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 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, tRNA(Arg)(CCU) and an ATP analog with Rfactor = 0.213 (Rfree = 0.253) at 2.0 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 carboxyl group of Arg induces both formation of Arg-AMP (Arg + ATP --> Arg-AMP + pyrophosphate) and pyrophosphorolysis of Arg-AMP (Arg-AMP + pyrophosphate --> Arg + ATP) at low pH. Furthermore, we obtained a structural model of the molecular mechanism for the Arg-tRNA synthetase-catalyzed deacylation of Arg-tRNA (Arg-tRNA + AMP --> Arg-AMP + tRNA at high pH), in which the deacylation of aminoacyl-tRNA bound on Arg-tRNA synthetase and Glu-tRNA synthetase is catalyzed by a quite similar mechanism, whereby the proton-donating group (-NH-C+(NH2)2 or -COOH) of Arg and Glu assists the aminoacyl transfer from the 2'-OH group of tRNA to the phosphate group of AMP at high pH.
Konno
Michiko
M
Department of Chemistry and Biochemistry, Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan. konno.michiko@ocha.ac.jp
Sumida
Tomomi
T
Uchikawa
Emiko
E
Mori
Yukie
Y
Yanagisawa
Tatsuo
T
Sekine
Shun-ichi
S
Yokoyama
Shigeyuki
S
Yokoyama
Shigeuki
S
D000266:Adenylyl Imidodiphosphate / Q000737:chemistry*; D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry*; D001126:Arginine-tRNA Ligase / Q000737:chemistry*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010755:Organophosphates / Q000737:chemistry; D011485:Protein Binding; D043902:Pyrococcus horikoshii / Q000201:enzymology; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D016963:Thermus thermophilus / Q000201:enzymology
D010755:Organophosphates; D012346:RNA, Transfer, Amino Acyl; D000266:Adenylyl Imidodiphosphate; D001120:Arginine; D001126:Arginine-tRNA Ligase