Aminoacylation reaction in the histidyl-tRNA synthetase: Fidelity mechanism of the activation step

Journal of Physical Chemistry B

Volumn 114, Issue 6, 2010, Pages 2301-2311

  Dutta Banik, S ^a   Nandi, N ^a  

^a UNIVERSITY OF KALYANI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ATOMS; BINDING ENERGY; BIOCHEMISTRY; CARBOXYLIC ACIDS; COMPLEXATION; ELECTROSTATICS; ESCHERICHIA COLI; ORGANIC ACIDS; OXYGEN; PHOSPHATASES; PHOSPHORUS;

ACTIVATION STEPS; ACTIVE SITE; ADENYLATE; AMINOACYLATION; ARG RESIDUES; BOND ANGLE; CARBOXYLIC ACID GROUPS; CATALYTIC ROLE; CLOSE PROXIMITY; D-AMINO ACID; ELECTROSTATIC INTERACTIONS; ELECTROSTATIC POTENTIALS; ENERGY SURFACE; FIDELITY MECHANISMS; IN-LINE; INTERMOLECULAR ENERGY; NANO-SPACE; NEGATIVE CHARGE; NUCLEOPHILIC ATTACK; OLIGOMERIC COMPLEXES; OXYGEN ATOM; PHOSPHATE GROUP; REACTION CENTER; STRUCTURAL REORGANIZATION; SYNTHETASES; TRANSITION STATE;

CRYSTAL STRUCTURE;

EID: 77649169683     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp910730s     Document Type: Article

References (29)

1. Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, 4th ed.; W. H. Freeman & Co.: New York, 2002; p 1044.
2. Ibba, M.; Söll, D. Annu. Rev. Biochem. 2000, 69, 617.
3. Berg, J. M.; Tymoczko, J. L.; Stryer, S. Biochemistry; W. H. Freeman & Co.: New York, 2002; p 671.
4. Arnez, J.; Harris, G.; Mitschier, D. C.; Rees, B.; Francklyn, C. S.; Moras, D. EMBO J. 1995, 14, 4143.
5. Åberg, A.; Yaremchuk, A.; Tukalo, M.; Rasmussen, B.; Cusack, S. Biochemistry 1991, 36, 3084.
6. Nandi, N. Int. Rev. Phys. Chem 2009, 28, 111.
7. Davie, E. W.; Konigsberger, V. V.; Lipman, F. Arch. Biochem. Biophys. 1956, 65, 21.
8. Calendar, R.; Berg, P. Biochemistry1966, 5, 1690.
9. Soutourina, J.; Plateau, P.; Blanquet, S. J. Biol. Chem. 2000, 275, 32535.
10. Bergmann, F.; Berg, P.; Dieckmann, M. J. Biol. Chem. 1961, 236, 1735.
11. Norton, S.; Ravel, J.; Lee, C.; Shive, W. Biol. Chem. 1963, 238, 269.
12. Yamane, T.; Miller, L.; Hopfield, J. J. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 4135.
13. Tamura, K.; Schimmel, P. Science 2004, 305, 1253.
14. Thompson, D.; Lazennec, C.; Plateau, P.; Simonson, T. J. Biol. Chem. 2007, 282, 30856.
15. (a) Dutta Banik, S.; Nandi, N. Coolid Surf. B 2009, 74, 468.
16. (b) Arnez, J. G.; Flanagan, K.; Moras, D.; Simonson, T. Proteins: Struct., Funct. and Genet. 1998, 32, 362.
17. Archontis, G.; Simonson, T.; Moras, D.; Karplus, M. J. Mol. Biol. 1998, 275, 823.
18. Wales, D. J.; Miller, M. A.; Walsh, T. R. Nature 1998, 394, 758.
19. Becker, O. M.; Karplus, M. J. Chem. Phys. 1997, 106, 1495.
20. Leach, A. R. Molecular Modelling: Principles and Applications, 2nd ed.; Pearson, Prentice Hall, 2001; p 279.
21. Lim, C.; Karplus, M. J. Am. Chem. Soc. 1990, 112, 5872.
22. Arnez, J. G.; Augstine, J. G.; Moras, D.; Francklyn, C. S. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 7144.
23. Colominus, C.; Seignovert, L.; Härtlein, M.; Grotli, M.; Cusack, S.; Leberman, R. EMBO J. 1998, 17, 2947.
24. Sjoberg, P.; Politzer, P. J. Phys. Chem. 1990, 94, 3959.
25. Frisch, M. J.; Tracks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Parkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
26. Kunitake, T. Thin Solid Films 1996, 284, 9-285.
27. Sakurai, M.; Tamagawa, H.; Inous, Y.; Ariga, K.; Kunitake, T. J. Phys, Chem. B 1997, 101, 4810.
28. Sakurai, M.; Tamagawa, H.; Inous, Y.; Ariga, K.; Kunitake, T. J. Phys. Chem., B 1997, 101, 4817.
29. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graphics 1996, 14, 33.