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. 1977 May;74(5):1903–1907. doi: 10.1073/pnas.74.5.1903

Aminoacyl-tRNA binding at the recognition site is the first step of the elongation cycle of protein synthesis.

J A Lake
PMCID: PMC431040  PMID: 266713

Abstract

Codon recognition occurs during protein synthesis with the aminoacyl-tRNA bound in the recognition (or R) tRNA-binding site. The recognition site is thought to be located on the external surface of the smaller ribosomal subunit distal from the interface between subunits, where the aminoacyl (A) and peptidyl (P) tRNA-binding sites are located. A molecular model describing the switching of the aminoacyl-tRNA from the R site to the A site is proposed. Details of the model include codon recognition at the R site by an aminoacyl-tRNA with its anticodon loop in the 5' stacked conformation; movement of the aminoacyl-tRNA from the R site to the A site by a switching in the anticodon loop from the 5' stacked conformation to the 3' stacked conformation; and recognition of the correct reading frame by a base-pairing interaction between the A and P site tRNAs that involves trans pairing of the invariant bases U-33 of both molecules.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bollen A., Heimark R. L., Cozzone A., Traut R. R., Hershey J. W. Cross-linking of initiation factor IF-2 to Escherichia coli 30 S ribosomal proteins with dimethylsuberimidate. J Biol Chem. 1975 Jun 10;250(11):4310–4314. [PubMed] [Google Scholar]
  2. Crick F. H. The origin of the genetic code. J Mol Biol. 1968 Dec;38(3):367–379. doi: 10.1016/0022-2836(68)90392-6. [DOI] [PubMed] [Google Scholar]
  3. Dahlberg A. E., Dahlberg J. E. Binding of ribosomal protein S1 of Escherichia coli to the 3' end of 16S rRNA. Proc Natl Acad Sci U S A. 1975 Aug;72(8):2940–2944. doi: 10.1073/pnas.72.8.2940. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Eisinger J., Spahr P. F. Binding of complementary pentanucleotides to the anticodon loop of transfer RNA. J Mol Biol. 1973 Jan;73(1):131–137. doi: 10.1016/0022-2836(73)90165-4. [DOI] [PubMed] [Google Scholar]
  5. Fuller W., Hodgson A. Conformation of the anticodon loop intRNA. Nature. 1967 Aug 19;215(5103):817–821. doi: 10.1038/215817a0. [DOI] [PubMed] [Google Scholar]
  6. Gorini L. Ribosomal discrimination of tRNAs. Nat New Biol. 1971 Dec 29;234(52):261–264. doi: 10.1038/newbio234261a0. [DOI] [PubMed] [Google Scholar]
  7. Gupta S. L., Waterson J., Sopori M. L., Weissman S. M., Lengyel P. Movement of the ribosome along the messenger ribonucleic acid during protein synthesis. Biochemistry. 1971 Nov 23;10(24):4410–4421. doi: 10.1021/bi00800a010. [DOI] [PubMed] [Google Scholar]
  8. Heimark R. L., Kahan L., Johnston K., Hershey J. W., Traut R. R. Cross-linking of initiation factor IF3 to proteins of the Escherichia coli 30 S ribosomal subunit. J Mol Biol. 1976 Aug 5;105(2):219–230. doi: 10.1016/0022-2836(76)90108-x. [DOI] [PubMed] [Google Scholar]
  9. Kim S. H., Suddath F. L., Quigley G. J., McPherson A., Sussman J. L., Wang A. H., Seeman N. C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. doi: 10.1126/science.185.4149.435. [DOI] [PubMed] [Google Scholar]
  10. Kurland C. G. Structure and function of the bacterial ribosome. Annu Rev Biochem. 1977;46:173–200. doi: 10.1146/annurev.bi.46.070177.001133. [DOI] [PubMed] [Google Scholar]
  11. Lake J. A., Kahan L. Ribosomal proteins S5, S11, S13 and S19 localized by electron microscopy of antibody-labeled subunits. J Mol Biol. 1975 Dec 25;99(4):631–644. doi: 10.1016/s0022-2836(75)80177-x. [DOI] [PubMed] [Google Scholar]
  12. Lake J. A., Pendergast M., Kahan L., Nomura M. Ribosome structure: three-dimensional distribution of proteins S14 and S4. J Supramol Struct. 1974;2(2-4):189–195. doi: 10.1002/jss.400020213. [DOI] [PubMed] [Google Scholar]
  13. Lake J. A. Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes. J Mol Biol. 1976 Jul 25;105(1):131–139. doi: 10.1016/0022-2836(76)90200-x. [DOI] [PubMed] [Google Scholar]
  14. Leder P. The elongation reactions in protein synthesis. Adv Protein Chem. 1973;27:213–242. doi: 10.1016/s0065-3233(08)60448-9. [DOI] [PubMed] [Google Scholar]
  15. Lucas-Lenard J., Tao P., Haenni A. L. Further studies on bacterial polypeptide elongation. Cold Spring Harb Symp Quant Biol. 1969;34:455–462. doi: 10.1101/sqb.1969.034.01.051. [DOI] [PubMed] [Google Scholar]
  16. Nomura M. Bacterial ribosome. Bacteriol Rev. 1970 Sep;34(3):228–277. doi: 10.1128/br.34.3.228-277.1970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Nomura M., Mizushima S., Ozaki M., Traub P., Lowry C. V. Structure and function of ribosomes and their molecular components. Cold Spring Harb Symp Quant Biol. 1969;34:49–61. doi: 10.1101/sqb.1969.034.01.009. [DOI] [PubMed] [Google Scholar]
  18. Piper P. W., Clark B. F. Primary structure of a mouse myeloma cell initiator transfer RNA. Nature. 1974 Feb 22;247(5442):516–518. doi: 10.1038/247516a0. [DOI] [PubMed] [Google Scholar]
  19. Richter D., Erdmann V. A., Sprinzl M. Specific recognition of GTpsiC loop (loop IV) of tRNA by 50S ribosomal subunits from E. coli. Nat New Biol. 1973 Dec 5;246(153):132–135. doi: 10.1038/newbio246132a0. [DOI] [PubMed] [Google Scholar]
  20. Riddle D. L., Carbon J. Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nat New Biol. 1973 Apr 25;242(121):230–234. doi: 10.1038/newbio242230a0. [DOI] [PubMed] [Google Scholar]
  21. Robertus J. D., Ladner J. E., Finch J. T., Rhodes D., Brown R. S., Clark B. F., Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974 Aug 16;250(467):546–551. doi: 10.1038/250546a0. [DOI] [PubMed] [Google Scholar]
  22. Schulman L. H., Pelka H. The structural basis for the resistance of Escherichia coli formylmethionyl transfer ribonucleic acid to cleavage by Escherichia coli peptidyl transfer ribonucleic acid hydrolase. J Biol Chem. 1975 Jan 25;250(2):542–547. [PubMed] [Google Scholar]
  23. Shine J., Dalgarno L. Determinant of cistron specificity in bacterial ribosomes. Nature. 1975 Mar 6;254(5495):34–38. doi: 10.1038/254034a0. [DOI] [PubMed] [Google Scholar]
  24. Simsek M., RajBhandary U. L., Boisnard M., Petrissant G. Nucleotide sequence of rabbit liver and sheep mammary gland cytoplasmic initiatory transfer RNAs. Nature. 1974 Feb 22;247(5442):518–520. doi: 10.1038/247518a0. [DOI] [PubMed] [Google Scholar]
  25. Steitz J. A., Jakes K. How ribosomes select initiator regions in mRNA: base pair formation between the 3' terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc Natl Acad Sci U S A. 1975 Dec;72(12):4734–4738. doi: 10.1073/pnas.72.12.4734. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Thach S. S., Thach R. E. Translocation of messenger RNA and "accommodation" of fMet-tRNA. Proc Natl Acad Sci U S A. 1971 Aug;68(8):1791–1795. doi: 10.1073/pnas.68.8.1791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tischendorf G. W., Zeichhardt H., Stöffler G. Determination of the location of proteins L14, L17, L18, L19, L22, L23 on the surface of the 5oS ribosomal subunit of Escherichia coli by immune electron microscopy. Mol Gen Genet. 1974;134(3):187–208. doi: 10.1007/BF00267715. [DOI] [PubMed] [Google Scholar]
  28. Uhlenbeck O. C. Complementary oligonucleotide binding to transfer RNA. J Mol Biol. 1972 Mar 14;65(1):25–41. doi: 10.1016/0022-2836(72)90489-5. [DOI] [PubMed] [Google Scholar]
  29. Wabl M. R. Electron microscopic localization of two proteins on the surface of the 50 S ribosomal subunit of Escherichia coli using specific antibody markers. J Mol Biol. 1974 Apr 5;84(2):241–247. doi: 10.1016/0022-2836(74)90582-8. [DOI] [PubMed] [Google Scholar]
  30. Woese C. Molecular mechanics of translation: a reciprocating ratchet mechanism. Nature. 1970 May 30;226(5248):817–820. doi: 10.1038/226817a0. [DOI] [PubMed] [Google Scholar]
  31. Yoon K., Turner D. H., Tinoco I., Jr The kinetics of codon-anticodon interaction in yeast phenylalanine transfer RNA. J Mol Biol. 1975 Dec 25;99(4):507–518. doi: 10.1016/s0022-2836(75)80169-0. [DOI] [PubMed] [Google Scholar]

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