Pathway · 3 proteins
tRNA charging
Synthetases and amidotransferases prepare aminoacyl-tRNA.
How it works
- Amino-acid supply and ATP feed synthetase-catalysed amino-acid activation.
- A matching tRNA receives the activated amino acid. Recognition involves tRNA identity features, not just the anticodon.
- Charged tRNAs connect the genetic code to the amino acids delivered to ribosomes. Editing and proofreading mechanisms help limit errors.
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 |
|---|---|---|---|---|---|
| tRNA(Ile)-lysidine synthase | 6.3.4.19 | cytidine(34) in tRNA(Ile2) + L-lysine + ATP = lysidine(34) in tRNA(Ile2) + AMP + diphosphate + H(+) | — | 317 | Unspecified |
| Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A | 3.5.1.2 | L-glutamine + H2O = L-glutamate + NH4(+) | — | 478 | Unspecified |
| Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 6.3.5.6; 6.3.5.7 | L-glutamyl-tRNA(Gln) + L-glutamine + ATP + H2O = L-glutaminyl-tRNA(Gln) + L-glutamate + ADP + phosphate + H(+) | Mg(2+) | 478 | Unspecified |
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 |
|---|---|---|---|---|---|
| Cysteine--tRNA ligaseHome: Translation interface | 6.1.1.16 | tRNA(Cys) + L-cysteine + ATP = L-cysteinyl-tRNA(Cys) + AMP + diphosphate | Zn(2+) | 495 | Step named |
| Lysine--tRNA ligaseHome: Translation interface | 6.1.1.6 | tRNA(Lys) + L-lysine + ATP = L-lysyl-tRNA(Lys) + AMP + diphosphate | Mg(2+) | 597 | Step named |
| Histidine--tRNA ligaseHome: Translation interface | 6.1.1.21 | tRNA(His) + L-histidine + ATP = L-histidyl-tRNA(His) + AMP + diphosphate + H(+) | — | 403 | Step named |
| Glutamate--tRNA ligaseHome: Translation interface | 6.1.1.17 | tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) + AMP + diphosphate | Zn(2+) | 473 | Step named |
| Methionine--tRNA ligaseHome: Translation interface | 6.1.1.10 | tRNA(Met) + L-methionine + ATP = L-methionyl-tRNA(Met) + AMP + diphosphate | Zn(2+) | 497 | Step named |
| Alanine--tRNA ligaseHome: Translation interface | 6.1.1.7 | tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) + AMP + diphosphate | Zn(2+) | 867 | Step named |
| Valine--tRNA ligaseHome: Translation interface | 6.1.1.9 | tRNA(Val) + L-valine + ATP = L-valyl-tRNA(Val) + AMP + diphosphate | — | 1165 | Step named |
| Threonine--tRNA ligaseHome: Translation interface | 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) ligaseHome: Translation interface | 6.1.1.23 | tRNA(Asx) + L-aspartate + ATP = L-aspartyl-tRNA(Asx) + AMP + diphosphate | — | 603 | Step named |
| Phenylalanine--tRNA ligase beta subunitHome: Translation interface | 6.1.1.20 | tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H(+) | Mg(2+) | 775 | Step named |
| Tyrosine--tRNA ligaseHome: Translation interface | 6.1.1.1 | tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H(+) | — | 392 | Step named |
| Leucine--tRNA ligase subunit betaHome: Translation interface | 6.1.1.4 | tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate | — | 289 | Step named |
| Glycine--tRNA ligase beta subunitHome: Translation interface | 6.1.1.14 | tRNA(Gly) + glycine + ATP = glycyl-tRNA(Gly) + AMP + diphosphate | — | 664 | Step named |
| Serine--tRNA ligaseHome: Translation interface | 6.1.1.11 | tRNA(Ser) + L-serine + ATP = L-seryl-tRNA(Ser) + AMP + diphosphate + H(+) | — | 425 | Step named |
| Isoleucine--tRNA ligaseHome: Translation interface | 6.1.1.5 | tRNA(Ile) + L-isoleucine + ATP = L-isoleucyl-tRNA(Ile) + AMP + diphosphate | Zn(2+) | 956 | Step named |
| Leucine--tRNA ligase subunit alphaHome: Translation interface | 6.1.1.4 | tRNA(Leu) + L-leucine + ATP = L-leucyl-tRNA(Leu) + AMP + diphosphate | — | 634 | Step named |
| Proline--tRNA ligaseHome: Translation interface | 6.1.1.15 | tRNA(Pro) + L-proline + ATP = L-prolyl-tRNA(Pro) + AMP + diphosphate | — | 570 | Step named |
| Methionyl-tRNA synthetase beta subunitHome: Translation interface | — | — | — | 111 | System only |
| Arginine--tRNA ligaseHome: Translation interface | 6.1.1.19 | tRNA(Arg) + L-arginine + ATP = L-arginyl-tRNA(Arg) + AMP + diphosphate | — | 583 | Step named |
| Glycine--tRNA ligase alpha subunitHome: Translation interface | 6.1.1.14 | tRNA(Gly) + glycine + ATP = glycyl-tRNA(Gly) + AMP + diphosphate | — | 285 | Step named |
| Phenylalanine--tRNA ligase alpha subunitHome: Translation interface | 6.1.1.20 | tRNA(Phe) + L-phenylalanine + ATP = L-phenylalanyl-tRNA(Phe) + AMP + diphosphate + H(+) | Mg(2+) | 338 | Step named |
| Tryptophan--tRNA ligaseHome: Translation interface | 6.1.1.2 | tRNA(Trp) + L-tryptophan + ATP = L-tryptophyl-tRNA(Trp) + AMP + diphosphate + H(+) | — | 395 | Step named |
Origins
How could transfer RNAs have been loaded with the right amino acids before synthetases existed?
All three basic reactions of translation (activating the amino acid, loading it onto RNA, and joining amino acids) have been reproduced with ribozymes. RNAs that load an amino acid onto themselves were found by laboratory selection with relative ease, and the best are faster and more specific than the protein enzymes.
The activated amino acids these reactions need are highly unstable, and the ribozymes were selected by researchers from large pools under chosen conditions.
Aquifex, like most bacteria, has no separate synthetase for glutamine. It loads tRNA-Gln with glutamate and then converts it with a three-part amidotransferase, so getting one amino acid right takes four proteins working in order.
From the books: Koonin, The Logic of Chance, PDF p. 233; Ruiz-Mirazo et al., Prebiotic Systems Chemistry, PDF p. 18; Koonin & Galperin, Sequence – Evolution – Function, PDF p. 288.
The wider question for this part of the cell: origins for conserved, but we cannot say what they do.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Nutrient and metabolic state · Biosynthesis of various nucleotide sugars · Purine metabolism · Bacterial secretion system · Glyoxylate and dicarboxylate metabolism · Starch and sucrose metabolism · Homologous recombination · Fructose and mannose metabolism · Streptomycin biosynthesis · Other carbon fixation pathways · Nicotinate and nicotinamide metabolism · Not yet placed in a pathway