Amino-acid activation and tRNA recognition help establish coding assignments.
FEATURED MACHINE 05 / 12
Aminoacyl-tRNA synthetases
Load amino acids onto the transfer RNAs used in translation.
LIBRARY BASIS · BACTERIAL ACCOUNT
The question behind this machine
The library makes the specificity of tRNA charging central to the genetic-code question: codon matching cannot generally reveal that a tRNA carries the wrong amino acid. Its origin discussion is retained as a question about how charging assignments, adaptors and translation became coupled.L1 L2 L3
Two selections before ribosomal decoding
A charging pathway must recognize a suitable amino acid and a suitable tRNA. These selections establish the amino-acid cargo that decoding subsequently delivers. The library’s general picture is useful, but bacteria do not invariably use exactly one direct synthetase for each amino acid; indirect charging pathways and different identity elements must be considered.
A tested two-site solution
The isoleucyl-tRNA synthetase structures studied by Nureki and colleagues distinguish an aminoacylation region from a separate editing region. The enzyme could activate closely related valine but then remove incorrect products through an additional selection step. This is a concrete experimental example of layered specificity, rather than an assertion that one binding event is absolutely error-free.P1
Editing is varied, not a universal identical attachment
A class II synthetase study also demonstrated hydrolytic editing. The broader lesson is to identify which chemical intermediate is checked and where the checking occurs. Some charging enzymes, separate editing factors and indirect pathways solve different recognition problems; the complete repertoire must be established for the organism of interest.P2
Construction, maintenance and origin assessment
The present system depends on encoded enzymes, functional tRNAs, activated substrates and the translation machinery that produces its protein parts. An origin account must explain how assignments became sufficiently stable and useful, while allowing that early catalysts need not have resembled every modern synthetase. Editing-rate measurements and modern dependency diagrams do not themselves yield a probability of the code’s origin.
Connected to the rest of the cell
This machine depends on resources and supporting systems, and its work supplies other cellular processes.
Explore the related system and its connections ↗FUNCTIONAL ORGANIZATION · AUTHOR’S FRAMEWORK
Hallmarks of design
Aminoacyl-tRNA synthetases illustrates the following organizational features in the supplied papers. These descriptions identify biological functions; interpreting their origin as design is the author’s comparative argument.H1, H2
Binding sites discriminate amino acids and tRNA identities.
Editing occurs in some synthetases; indirect charging and separate editing routes also matter.
Origin hurdles and abductive assessment · Assessment method · All 40 hallmarks. Biological evidence: the mechanism, accession records and scientific references on this page.
Origins and explanatory assessment
Represented in the 912-protein inventory
22 selected protein entries. This is a family of enzymes, not a single complex.
| Gene / locus | Protein entry | Source record |
|---|---|---|
| cysSaq_1068 | Cysteine--tRNA ligase (EC 6.1.1.16) (Cysteinyl-tRNA synthetase) (CysRS) | O67163 ↗ |
| lysSaq_1202 | Lysine--tRNA ligase (EC 6.1.1.6) (Lysyl-tRNA synthetase) (LysRS) | O67258 ↗ |
| hisSaq_122 | Histidine--tRNA ligase (EC 6.1.1.21) (Histidyl-tRNA synthetase) (HisRS) | O66522 ↗ |
| gltXaq_1221 | Glutamate--tRNA ligase (EC 6.1.1.17) (Glutamyl-tRNA synthetase) (GluRS) | O67271 ↗ |
| metGaq_1257 | Methionine--tRNA ligase (EC 6.1.1.10) (Methionyl-tRNA synthetase) (MetRS) | O67298 ↗ |
| alaSaq_1293 | Alanine--tRNA ligase (EC 6.1.1.7) (Alanyl-tRNA synthetase) (AlaRS) | O67323 ↗ |
| valSaq_1413 | Valine--tRNA ligase (EC 6.1.1.9) (Valyl-tRNA synthetase) (ValRS) | O67411 ↗ |
| thrSaq_1667 | Threonine--tRNA ligase (EC 6.1.1.3) (Threonyl-tRNA synthetase) (ThrRS) | O67583 ↗ |
| aspSaq_1677 | Aspartate--tRNA(Asp/Asn) ligase (EC 6.1.1.23) (Aspartyl-tRNA synthetase) (AspRS) (Non-discriminating aspartyl-tRNA synthetase) (ND-AspRS) | O67589 ↗ |
| pheTaq_1730 | Phenylalanine--tRNA ligase beta subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase beta subunit) (PheRS) | O67620 ↗ |
| tyrSaq_1751 | Tyrosine--tRNA ligase (EC 6.1.1.1) (Tyrosyl-tRNA synthetase) (TyrRS) | O67632 ↗ |
| leuS'aq_1770 | Leucine--tRNA ligase subunit beta (EC 6.1.1.4) (Leucyl-tRNA synthetase subunit beta) (LeuRS) | O67646 ↗ |
| glySaq_2141 | Glycine--tRNA ligase beta subunit (EC 6.1.1.14) (Glycyl-tRNA synthetase beta subunit) (GlyRS) | O67898 ↗ |
| serSaq_298 | Serine--tRNA ligase (EC 6.1.1.11) (Seryl-tRNA synthetase) (SerRS) (Seryl-tRNA(Ser/Sec) synthetase) | O66647 ↗ |
| ileSaq_305 | Isoleucine--tRNA ligase (EC 6.1.1.5) (Isoleucyl-tRNA synthetase) (IleRS) | O66651 ↗ |
| leuSaq_351 | Leucine--tRNA ligase subunit alpha (EC 6.1.1.4) (Leucyl-tRNA synthetase subunit alpha) (LeuRS) | O66680 ↗ |
| proSaq_365 | Proline--tRNA ligase (EC 6.1.1.15) (Prolyl-tRNA synthetase) (ProRS) | O66690 ↗ |
| metG'aq_422 | Methionyl-tRNA synthetase beta subunit | O66738 ↗ |
| argSaq_923 | Arginine--tRNA ligase (EC 6.1.1.19) (Arginyl-tRNA synthetase) (ArgRS) | O67068 ↗ |
| glyQaq_945 | Glycine--tRNA ligase alpha subunit (EC 6.1.1.14) (Glycyl-tRNA synthetase alpha subunit) (GlyRS) | O67081 ↗ |
| pheSaq_953 | Phenylalanine--tRNA ligase alpha subunit (EC 6.1.1.20) (Phenylalanyl-tRNA synthetase alpha subunit) (PheRS) | O67087 ↗ |
| trpSaq_992 | Tryptophan--tRNA ligase (EC 6.1.1.2) (Tryptophanyl-tRNA synthetase) (TrpRS) | O67115 ↗ |
Follow the evidence
Each source-record link opens its UniProt entry. Gene links open the corresponding entry in this atlas’s working inventory.
Related scientific references ↗Sources for the developed article
Library essays and topic discussions
- L1. Otangelo Grasso, Aminoacyl-tRNA synthetases point to design. Machine or family-level discussion.
- L2. Otangelo Grasso, Origin of Aminoacyl tRNA synthetase. Machine or family-level discussion.
- L3. Otangelo Grasso, Aminoacyl-tRNA synthetases. Machine or family-level discussion.
Primary scientific evidence
- P1. Nureki et al. (1998), Enzyme structure with two catalytic sites for double-sieve selection of substrate.
- P2. Beuning & Musier-Forsyth (2000), Hydrolytic editing by a class II aminoacyl-tRNA synthetase.
Numbered protein records establish the selected inventory entries; these experimental examples establish the mechanisms identified above. Results from another bacterial species are not automatically Aquifex-specific measurements. Explore the library-to-atlas source guide →