Crystal structure at 1.8 Å resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase

Biochemistry

Volumn 44, Issue 11, 2005, Pages 4294-4301

  Fromant, Michel ^a   Schmitt, Emmanuelle ^a   Mechulam, Yves ^a   Lazennec, Christine ^a   Plateau, Pierre ^a   Blanquet, Sylvain ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CATALYSIS; CRYSTAL STRUCTURE; CRYSTALLINE MATERIALS; DIMERS; RNA; VAN DER WAALS FORCES;

ACTIVE SITES; HOMOLOGUES; NUCLEOPHILES; PROTOMERS;

ENZYMES;

HYDROLASE; PEPTIDE TRANSFER RIBONUCLEIC ACID HYDROLASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; CATALYSIS; ENZYME ACTIVE SITE; ENZYME ACTIVITY; NONHUMAN; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; SULFOLOBUS SOLFATARICUS;

AMINO ACID SEQUENCE; ANIMALS; ARCHAEAL PROTEINS; ASPARTIC ACID; BINDING SITES; CARBOXYLIC ESTER HYDROLASES; CATALYTIC DOMAIN; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ENZYME ACTIVATION; HUMANS; LYSINE; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN STRUCTURE, SECONDARY; SUBSTRATE SPECIFICITY; SULFOLOBUS SOLFATARICUS; THREONINE;

EID: 15544363359     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047711k     Document Type: Article

References (22)

1. Atherly, A. G., and Menninger, J. R. (1972) Mutant E.coli strain with temperature sensitive peptidyl-transfer RNA hydrolase, Nat. New Biol. 240, 245-246.
2. Garcia-Villegas, M. R., De La Vega, F. M., Galindo, J. M., Segura, M., Buckingham, R. H., and Guarneros, G. (1991) Peptidyl-tRNA hydrolase is involved in λ inhibition of host protein synthesis, EMBO J. 10, 3549-3555.
3. Menninger, J. R., and Coleman, R. A. (1993) Lincosamide antibiotics stimulate dissociation of peptidyl-tRNA from ribosomes, Antimicrob. Agents Chemother. 37, 2027-2029.
4. Schmitt, E., Mechulam, Y., Fromant, M., Plateau, P., and Blanquet, S. (1997) Crystal structure at 1.2 Å resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase, EMBO J. 16, 4760-4769.
5. Bonin, P. D., Choi, G. H., Trepod, C. M., Mott, J. E., Lyle, S. B., Cialdella, J. I., Sarver, R. W., Marshall, V. P., and Erickson, L. A. (2002) Expression, purification and characterization of peptidyl-tRNA hydrolase from Staphylococcus aureus, Protein Expression Purif. 24, 123-130.
6. Goodall, J. J., Chen, G. J., and Page, M. G. (2004) Essential role of histidine 20 in the catalytic mechanism of Escherichia coli peptidyl-tRNA hydrolase, Biochemistry 43, 4583-4591.
7. Rosas-Sandoval, G., Ambrogelly, A., Rinehart, J., Wei, D., Cruz-Vera, L. R., Graham, D. E., Stetter, K. O., Guarneros, G., and Söll, D. (2002) Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast, Proc. Natl. Acad. Sci. U.S.A. 99, 16707-16712.
8. Fromant, M., Ferri-Fioni, M. L., Plateau, P., and Blanquet, S. (2003) Peptidyl-tRNA hydrolase from Sulfolobus solfataricus, Nucleic Acids Res. 31, 3227-3235.
9. De Pereda, J. M., Waas, W. F., Jan, Y., Ruoslahti, E., Schimmel, P., and Pascual, J. (2004) Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity, J. Biol. Chem. 279, 8111-8115.
10. Jan, Y., Matter, M., Pai, J. T., Chen, Y. L., Pilch, J., Komatsu, M., Ong, E., Fukuda, M., and Ruoslahti, E. (2004) A mitochondrial protein, Bit1, mediates apoptosis regulated by integrins and Groucho/TLE corepressors, Cell 116, 751-762.
11. Jancarik, J., and Kim, S. H. (1991) Sparse matrix sampling: a screening method for crystallization of proteins, J. Appl. Crystallogr. 24, 409-411.
12. Leslie, A. (1990) Crystallographic computing V, Oxford University Press, Oxford, U.K.
13. Collaborative Computational Project No. 4 (1994) The CCP4 suite: programs from protein crystallography, Acta Crystallogr. D50, 760-763.
14. Terwilliger, T. C., and Berendzen, J. (1999) Automated MAD and MIR structure solution, Acta Crystallogr., Sect. D: Biol. Crystallogr. 55 (Part 4), 849-861.
15. Terwilliger, T. C. (2003) SOLVE and RESOLVE: automated structure solution and density modification, Methods Enzymol. 374, 22-37.
16. Cowtan, K. (1994) Jt. CCP4 and ESF-EACBM Newsl. Protein Crystollagr. 31, 34-38.
17. 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 Cystallogr. A47, 110-119.
18. Adams, P. D., Pannu, N. S., Read, R. J., and Brunger, A. T. (1997) Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement, Proc. Natl. Acad. Sci. U.S.A. 94, 5018-5023.
19. Dardel, F. (1994) MC-Fit: Using Monte-Carlo methods to get accurate confidence limits on enzyme parameters, Comput. Appl. Biosci. 10, 273-275.
20. Evans, S. V. (1993) Setor: hardware lighted three-dimensional solid model representation of macromolecules, J. Mol. Graphics 11, 134-138.
21. 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.
22. 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.