Summary
The changes in the catalytic activity resulting from amino acid substitutions in the active site region have been theoretically modeled for tyrosyl tRNA synthetase (Tyr-RS). The catalytic activity was calculated as the differential stabilization of the transition state using electrostatic approximation. The results indicate that charged residues His45, His48, Asp78, Asp176, Asp194, Lys225, Lys230, Lys233, Arg265, and Lys268 play essential roles in catalysis of aminoacyl adenylate formation in Tyr-RS, which is in general agreement with previously known experimental data for residues 45, 48, 194, 230, and 233. These catalytic residues have also been used to search for sequence homology patterns among class I aminoacyl RSs of which HIGH and KMSKS conserved sequence motifs are well known. His45 and His48 belong to the HIGH signature sequence of class I aminoacyl tRNA synthetases (aRSs), whereas Arg265 and Lys268 can constitute a part of the KMSKS charge pattern. Lys225, Lys230, and Lys233 may be part of the conservative substitution pattern [HKR]-X(4)-[HKR]-X(2)-[HKR], and Asp 194 is part of the new GSDQ motif. This demonstrates that the three dimensional charge distribution near the active site is an essential feature of the catalytic activity of aRS and that the theoretical technique used in this work can be utilized in searches for the catalytically important residues that may provide a clue for a charge residue pattern conserved in evolution. The appearance of patterns I–IV in Arg-, Gln-, Met-, Ile-, Leu-, Trp-, Val-, Glu-, Cys-, and Tyr-RS indicates that all these enzymes could have the same ancestor.
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References
Bajorath J, Kitson DH, Fitzgerald G, Andzelm J, Kraut J, Hagler AT (1991) Electron redistribution on binding of a substrate to an enzyme folate and dihydrofolate reductase. Proteins Struct Funct Genet 9:217–224.
Bhat TN, Blow DM, Brick P, Nyborg J (1982) Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold. J Mol Biol 158:699–709
Breton R, Watson D, Yaguchi M, Lapointe J (1990) Glutamyl-tRNA synthetases ofBacillus subtilis 168T and ofBacillus stearothermopilus. J Biol Chem 265:18248–18255
Brick P, Bhat TN, Blow DM (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J Mol Biol 208:83–98
Burbaum JJ, Starzyk RM, Schimmel P (1990) Understanding structural relationships in proteins of unsolved three-dimensional structure. Proteins Struct Funct Genet 7:99–111
Carter PJ, Winter G, Wilkinson AJ, Fersht AR (1984) The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermopilus). Cell 38:835–840
de Duve C (1988) The second genetic code. Nature 333:117–118
Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347:203–206
Eriani G, Dirheimer G, Gaugloff J (1991) Cysteinyl-tRNA synthetase determination of the lastE. coli aminoacyl-tRNA synthetase primary structure. Nucleic Acids Res 19:265–269
Fersht AR (1987) Dissection of the structure and activity of enzyme. Proc R.A. Welch Found Conf Chem Res 31:158–182
Fersht AR, Knill-Jones JW, Bedouelle H, Winter G (1988) Reconstruction by site-directed mutagenesis of the transition state for the activation of tyrosine by the tyrosyl-tRNA synthetase. Biochemistry 27:1581–1587
Garcia GA, Leatherbarrow RJ, Eckstein F, Fersht AR (1990) Metal ion dependence of phosphothioate ATP analogues in theBacillus stearothermopilus tyrosyl-tRNA synthetase reaction. Biochemistry 29:1643–1648
George DG, Barker WC, Hunt LT (1986) The protein identification resource. Nucleic Acids Res 14:11–16
Halgren TA, Lipscomb WN (1977) The synchronous-transit method for determining reaction pathways and locating pathways and locating molecular transition states. Chem Phys Lett 49:225–232
Hountondji C, Dessen P, Blanquet S (1986) Sequence similarities among the family of aminoacyl-tRNA synthetases. Biochimie 68:1071–1078
Hountondji C, Schmitter J-M, Beauvallet C, Blanquet S (1990) Mapping of the active site ofEscherichia coli methionyl-tRNA synthetase: identification of amino acid residues labeled by periodate-oxydized tRNAfMet molecules having modified lengths at the 3′-acceptor end. Biochemistry 29:8190–8198
Hwang JH, Warshel A (1987) Semiquantitative calculations of catalytic free energies in genetically modified enzymes. Biochemistry 26:2669–2673
Krauss M, Garmer DR (1990) Active site ionicity and the mechanism of carbonic anhydrase. J Am Chem Soc (in press)
Leatherbarrow RJ, Fersht AR (1987) Investigation of transition-state stabilization by residues histidine-45 and threonine-40 in the fyrosyl-tRNA synthetase. Biochemistry 26: 8524–8528
Leatherbarrow RJ, Fersht AR, Winter G (1985) Transition state stabilization on the mechanism of tyrosyl tRNA synthetase revealed by protein engineering. Proc Natl Acad Sci USA 82: 7804–7844
Lowe DM, Fersht AR, Wilkinson AJ, Carter P, Winter G (1985) Probing histidine-substrate interactions in tyrosyl-tRNA synthetase using asparagine and glutamine replacements. Biochemistry 24:5106–5109
Mechulam Y, Dardel F, Le Carre D, Blanquet S, Fayat G (1991) Lysine 335, part of KMSKS sequence plays a crucial role in amino acid activation catalysed by the methionyl-tRNA synthetase fromEscherichia coli. J Mol Biol 217:465–475
Meinnel T, Mechulam Y, Dordel F, Schmitter JM, Mountondji C, Brunie S, Dessen P, Fayat G, Blanquet S (1990) Methionyl-tRNA synthetase fromE. coli-a review. Biochimie 72:625–632
Monteilhet C, Blow DM (1978) Binding of tyrosine adenosine triphosphate and analogues to crystalline tyrosyl transfer RNA synthetase. J Mol Biol 122:407–417
Naray-Szabo G (1988) Electrostatic catalysis in enzymes. J Mol Catal 47:281–287
Rein R, Srinivasan S, McDonald J, Raghunathan G, Shibata M (1987) Structural elements and organization of the ancestral translational machinery. Origins Life 17:431–438
Sawaryn A, Sokalski WA (1989) Cumulative atomic multipole moments and point charge models describing molecular charge distribution. Comp Phys Comm 52:397–408
Schimmel P (1989) Parameters for the molecular recognition of transfer RNAs. Biochemistry 28:2747–2759
Schimmel P (1991) Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code. Trends Biochem Sci 16:1–3
Sokalski WA (1985) The physical nature of catalytic activity due to the molecular environment in terms of intermolecular interaction theory: derivation of simplified models. J Mol Catal 30:395–410
Sokalski WA, Maruszewski K, Hariharan PC, Kaufman JJ (1989) Library of cumulative atomic multipole moments: II. Neutral and charged amino acids. Int J Quantum Chem Quantum Biol Symp 16:119–164
Webster TA, Tsai M, Kula M, Mackie G, Schimmel P (1984) Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase. Science 226:1315–1317
Wells TNC, Fersht AR (1985) Hydrogen bonding in enzymatic catalysis analyzed by protein engineering. Nature 316:656–657
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Sokalski, W.A., Shibata, M., Barak, D. et al. Catalytic activity of aminoacyl tRNA synthetases and its implications for the origin of life. I. Aminoacyl adenylate formation in tyrosyl tRNA synthetase. J Mol Evol 33, 405–411 (1991). https://doi.org/10.1007/BF02103131
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DOI: https://doi.org/10.1007/BF02103131