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Literature summary for 6.1.1.11 extracted from
- Classical molecular dynamics simulation of seryl tRNA synthetase and threonyl tRNA synthetase bound with tRNA and aminoacyl adenylate (2018), J. Biomol. Struct. Dyn., 2018, 1-23 .
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Thermus thermophilus |  |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + L-serine + tRNASer | Thermus thermophilus | - |
AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 | - |
AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | Thermus thermophilus DSM 7039 | - |
AMP + diphosphate + L-seryl-tRNASer | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Thermus thermophilus | P34945 | - |
- |
| Thermus thermophilus DSM 7039 | P34945 | - |
- |
| Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 | P34945 | - |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + L-serine + tRNASer | - |
Thermus thermophilus | AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | tttRNASer | Thermus thermophilus | AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | - |
Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 | AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | tttRNASer | Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 | AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | - |
Thermus thermophilus DSM 7039 | AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| ATP + L-serine + tRNASer | tttRNASer | Thermus thermophilus DSM 7039 | AMP + diphosphate + L-seryl-tRNASer | - |
? | |
| additional information | the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme | Thermus thermophilus | ? | - |
? | |
| additional information | the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme | Thermus thermophilus HB27 / ATCC BAA-163 / DSM 7039 | ? | - |
? | |
| additional information | the interaction of ttRNASer with the enzyme, interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free State, which is significantly reduced down within the active site bound with adenylate. The loops change their conformation via multimodal dynamics. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme | Thermus thermophilus DSM 7039 | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | - |
Thermus thermophilus |
| homodimer | - |
Thermus thermophilus |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| SerRS | - |
Thermus thermophilus |
| serS | - |
Thermus thermophilus |
| seryl tRNA synthetase | - |
Thermus thermophilus |
| subclass IIa dimeric SerRS | - |
Thermus thermophilus |
| ttSerRS | - |
Thermus thermophilus |
| TT_C0520 | - |
Thermus thermophilus |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| ATP | - |
Thermus thermophilus | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the class II, subclass IIa, of aminoacyl-tRNA sythetases | Thermus thermophilus |
| additional information | the interactions between the catalytically important loops and tRNA contribute to the change in dynamics of tRNA in free and bound states, respectively. These interactions help in the development of catalytically effective organization of the active site. The A76 end of the tttRNASer exhibits fast dynamics in free state, which is significantly reduced within the active site bound with adenylate. Presence of bound Mg2+ ions around tRNA and dynamically slow bound water are other common features of the enzyme, dynamics of dimeric ttSerRS bound with adenylate and tttRNASer with a focus to the molecular process of the dynamic development of the catalytically competent active site organization essential for the second step, molecular dynamic simulations, overview | Thermus thermophilus |
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