2ZUF

Crystal structure of Pyrococcus horikoshii arginyl-tRNA synthetase complexed with tRNA(Arg)

Summary for 2ZUF

• Entry DOI: 10.2210/pdb2zuf/pdb
• Related: 2ZUE
• Descriptor: Arginyl-tRNA synthetase, tRNA-Arg (3 entities in total)
• Functional Keywords: rrs/trna(arg), aminoacyl-trna synthetase, atp-binding, cytoplasm, ligase, nucleotide-binding, protein biosynthesis, ligase-rna complex, ligase/rna
• Biological source: Pyrococcus horikoshii; More
• Cellular location: Cytoplasm: O59147
• Total number of polymer chains: 2
• Total formula weight: 97605.67

Authors

Konno, M.,Sumida, T.,Uchikawa, E.,Mori, Y.,Yanagisawa, T.,Sekine, S.,Yokoyama, S. (deposition date: 2008-10-16, release date: 2009-08-18, Last modification date: 2023-11-08)

Primary citation

Konno, M.,Sumida, T.,Uchikawa, E.,Mori, Y.,Yanagisawa, T.,Sekine, S.,Yokoyama, S.
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)
Febs J., 276:4763-4779, 2009

PubMed Abstract: 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.

PubMed: 19656186
DOI: 10.1111/j.1742-4658.2009.07178.x

Experimental method

X-RAY DIFFRACTION (2.3 Å)