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2. Structural aspects of RbfA action during small ribosomal subunit assembly.

Author

Datta PP, Wilson DN, Kawazoe M, Swami NK, Kaminishi T, Sharma MR, Booth TM, Takemoto C, Fucini P, Yokoyama S, and Agrawal RK

Subjects
Bacterial Proteins metabolism, Bacterial Proteins physiology, Binding Sites, Cryoelectron Microscopy, Models, Molecular, Protein Structure, Tertiary, RNA, Bacterial metabolism, RNA, Ribosomal, 16S metabolism, RNA-Binding Proteins metabolism, Ribosomal Proteins metabolism, Ribosomal Proteins physiology, Bacterial Proteins chemistry, RNA-Binding Proteins chemistry, Ribosomal Proteins chemistry, Ribosome Subunits, Small, Bacterial metabolism, Thermus thermophilus metabolism
Abstract

Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock.

Published
2007
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3. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process.

Author

Valle M, Sengupta J, Swami NK, Grassucci RA, Burkhardt N, Nierhaus KH, Agrawal RK, and Frank J

Subjects
Anticodon genetics, Codon genetics, Escherichia coli chemistry, Escherichia coli Proteins chemistry, Escherichia coli Proteins ultrastructure, Guanosine Diphosphate chemistry, Guanosine Triphosphate metabolism, Image Processing, Computer-Assisted, Macromolecular Substances, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor Tu chemistry, Peptide Elongation Factor Tu ultrastructure, Protein Conformation, Pyridones pharmacology, RNA, Transfer chemistry, RNA, Transfer, Amino Acyl chemistry, RNA, Transfer, Amino Acyl metabolism, RNA, Transfer, Amino Acyl ultrastructure, RNA, Transfer, Phe chemistry, RNA, Transfer, Phe metabolism, Ribosomes chemistry, Ribosomes drug effects, Structure-Activity Relationship, Cryoelectron Microscopy, Peptide Chain Elongation, Translational, RNA, Transfer, Amino Acyl physiology, Ribosomes ultrastructure
Abstract

During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition.

Published
2002
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