Structural Characterization of the D-Tyr-tRNA^Tyr Deacylase from Bacillus lichenformis, an Organism of Great Industrial Importance

Angshuman Bagchi

.

DOI: 10.4236/cmb.2011.11001                

Abstract

A new class of enzyme was established that hydrolyze the ester bond between D-Tyr bound onto its cognate t-RNA. The enzyme is called D-Tyr-tRNA deacylase. The three dimensional structure of the D-Tyr-tRNA deacylase from industrially important microorganism Bacillus lichenformis DSM13 was predicted by comparative modeling approach. Since the protein acts as a dimer a dimeric model of the enzyme was constructed. The interactions responsible for dimerization were also predicted. With the help of docking and molecular dynamics simulations the favourable binding mode of the enzyme was predicted. The probable biochemical mechanism of the hydrolysis process was elucidated. This study provides a rational framework to interpret the molecular mechanistic details of the removal of toxic D-Tyr-tRNA from the cells of industrially important microorganism Bacillus lichenformis DSM13 using the enzyme D-Tyr-tRNA deacylase.

Keywords

Molecular Modeling, Molecular Docking, Molecular Dynamics, Industrially Important Microorganism, Ester Hydrolysis, D-Tyr-tRNA Deacylase

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	R. Calender and P. Berg, “Valyl t-RNA Synthetase from Staphylococcus aureaus,” Biochemistry, Vol. 5, No. 5, 1966, pp. 1681-1690.
[2]	M. L. F-Fioni, E. Schmitt, J. Soutourina, P. Plateau, Y. Mechulam and S. Blanquet, “Structure of Crystalline D- Tyr-t-RNATyr Deacylase,” Journal of Biological Chemistry, Vol. 14, 2001, pp. 47285-47290.
[3]	J. Soutourina, P. Plateau and S. Blanquet, “Metabolism of D-Aminoacyl-tRNAs in Escherichia coli and Saccharomyces cerevisiae Cells,” Journal of Biological Chemistry, Vol. 275, 2000, pp. 32535-32542. doi:10.1074/jbc.M005166200
[4]	B. Veith, C. Herzberg, S. Steckel, J. Feesche, K. H. Maurer, P. Ehrenreich, S. Baumer, A. Henne, H. Liesegang, R. Merkl, A. Ehrenreich and G. Gottschalk, “The Complete Genome Sequence of Bacillus licheniformis DSM13, an Organism with Great Industrial Potential,” Journal of Molecular Microbiology and Biotechnology, Vol. 7, No. 4, 2004, pp. 204-211. doi:10.1159/000079829
[5]	M. H. Berman, J. Westbrook, J. Feng, G. Gillilang, T. N. Bhat, H. Weissig and I. N. Sindyalov, “The Protein Data Bank,” Nucleic Acids Research, Vol. 28, No. 1, 2000, pp. 235-242. doi:10.1093/nar/28.1.235
[6]	S. F. Altschul, W. Gisli, W. Miller, E. W. Mayer and D. J. Lipman, “Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs,” Nucleic Acids Research, Vol. 25, No. 17, 1997, pp. 3389-3402. doi:10.1093/nar/25.17.3389
[7]	A. Sali and T. L. Blundell, “Comparative Protein Modeling by Satisfaction of Spatial Restraints,” Journal of Molecular Biology, Vol. 234, No. 3, 1993, pp. 779-815. doi:10.1006/jmbi.1993.1626
[8]	P. Dauber-Osguthorpe, V. A. Roberts, D. J. Osguthorpe, J. Wolff, M. Genest and A. T. Hagler, “Structure and Energetics of Ligand Binding to Proteins: Escherichia coli Dihydrofolate Reductase Trimethoprim, a Drug Receptor System,” Proteins, Vol. 4, No. 1, 1988, pp. 31-47. doi:10.1002/prot.340040106
[9]	M. J. Sippl, “Recognition of Errors in Three-Dimensional Structures of Proteins,” Proteins, Vol. 17, No. 4, 1993, pp. 355-362. doi:10.1002/prot.340170404
[10]	M. Wiederstein, P. Lackner and F. Kieberger, “Direct in Silico Mutagenesis,” in: S. Brankmann and A. Schwienhorst, Eds., Evolutionary Methods in Biotechnology, Wiley-VCH, New York, 2004
[11]	D. Eisenberg, R. Luthy and J. U. Bowie, “VERIFY3D: Assessment of Protein Models with Three-Dimensional Profiles,” Methods in Enzymology, Vol. 277, 1997, pp. 396-404. doi:10.1016/S0076-6879(97)77022-8
[12]	R. A. Laskowski, M. W. MacArthur, D. S. Moss and J. M. Thornton, “PROCHECK: A Program to Check the Stereochemistry of Protein Structures,” Journal of Applied Crystallography, Vol. 26, 1993, pp. 283-291. doi:10.1107/S0021889892009944
[13]	G. N. Ramachandran and V. Sashisekharan, “Conformation of Polypeptides and Proteins,” Advances in Protein Chemistry, Vol. 23, 1968, pp. 283-438. doi:10.1016/S0065-3233(08)60402-7
[14]	D. Schneidman-Duhovny, Y. Inbar, V. Polak, M. Shatsky, I. Halperin, H. Benyamini, A. Barzilai, O. Dror, N. Haspel, R. Nussinov and H. J. Wolfson, “Taking Geometry to Its Edge: Fast Unbound Rigid (and Hinge-Bent) Docking,” Proteins, Vol. 52, No. 1, 2003, pp. 107-112. doi:10.1002/prot.10397
[15]	L. Verlet, “Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lenard-Jones Molecules,” Physical Review, Vol. 159, No. 1, 1967, pp. 98-103. doi:10.1103/PhysRev.159.98
[16]	J. P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, “Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alokanes,” Advances in Protein Chemistry, Vol. 23, No. 3, 1977, pp. 327-331. doi:10.1016/0021-9991(77)90098-5
[17]	G. Vriend, “WHAT IF: A Molecular Modeling and Drug Design Program,” Journal of Molecular Graphics, Vol. 8, No. 1, 1990, pp. 52-58. doi:10.1016/0263-7855(90)80070-V
[18]	P. Lavigne, J. R. Bagu, R. Boyko, L. Willard, C. F. Holmes and B. D. Sykes, “Structure-Based Thermodynamic Analysis of the Dissociation of Protein Phosphatase-1 Catalytic Subunit and Microcystin-LR Docked Complexes,” Protein Science, Vol. 9, No. 2, 2000, pp. 252-264. doi:10.1110/ps.9.2.252
[19]	P. J. Kraulis, “Molscript: A Program to Produce Both Detailed and Schematic Plots of Protein Structures,” Journal of Applied Crystallography, Vol. 24, No. 1991, pp. 946-950.