7 RNA polymerase and rare ArgtRNAs, BioTechniques 19, 196-200.
15. Leslie, A. (1990) in Crystallographic computing V, Oxford University Press, New York.
16. Collaborative Computational Project No. 4 (1994) The CCP4 suite: Programs from protein crystallography, Acta Crystallogr. D50, 760-763.
17. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr. D55, 849-861.
18. Terwilliger, T. C. (1999) Reciprocal-space solvent flattening, Acta Crystallogr. D55, 1863-1871.
19. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for the building of proteins model in electron density maps and the location of errors in these models. Acta Crystallogr. A47, 110-119.
20. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D54, 905-921.
21. Storoni, L. C., McCoy, A. J., and Read, R. J. (2004) Likelihood-enhanced fast rotation functions, Acta Crystallogr. D60, 432-438.
22. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res. 25, 4876-4882.
23. Samuel, C. E. (1993) The eIF-2 α protein kinases, regulators of translation in eukaryotes from yeasts to humans, J. Biol. Chem. 268, 7603-7606.
24. Nagai, K., Oubridge, C., Jessen, T. H., Li, J., and Evans, P. R. (1990) Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A, Nature 348, 515-520.
25. Rosenzweig, A. C., Huffman, D. L., Hou, M. Y., Wernimont, A. K., Pufahl, R. A., and O'Halloran, T. V. (1999) Crystal structure of the Atx1 metallochaperone protein at 1.02 Å resolution, Structure 7, 605-617.
26. Jue, R. A., Woodbury, N. W., and Doolittle, R. F. (1980) Sequence homologies among E. coli ribosomal proteins: Evidence for evolutionarily related groupings and internal duplications, J. Mol. Evol. 15, 129-148.
27. Mosyak, L., Reshetnikova, L., Goldgur, Y., Delarue, M., and Safro, M. G. (1995) Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus, Nat. Struct. Biol. 2, 537-547.
28. Xiong, Y., and Steitz, T. A. (2004) Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template, Nature 430, 640-645.
29. Jorgensen, R., Ortiz, P. A., Carr-Schmid, A., Nissen, P., Kinzy, T. G., and Andersen, G. R. (2003) Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase, Nat. Struct. Biol. 10, 379-385.
30. Andersen, G. R., Pedersen, L., Valente, L., Chatterjee, I. I., Kinzy, T. G., Kjeldgaard, M., and Nyborg, J. (2000) Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Bα, Mol. Cell 6, 1261-1266.
31. Donahue, T. F., Cigan, A. M., Pabich, E. K., and Valavicius, B. C. (1988) Mutations at a Zn(II) finger motif in the yeast eIF-2β gene alter ribosomal start-site selection during the scanning process, Cell 54, 621-632.
32. Cigan, A. M., Pabich, E. K., Feng, L., and Donahue, T. F. (1989) Yeast translation initiation suppressor sui2 encodes the α subunit of eukaryotic initiation factor 2 and shares sequence identity with the human α subunit, Proc. Natl. Acad. Sci. U.S.A. 86, 2784-2788.
33. Fromme, J. C., and Verdine, G. L. (2003) Structure of a trapped endonuclease III-DNA covalent intermediate, EMBO J. 22, 3461-3471.
34. Evans, S. V. (1993) Setor: Hardware lighted three-dimensional solid model representation of macromolecules. J. Mol. Graphics 11, 134-138.
35. Barton, G. J. (1993) ALSCRIPT: A tool to format multiple sequence alignments, Protein Eng. 6, 37-40.
36. Nicholls, A., and Honig, B. (1991) A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation, J. Comput. Chem. 12, 435-445.
37. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins 11, 281-286.
38. Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures, J. Mol. Graphics 14, 51-55.