Contact areas of the XXXX tRNA-like structure interacting with @entity375 valyl-tRNA synthetase.

@entity2036 @entity535 @entity330 @entity6546 @entity71166 @entity2774 @entity1391 @entity4857 @entity375 @entity56040
The tRNA-like structure of @entity71166 is known to be efficiently recognized and aminoacylated by valyl-tRNA synthetase. The present work reports domains in the isolated tRNA-like fragment (159 terminal @entity2036 at the 3'-end of the two viral RNAs) in contact with purified @entity375 valyl-tRNA synthetase. These domains were determined in protection experiments using chemical and enzymatic structural probes. In addition, new data, re-enforcing the validity of the tertiary folding model for the native RNA, are given. In particular, at the level of the @entity535 accepting arm it was found that the two @entity1391 groups flanking the three @entity2774 residues of loop I are inaccessible to @entity330 . This is in agreement with a higher-order structure of this loop involving "pseudo knotting", as proposed by Rietveld et al. (1982). @entity56040 -tRNA synthetase efficiently protects the viral RNA against digestion by single-strand-specific S1 nuclease at the level of the anticodon loop. With cobra venom ribonuclease, specific for double-stranded regions of RNA, protection was detected on both sides of the anticodon arm and at the 5'-ends of loop I, a region that is involved in the building up of the acceptor arm. Loop II, which is topologically homologous to the T-loop of canonical tRNA was likewise protected. Weak protection was observed between arms I and II, and at the 3'-side of arm V. This arm, located at the 5'-side of arm IV (homologous to the D-arm of tRNA), does not participate in the pseudo-knotted model of the @entity4857 acceptor arm. Ethylnitrosourea was used to determine the @entity6546 of the tRNA-like structure in close contact with the synthetase. These are grouped in several stretches scattered over the RNA molecule. In agreement with the nuclease digestion results, protected @entity6546 are located in arms I, II, and III. Additionally, this chemical probe permits detection of other protected @entity6546 on the 3'-side of arm IV and on both sides of arm V. When displayed in the three-dimensional model of the tRNA-like structure, protected areas are localized on both limbs of the L-shaped RNA. It appears that valyl-tRNA synthetase embraces the entire tRNA-like structure. This is reminiscent of the interaction model of canonical @entity375 tRNAVal with its cognate synthetase.
