Home LiteratureArticle Details
PMID: 20694005 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Structural rearrangements of the ribosome at the tRNA proofreading step.

Nature structural & molecular biology ·Vol. 17 ·No. 9 ·2010-09-00 ·Pages 1072-8

Jenner L, Demeshkina N, Yusupova G, Yusupov M

Abstract

Discrimination of tRNA on the ribosome occurs in two consecutive steps: initial selection and proofreading. Here we propose a proofreading mechanism based on comparison of crystal structures of the 70S ribosome with an empty A site or with the A site occupied by uncharged cognate or near-cognate tRNA. We observe that ribosomal proteins S13, S19, L16, L25, L27 and L31 are actively involved in the proofreading of tRNA. We suggest that proofreading begins with the monitoring of the entire anticodon loop of tRNA by nucleotides from 16S rRNA (helices 18 and 44) of the small subunit and 23S rRNA (helix 69) of the large subunit with involvement of magnesium ions. Subsequently, the elbow region is scanned by rRNA (helices 38 and 89) and proteins from the large subunit determining whether to accommodate the acceptor end of tRNA in the peptidyl transferase center or not.

MeSH Terms
Crystallography, X-Ray Models, Molecular Protein Structure, Quaternary RNA, Transfer/chemistry Ribosomes/chemistry Thermus thermophilus/chemistry
Chemicals
RNA, Transfer
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Jenner Lasse
Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
Demeshkina Natalia
Yusupova Gulnara
Yusupov Marat
References (52)
52 references, click to expand
  1. Structural basis for mRNA and tRNA positioning on the ribosome.
    Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15830-4 PMID: 17038497
  2. Kinetic amplification of enzyme discrimination.
    Biochimie. 1975;57(5):587-95 PMID: 1182215
  3. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome.
    Science. 2009 Aug 21;325(5943):966-70 PMID: 19696344
  4. Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.
    PLoS One. 2007 Jun 13;2(6):e517 PMID: 17565370
  5. Application of a Theory of Enzyme Specificity to Protein Synthesis.
    Proc Natl Acad Sci U S A. 1958 Feb;44(2):98-104 PMID: 16590179
  6. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.
    Science. 2009 Oct 30;326(5953):688-694 PMID: 19833920
  7. An active role for tRNA in decoding beyond codon:anticodon pairing.
    Science. 2005 May 20;308(5725):1178-80 PMID: 15905403
  8. The contribution of metal ions to the structural stability of the large ribosomal subunit.
    RNA. 2004 Sep;10(9):1366-79 PMID: 15317974
  9. The role of 23S ribosomal RNA residue A2451 in peptide bond synthesis revealed by atomic mutagenesis.
    Chem Biol. 2008 May;15(5):485-92 PMID: 18439847
  10. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms.
    Annu Rev Biochem. 2001;70:415-35 PMID: 11395413
  11. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome.
    Mol Cell. 2004 Jan 30;13(2):191-200 PMID: 14759365
  12. The accuracy of protein biosynthesis is limited by its speed: high fidelity selection by ribosomes of aminoacyl-tRNA ternary complexes containing GTP[gamma S].
    Proc Natl Acad Sci U S A. 1982 Aug;79(16):4922-6 PMID: 6750613
  13. The ribosome's response to codon-anticodon mismatches.
    Biochimie. 2006 Aug;88(8):1001-11 PMID: 16716484
  14. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
    EMBO J. 2004 Mar 10;23(5):1008-19 PMID: 14976550
  15. Ribosomal catalysis: the evolution of mechanistic concepts for peptide bond formation and peptidyl-tRNA hydrolysis.
    RNA Biol. 2008 Jan-Mar;5(1):5-12 PMID: 18388484
  16. Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions.
    RNA. 2004 Jan;10(1):90-101 PMID: 14681588
  17. Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA.
    J Mol Biol. 1998 Mar 27;277(2):333-45 PMID: 9514734
  18. Structure of the 70S ribosome complexed with mRNA and tRNA.
    Science. 2006 Sep 29;313(5795):1935-42 PMID: 16959973
  19. Initiator tRNAs have a unique anticodon loop conformation.
    Proc Natl Acad Sci U S A. 1979 Jul;76(7):3289-93 PMID: 386336
  20. Structure of the 30S ribosomal subunit.
    Nature. 2000 Sep 21;407(6802):327-39 PMID: 11014182
  21. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome.
    Mol Cell. 2008 Oct 24;32(2):190-7 PMID: 18951087
  22. Structures of the ribosome in intermediate states of ratcheting.
    Science. 2009 Aug 21;325(5943):1014-7 PMID: 19696352
  23. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.
    RNA. 2002 Oct;8(10):1189-232 PMID: 12403461
  24. Crystal structure of a translation termination complex formed with release factor RF2.
    Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19684-9 PMID: 19064930
  25. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome.
    Nat Struct Mol Biol. 2009 May;16(5):528-33 PMID: 19363482
  26. Selection of tRNA by the ribosome requires a transition from an open to a closed form.
    Cell. 2002 Nov 27;111(5):721-32 PMID: 12464183
  27. Selective perturbation of G530 of 16 S rRNA by translational miscoding agents and a streptomycin-dependence mutation in protein S12.
    J Mol Biol. 1994 Jan 7;235(1):156-72 PMID: 8289238
  28. tRNA selection and kinetic proofreading in translation.
    Nat Struct Mol Biol. 2004 Oct;11(10):1008-14 PMID: 15448679
  29. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome.
    EMBO J. 1999 Jul 1;18(13):3800-7 PMID: 10393195
  30. Transfer RNA structure and coding specificity. I. Evidence that a D-arm mutation reduces tRNA dissociation from the ribosome.
    J Mol Biol. 1989 Apr 5;206(3):489-501 PMID: 2469803
  31. The RNA Modification Database: 1999 update.
    Nucleic Acids Res. 1999 Jan 1;27(1):196-7 PMID: 9847178
  32. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition.
    RNA. 2007 Jan;13(1):87-96 PMID: 17095544
  33. Multiple effects of S13 in modulating the strength of intersubunit interactions in the ribosome during translation.
    J Mol Biol. 2005 May 27;349(1):47-59 PMID: 15876367
  34. Structural aspects of messenger RNA reading frame maintenance by the ribosome.
    Nat Struct Mol Biol. 2010 May;17(5):555-60 PMID: 20400952
  35. Possibilities for the evolution of the genetic code from a preceding form.
    Nature. 1973 Nov 2;246(5427):22-6 PMID: 4585842
  36. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity.
    Proc Natl Acad Sci U S A. 1974 Oct;71(10):4135-9 PMID: 4530290
  37. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA.
    Nature. 2005 Nov 24;438(7067):520-4 PMID: 16306996
  38. Effect of photochemical crosslink S4U(8)-C(13) on suppressor activity of su+ tRNATrp from Escherichia coli.
    J Mol Biol. 1979 Apr 5;129(2):287-94 PMID: 383994
  39. Interaction of antibiotics with functional sites in 16S ribosomal RNA.
    Nature. 1987 Jun 4-10;327(6121):389-94 PMID: 2953976
  40. Effect of Mg2+ concentration, polyamines, streptomycin, and mutations in ribosomal proteins on the accuracy of the two-step selection of aminoacyl-tRNAs in protein biosynthesis.
    J Biol Chem. 1981 Jul 10;256(13):6676-81 PMID: 6113247
  41. A uniform response to mismatches in codon-anticodon complexes ensures ribosomal fidelity.
    Mol Cell. 2006 Feb 3;21(3):369-77 PMID: 16455492
  42. Fidelity at the molecular level: lessons from protein synthesis.
    Cell. 2009 Feb 20;136(4):746-62 PMID: 19239893
  43. Recognition of the codon-anticodon helix by ribosomal RNA.
    Science. 1999 Sep 10;285(5434):1722-5 PMID: 10481006
  44. Recognition of cognate transfer RNA by the 30S ribosomal subunit.
    Science. 2001 May 4;292(5518):897-902 PMID: 11340196
  45. Recognition and selection of tRNA in translation.
    FEBS Lett. 2005 Feb 7;579(4):938-42 PMID: 15680978
  46. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA.
    J Mol Biol. 1990 Jan 5;211(1):135-45 PMID: 2405162
  47. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: structure of the proteins and their interactions with 16 S RNA.
    J Mol Biol. 2002 Feb 22;316(3):725-68 PMID: 11866529
  48. A ratchet-like inter-subunit reorganization of the ribosome during translocation.
    Nature. 2000 Jul 20;406(6793):318-22 PMID: 10917535
  49. Mutants of initiator tRNA that function both as initiators and elongators.
    J Biol Chem. 1991 Sep 25;266(27):18018-24 PMID: 1917940
  50. Crystal structure of the ribosome at 5.5 A resolution.
    Science. 2001 May 4;292(5518):883-96 PMID: 11283358
  51. Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem.
    J Biol Chem. 1991 Sep 25;266(27):18012-7 PMID: 1917939
  52. Counting cycles of EF-Tu to measure proofreading in translation.
    Biochimie. 1986 Mar;68(2):261-73 PMID: 3089318
Article Info
Journal
Nature structural & molecular biology
Abbr.
Nat Struct Mol Biol
ISSN
1545-9985
DOI
10.1038/nsmb.1880
Published
2010-09-00
Epub
2010-00-08
Pages
1072-8
Language
English
Region
United States
NLM ID
101186374
Subset
IM
Databases
PDB
3I8F, 3I8G, 3I8H, 3I8I, 3I9B, 3I9C, 3I9D, 3I9E
External Links
PubMed source DOI: 10.1038/nsmb.1880 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2