Pathway · 22 proteins
Translation interface
Aminoacyl-tRNA synthetases attach amino acids to tRNA.
How it works
- An aminoacyl-tRNA synthetase recognises an amino acid and appropriate tRNA identity features.
- ATP-dependent activation forms an aminoacyl-adenylate intermediate, followed by transfer of the amino acid to the tRNA’s terminal adenosine.
- The charged tRNA delivers its amino acid during translation. Editing mechanisms in many synthetases reduce mischarging; tRNA charging is downstream of amino-acid biosynthesis.
Grouped by the atlas’s curated pathway map. The table order is not a proven reaction order.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Cysteine--tRNA ligase | 6.1.1.16 | tRNA(Cys) + L-cysteine + ATP = L-cysteinyl-tRNA(Cys) + AMP + diphosphate | Zn(2+) | 495 | Step named |
| Lysine--tRNA ligase | 6.1.1.6 | tRNA(Lys) + L-lysine + ATP = L-lysyl-tRNA(Lys) + AMP + diphosphate | Mg(2+) | 597 | Step named |
| Histidine--tRNA ligase | 6.1.1.21 | tRNA(His) + L-histidine + ATP = L-histidyl-tRNA(His) + AMP + diphosphate + H(+) | — | 403 | Step named |
| Glutamate--tRNA ligase | 6.1.1.17 | tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) + AMP + diphosphate | Zn(2+) | 473 | Step named |
| Methionine--tRNA ligase | 6.1.1.10 | tRNA(Met) + L-methionine + ATP = L-methionyl-tRNA(Met) + AMP + diphosphate | Zn(2+) | 497 | Step named |
| Alanine--tRNA ligase | 6.1.1.7 | tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) + AMP + diphosphate | Zn(2+) | 867 | Step named |
| Valine--tRNA ligase | 6.1.1.9 | tRNA(Val) + L-valine + ATP = L-valyl-tRNA(Val) + AMP + diphosphate | — | 1165 | Step named |
| Threonine--tRNA ligase | 6.1.1.3 | tRNA(Thr) + L-threonine + ATP = L-threonyl-tRNA(Thr) + AMP + diphosphate + H(+) | Zn(2+) | 638 | Step named |
| Aspartate--tRNA(Asp/Asn) ligase | 6.1.1.23 | tRNA(Asx) + L-aspartate + ATP = L-aspartyl-tRNA(Asx) + AMP + diphosphate | — | 603 | Step named |
| Phenylalanine--tRNA ligase beta subunit | 6.1.1.20 | tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H(+) | Mg(2+) | 775 | Step named |
| Tyrosine--tRNA ligase | 6.1.1.1 | tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H(+) | — | 392 | Step named |
| Leucine--tRNA ligase subunit beta | 6.1.1.4 | tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate | — | 289 | Step named |
| Glycine--tRNA ligase beta subunit | 6.1.1.14 | tRNA(Gly) + glycine + ATP = glycyl-tRNA(Gly) + AMP + diphosphate | — | 664 | Step named |
| Serine--tRNA ligase | 6.1.1.11 | tRNA(Ser) + L-serine + ATP = L-seryl-tRNA(Ser) + AMP + diphosphate + H(+) | — | 425 | Step named |
| Isoleucine--tRNA ligase | 6.1.1.5 | tRNA(Ile) + L-isoleucine + ATP = L-isoleucyl-tRNA(Ile) + AMP + diphosphate | Zn(2+) | 956 | Step named |
| Leucine--tRNA ligase subunit alpha | 6.1.1.4 | tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate | — | 634 | Step named |
| Proline--tRNA ligase | 6.1.1.15 | tRNA(Pro) + L-proline + ATP = L-prolyl-tRNA(Pro) + AMP + diphosphate | — | 570 | Step named |
| Methionyl-tRNA synthetase beta subunit | — | — | — | 111 | System only |
| Arginine--tRNA ligase | 6.1.1.19 | tRNA(Arg) + L-arginine + ATP = L-arginyl-tRNA(Arg) + AMP + diphosphate | — | 583 | Step named |
| Glycine--tRNA ligase alpha subunit | 6.1.1.14 | tRNA(Gly) + glycine + ATP = glycyl-tRNA(Gly) + AMP + diphosphate | — | 285 | Step named |
| Phenylalanine--tRNA ligase alpha subunit | 6.1.1.20 | tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H(+) | Mg(2+) | 338 | Step named |
| Tryptophan--tRNA ligase | 6.1.1.2 | tRNA(Trp) + L-tryptophan + ATP = L-tryptophyl-tRNA(Trp) + AMP + diphosphate + H(+) | — | 395 | Step named |
Also part of this pathway
These proteins are described under another pathway, but also take part here.
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| tRNA(Ile)-lysidine synthaseHome: tRNA charging | 6.3.4.19 | cytidine(34) in tRNA(Ile2) + L-lysine + ATP = lysidine(34) in tRNA(Ile2) + AMP + diphosphate + H(+) | — | 317 | Unspecified |
Origins
How did the genetic code, the rule that links each codon to one amino acid, come to be?
How it was discovered
- 1967–68Carl Woese, Francis Crick and Leslie Orgel publish the first detailed discussions of the origin of the genetic code.Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, p. 395
The question has been discussed since the late 1960s. A biology textbook states it plainly: the code must have arisen very early because all organisms have it, but how it originated remains a question for scientists to address.
The code is carried out by aminoacyl-tRNA synthetases: each recognises one amino acid and the transfer RNAs that belong to it. That pairing is the code, and it is virtually the same in all organisms.
Twenty-two proteins of the minimal set work at this interface, and each is itself made by translation using the code it carries out.
From the books: Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, p. 395; Solomon, Berg & Martin, Biology, PDF p. 484; Garrett & Grisham, Biochemistry, p. 1094.
The wider question for this part of the cell: origins for building proteins and folding them.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Ribosomal subunits · RNA maturation · Translation cycle · Protein translocation · Protein turnover · Folding and stabilization · Recycling and rescue · Early folding support · Protein targeting · Ribosome · Protein export · Not yet placed in a pathway