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Interaction of Human Phenylalanyl-tRNA Synthetase with Specific tRNA According to Thiophosphate Footprinting

I. A. Vasil’eva1, E. A. Semenova2, and N. A. Moor1*

1Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, pr. Lavrentieva 8, 630090 Novosibirsk, Russia; fax: (383) 333-3677; E-mail: moor@niboch.nsc.ru

2Novosibirsk State University, ul. Pirogova 2, 630090 Novosibirsk, Russia

* To whom correspondence should be addressed.

Received June 23, 2008; Revision received July 10, 2008
The interaction of human cytoplasmic phenylalanyl-tRNA synthetase (an enzyme with yet unknown 3D-structure) with homologous tRNAPhe under functional conditions was studied by footprinting based on iodine cleavage of thiophosphate-substituted tRNA transcripts. Most tRNAPhe nucleotides recognized by the enzyme in the anticodon (G34), anticodon stem (G30–C40, A31–U39), and D-loop (G20) have effectively or moderately protected phosphates. Other important specificity elements (A35 and A36) were found to form weak nonspecific contacts. The D-stem, T-arm, and acceptor stem are also among continuous contacts of the tRNAPhe backbone with the enzyme, thus suggesting the presence of additional recognition elements in these regions. The data indicate that mechanisms of interaction between phenylalanyl-tRNA synthetases and specific tRNAs are different in prokaryotes and eukaryotes.
KEY WORDS: nucleoside-5′-O-(1-thiotriphosphate), tRNAPhe, human phenylalanyl-tRNA synthetase, footprinting

DOI: 10.1134/S0006297909020084