Ribosome Structure, Function, and Early Evolution
Abstract
1. Introduction
2. Initiation of Translation
2.1. Homologous GTPases in Initiation and Elongation of Translation
2.2. Mechanism of Initiation
3. Elongation of Translation
3.1. Molecular Motor
3.2. tRNA as a Relatively Stiff Adapter
3.3. tRNA Entry
3.4. Forming the Accurate Codon-Anticodon Latch and Closing the 30S Subunit Conformation
3.5. Accommodation
3.6. Peptide Bond Formation
3.7. Translocation
3.8. EF-G·GTP/GDP in Translocation
3.9. 30S-50S Intersubunit Bridges in Translocation
3.10. Ratchet Pawls
3.11. Kink-Turns and Micro-Motions
4. Evolution of Translation
4.1. tRNA Evolution
4.2. tRNA as Core Evolutionary Intellectual Property
4.3. Aminoacyl-tRNA Synthetase Evolution
4.4. rRNA Evolution
4.5. Evolution of the Genetic Code
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
MDPI | Multidisciplinary Digital Publishing Institute |
DOAJ | Directory of open access journals |
aaRS | Aminoacyl-tRNA synthetase (i.e., GlyRS) |
A-site | Aminoacyl site |
As | Acceptor stems |
ASL | Anticodon stem loop |
Ac loop | Anticodon loop |
EF | Elongation Factor |
E-site | Exit site |
IF | Initiation Factor |
LUCA | Last universal common (cellular) ancestor |
P-site | Peptidyl site |
PTC | Peptidyl Transferase Center |
SRL | Sarcin-ricin loop |
T loop | T loop or TΨC loop |
V loop | Variable loop |
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Intermediate | Stage | Ternary Complex | EF-G | A Site | P Site | E Site | PDB | Proofreading | |||
---|---|---|---|---|---|---|---|---|---|---|---|
(Figure 1) | ASL | CCA/PTC | ASL | CCA/PTC | ASL | CCA | |||||
A | aa-tRNA.EF-Tu.GTP (free) | empty | empty | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA-peptide | E site | E site U2431, A2432 | 1TTT | |||
B | Cplx 1 | aa-tRNA.EF-Tu.GTP (bound) | A/T, open | empty | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA-peptide | E site | E site U2431, A2432 | 5UYK | ||
Cplx 2 | aa-tRNA.EF-Tu.GTP (bound) | A/T, latched | empty | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA-peptide | E site | E site U2431, A2432 | 5UYL | !! | ||
C | Cplx 3 | aa-tRNA.EF-Tu.GTP (bound) | A/T, latched | empty | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA-peptide | E site | E site U2431, A2432 | 5UYM | !! | |
D | Elbow | aa-tRNA.EF-Tu.GDP (bound) | EA, latched | empty | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA-peptide | E site | E site U2431, A2432 | !!!! | ||
E | CCA | EF-G.GTP (binds) | A, latched | CCA-aa, C75:G2553 | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA-peptide | E site | E site U2431, A2432 | 5IBB, 4WPO | ||
F | EF-G.GTP | A, latched | CCA-peptide, C75:G2553 | P site | A2451, C2452, U2585, G2252:C74, G2251:C75, CCA | E site | E site U2431, A2432 | ||||
G | pre | EF-G.GDP | ap, open | (CCA-peptide, C75:G2553) | empty | (ap/A<-->ap/ap tRNA-peptide) | pe | pe/E tRNA: U2431, A2432 | 4W29, 4V5M | ||
pre/post | EF-G.GDP | ap, open | (CCA-peptide, C75:G2553) | empty | (ap/A<-->ap/ap tRNA-peptide) | pe | pe/E tRNA: U2431, A2432 | ||||
H | post | EF-G.GDP | ap, open | (CCA-peptide, C75:G2553) | empty | (ap/A<-->ap/ap tRNA-peptide) | pe | pe/E tRNA: U2431, A2432 | 4V5N, 5OT7 | ||
latch: 30S: S12, 16S: G530~A1492, A1493; 23S: A1913 |
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Opron, K.; Burton, Z.F. Ribosome Structure, Function, and Early Evolution. Int. J. Mol. Sci. 2019, 20, 40. https://doi.org/10.3390/ijms20010040
Opron K, Burton ZF. Ribosome Structure, Function, and Early Evolution. International Journal of Molecular Sciences. 2019; 20(1):40. https://doi.org/10.3390/ijms20010040
Chicago/Turabian StyleOpron, Kristopher, and Zachary F. Burton. 2019. "Ribosome Structure, Function, and Early Evolution" International Journal of Molecular Sciences 20, no. 1: 40. https://doi.org/10.3390/ijms20010040
APA StyleOpron, K., & Burton, Z. F. (2019). Ribosome Structure, Function, and Early Evolution. International Journal of Molecular Sciences, 20(1), 40. https://doi.org/10.3390/ijms20010040