Cross-crystal averaging reveals that the structure of the peptidyl-transferase center is the same in the 70S ribosome and the 50S subunit

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 2, 2008, Pages 500-505

  Simonović, Miljan ^a   Steitz, Thomas A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDYLTRANSFERASE;

ARTICLE; CRYSTAL STRUCTURE; HALOARCULA MARISMORTUI; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN QUATERNARY STRUCTURE; PROTEIN STRUCTURE; RIBOSOME; THERMUS THERMOPHILUS;

ANTICODON; CATALYSIS; CODON; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; HALOARCULA MARISMORTUI; KINETICS; MAGNESIUM; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PEPTIDES; PEPTIDYL TRANSFERASES; PROTEIN STRUCTURE, TERTIARY; RIBOSOMES; RNA, TRANSFER; THERMUS THERMOPHILUS; ZINC;

HALOARCULA MARISMORTUI; THERMUS THERMOPHILUS;

EID: 38649126163     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0711076105     Document Type: Article

References (34)

1. Wimberly BT, et al. (2000) Structure of the 30S ribosomal subunit. Nature 407:327-339.
2. Carter AP, et al. (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407:340-348.
3. Ogle JM, et al. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292:897-902.
4. Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111:721-732.
5. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000) The structural basis of ribosome activity in peptide bond synthesis. Science 289:920-930.
6. Schmeing TM, et al. (2002) A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits. Nat Struct Biol 9:225-230.
7. Schmeing TM, Moore PB, Steitz TA (2003) Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. RNA 9:1345-1352.
8. Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA (2005) Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell 20:437-448.
9. Schmeing TM, Huang KS, Strobel SA, Steitz TA (2005) An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438:520-524.
10. Das GK, Bhattacharyya D, Burma DP (1999) A possible mechanism of peptide bond formation on ribosome without mediation of peptidyl transferase. J Theor Biol 200:193-205.
11. Chamberlin SI, Merino EJ, Weeks KM (2002) Catalysis of amide synthesis by RNA phosphodiester and hydroxyl groups. Proc Natl Acad Sci USA 99:14688-14693.
12. Hansen JL, Schmeing TM, Moore PB, Steitz TA (2002) Structural insights into peptide bond formation. Proc Natl Acad Sci USA 99:11670-11675.
13. Dorner S, Panuschka C, Schmid W, Barta A (2003) Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2′-OH to activity. Nucleic Acids Res 31:6536-6542.
14. Weinger JS, Parnell KM, Dorner S, Green R, Strobel SA (2004) Substrate-assisted catalysis of peptide bond formation by the ribosome. Nat Struct Mol Biol 11:1101-1106.
15. Sharma PK, Xiang Y, Kato M, Warshel A (2005) What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome? Biochemistry 44:11307-11314.
16. Trobro S, Aqvist J (2005) Mechanism of peptide bond synthesis on the ribosome. Proc Natl Acad Sci USA 102:12395-12400.
17. Trobro S, Aqvist J (2006) Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer. Biochemistry 45:7049-7056.
18. Rangelov MA, Vayssilov GN, Yomtova VM, Petkov DD (2006) The syn-oriented 2′-OH provides a favorable proton transfer geometry in 1,2-diol monoester aminolysis: Implications for the ribosome mechanism. J Am Chem Soc 128:4964-4965.
19. Rodnina MV, Beringer M, Wintermeyer W (2007) How ribosomes make peptide bonds. Trends Biochem Sci 32:20-26.
20. Selmer M, et al. (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935-1942.
21. Korostelev A, Trakhanov S, Laurberg M, Noller HF (2006) Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126:1065-1077.
22. Cowtan K (1999) Error estimation and bias correction in phase-improvement calculations. Acta Crystallogr D 55:1555-1567.
23. Elkins PA, et al. (2000) Ternary complex between placental lactogen and the extracellular domain of the prolactin receptor. Nat Struct Biol 7:808-815.
24. Brejc K, et al. (2001) Crystal structure of an ACh-binding protein reveals the ligand-binding domain of nicotinic receptors. Nature 411:269-276.
25. Li J, Edwards PC, Burghammer M, Villa C, Schertler GF (2004) Structure of bovine rhodopsin in a trigonal crystal form. J Mol Biol 343:1409-1438.
26. Lomakin IB, Xiong Y, Steitz TA (2007) The crystal structure of yeast fatty acid synthase, a cellular machine with eight active sites working together. Cell 129:319-332.
27. Tung CS, Sanbonmatsu KY (2004) Atomic model of the Thermus thermophilus 70S ribosome developed in silico. Biophys J 87:2714-2722.
28. Yusupov MM, et al. (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science 292:883-896.
29. Schuwirth BS, et al. (2005) Structures of the bacterial ribosome at 3.5 Å resolution. Science 310:827-834.
30. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D 53:240-255.
31. Kleywegt GJ, Jones TA (1999) Software for handling macromolecular envelopes. Acta Crystallogr D 55:941-944.
32. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D 60:2126-2132.
33. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47:110-119.
34. Cowtan KD, Zhang KY (1999) Density modification for macromolecular phase improvement. Prog Biophys Mol Biol 72:245-270.