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The interactive recognition of nucleic acids by proteins is a central process in the regulation of gene expression. To gain insight into such interactions requires a knowledge of appropriate three-dimensional structures and information on biochemical function. Only a few native biological supramacromolecular protein-nucleic acid complexes are currently accessible for such detailed investigations. One convenient object for such study is the ternary complex composed of aminoacyl-tRNA (aa-tRNA) and elongation factor (EF-Tu) bound to GTR. This chapter brings up to date two earlier reviews addressing the problem of aa-tRNA and EF-Tu:GTP interaction. It summarizes the most recent published studies that contribute to an understanding of the recognitory interactions between tRNA and the protein elongation factor, and the chapter puts these studies in perspective. Finally, it proposes a new model for the three-dimensional structure of the ternary complex (TC). This model accommodates all existing structural experimental data obtained during the studies of the TC.
Hydrogen bonding interactions between GDP and E. coli EF-Tu.
Secondary structure model of tRNA ( 94 ) with marked nucleotides whose reactivity is reduced in the presence of elongation factor Tu ( 24 , 110 ) or cross-linked to the EF-Tu ( 67 , 109 ). Large filled arrows mean protected nucleotides, large empty arrows mean exposed nucleotides, and small filled arrows mean neutral cuts.
Cartoon model of conformational changes of elongation factor from GDP to GTP form. Domain 2 moves 35-40 Å to form a cleft with domain 1, which contains the amino acid binding site of aa-tRNA. The effector region comprises the amino acid residues 40–60 in the case of EF-Tu of T. thermophilus.
Panels A and B show two views of a tertiary structural model of the ternary complex of EF-Tu:GTP-aa-tRNA. The stretched CCA end is assumed to be bent back to the EF-Tu with the amino acid attached (not shown) (compare with reference 47 ).
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