tailieunhanh - Báo cáo khoa học: Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)

The ATP–pyrophosphate exchange reaction catalyzed by Arg-tRNA, Gln-tRNA and Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also assists Arg-tRNA synthetase in catalyzing the pyro-phosphorolysis of synthetic Arg-AMP at low pH. The mechanism by which the 3¢-end A76, and in particular its hydroxyl group, of the cognate tRNA is involved with the exchange reaction catalyzed by those enzymes has yet to be established. | ỊFEBS Journal Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase tRNA and an ATP analog ANP Michiko Konno1 Tomomi Sumida1 z Emiko Uchikawa1 Yukie Mori1 Tatsuo Yanagisawa2 Shun-ichi Sekine2 and Shigeuki Yokoyama2 1 Department of Chemistry and Biochemistry Graduate Schoolof Humanities and Sciences Ochanomizu University Tokyo Japan 2 Department of Biophysics and Biochemistry Graduate Schoolof Science University of Tokyo Japan Keywords aminoacyl-AMP formation Arg-tRNA synthetase deacylation reaction pyrophosphorolysis tRNA Correspondence M. Konno Department of Chemistry and Biochemistry Graduate School of Humanities and Sciences Ochanomizu University 2-1-1 Otsuka Bunkyo-Ku Tokyo 112-8610 Japan Fax 81 359785717 Tel 81 359875718 E-mail Present address RIKEN Systems and StructuralBiology Center 1-7-22 Suehiro-cho Tsurumi Yokohama 230-0045 Japan Database The atomic coordinates and the structure factors have been deposited in the Protein Data Bank ID 2ZUE for the ternary complex of ArgRS tRNAArgCCU and ANP and ID 2ZUF for the binary complex of ArgRS and tRNAArgCCU The ATP-pyrophosphate exchange reaction catalyzed by Arg-tRNA Gln-tRNA and Glu-tRNA synthetases requires the assistance of the cognate tRNA. tRNA also assists Arg-tRNA synthetase in catalyzing the pyrophosphorolysis of synthetic Arg-AMP at low pH. The mechanism by which the 3 -end A76 and in particular its hydroxyl group of the cognate tRNA is involved with the exchange reaction catalyzed by those enzymes has yet to be established. We determined a crystal structure of a complex of Arg-tRNA synthetase from Pyrococcus horikoshii tRNAArgCCU and an ATP analog with Rfactor Rfree at A resolution. On the basis of newly obtained structural information about the position of ATP bound on the enzyme we constructed a structural model for a mechanism in which the formation of a hydrogen bond between the 2 -OH group of A76 of tRNA and the .