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Literature summary for 2.9.1.3 extracted from
- Selenomodification of tRNA in archaea requires a bipartite rhodanese enzyme (2012), FEBS Lett., 586, 717-721 .
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanocaldococcus jannaschii | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? |  |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanococcus aeolicus | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanococcus maripaludis | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanococcus voltae | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanococcus vannielii | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanocaldococcus fervens | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanocaldococcus infernus | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanocaldococcus vulcanius | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanocaldococcus sp. FS406-22 | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | Methanothermococcus okinawensis | - |
5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Methanocaldococcus fervens | - |
- |
- |
| Methanocaldococcus infernus | - |
- |
- |
| Methanocaldococcus jannaschii | - |
- |
- |
| Methanocaldococcus sp. FS406-22 | - |
- |
- |
| Methanocaldococcus vulcanius | - |
- |
- |
| Methanococcus aeolicus | - |
- |
- |
| Methanococcus maripaludis | - |
- |
- |
| Methanococcus maripaludis | Q6LYT8 | ATP/GTP-binding site motif A (P-loop) | - |
| Methanococcus vannielii | - |
- |
- |
| Methanococcus voltae | - |
- |
- |
| Methanothermococcus okinawensis | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanocaldococcus jannaschii | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanococcus aeolicus | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanococcus maripaludis | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanococcus voltae | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanococcus vannielii | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanocaldococcus fervens | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanocaldococcus infernus | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanocaldococcus vulcanius | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanocaldococcus sp. FS406-22 | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
| selenophosphate + geranyl diphosphate + 5-methylaminomethyl-2-thiouridine34 in tRNA + H2O | - |
Methanothermococcus okinawensis | 5-methylaminomethyl-2-selenouridine34 in tRNA + (2E)-3,7-dimethylocta-2,6-diene-1-thiol + diphosphate + phosphate | - |
? | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanocaldococcus jannaschii |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanococcus aeolicus |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanococcus maripaludis |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanococcus voltae |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanococcus vannielii |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanocaldococcus fervens |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanocaldococcus infernus |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanocaldococcus vulcanius |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanocaldococcus sp. FS406-22 |
| evolution | the putative bipartite ortholog of the bacterial YbbB gene is identified in twelve additional archaeal genomes. Its function is confirmed as a tRNA 2-selenouridine synthase through biochemical and genetic experiments. A phylogenetic analysis of bacterial and archaeal versions of this enzyme provides insights into the early evolution of tRNA 2-selenouridine synthase. The active site loop containing the YbbB-characteristic CXRGGXRS motif near the C-terminus of the rhodanese domain and the Walker A motif (GX4GKT) at the N-terminus of the P-loop domain are highly conserved among the archaeal and bacterial YbbB sequences. The identified archaeal YbbB orthologs represent a bipartite version of bacterial tRNA 2-selenouridine synthase | Methanothermococcus okinawensis |
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