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  Ribosomal crystallography: peptide bond formation and its inhibition

Bashan, A., Zarivach, R., Schluenzen, F., Agmon, I., Harms, J., Auerbach, T., et al. (2003). Ribosomal crystallography: peptide bond formation and its inhibition. Biopolymers, 70(1), 19-41. doi:10.1002/bip.10412.

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Genre: Journal Article
Alternative Title : Biopolymers

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 Creators:
Bashan, Anat, Author
Zarivach, Raz, Author
Schluenzen, Frank, Author
Agmon, Ilana, Author
Harms, Jörg, Author
Auerbach, Tamar, Author
Baram, David, Author
Berisio, Rita1, Author           
Bartels, Heike, Author
Hansen, Harly A. S., Author
Fucini, Paola1, Author           
Wilson, Daniel2, Author
Peretz, Moshe, Author
Kessler, Maggie, Author
Yonath, Ada, Author
Affiliations:
1Ribosomes, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433558              
2Max Planck Society, ou_persistent13              

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Free keywords: ribosomes; peptide-bond formation; translocation; tunnel gating; elongation arrest
 Abstract: Ribosomes, the universal cellular organelles catalyzing the translation of genetic code into proteins, are protein/RNA assemblies, of a molecular weight 2.5 mega Daltons or higher. They are built of two subunits that associate for performing protein biosynthesis. The large subunit creates the peptide bond and provides the path for emerging proteins. The small has key roles in initiating the process and controlling its fidelity. Crystallographic studies on complexes of the small and the large eubacterial ribosomal subunits with substrate analogs, antibiotics, and inhibitors confirmed that the ribosomal RNA governs most of its activities, and indicated that the main catalytic contribution of the ribosome is the precise positioning and alignment of its substrates, the tRNA molecules. A symmetry-related region of a significant size, containing about two hundred nucleotides, was revealed in all known structures of the large ribosomal subunit, despite the asymmetric nature of the ribosome. The symmetry rotation axis, identified in the middle of the peptide-bond formation site, coincides with the bond connecting the tRNA double-helical features with its single-stranded 3 end, which is the moiety carrying the amino acids. This thus implies sovereign movements of tRNA features and suggests that tRNA translocation involves a rotatory motion within the ribosomal active site. This motion is guided and anchored by ribosomal nucleotides belonging to the active site walls, and results in geometry suitable for peptide-bond formation with no significant rearrangements. The sole geometrical requirement for this proposed mechanism is that the initial P-site tRNA adopts the flipped orientation. The rotatory motion is the major component of unified machinery for peptide-bond formation, translocation, and nascent protein progression, since its spiral nature ensures the entrance of the nascent peptide into the ribosomal exit tunnel. This tunnel, assumed to be a passive path for the growing chains, was found to be involved dynamically in gating and discrimination.

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Language(s): eng - English
 Dates: 2003-07-30
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 174589
DOI: 10.1002/bip.10412
 Degree: -

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Title: Biopolymers
  Alternative Title : Biopolymers
Source Genre: Journal
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Publ. Info: -
Pages: - Volume / Issue: 70 (1) Sequence Number: - Start / End Page: 19 - 41 Identifier: ISSN: 1097-0282