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IPR006463 is a tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB.
<p>This entry represents the MiaB enzyme and homologues that are responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil (all except tRNA(I,V) Ser). Adenine-37 is next to the anticodon on the 3' side in these tRNA's, and lack of modification at this site leads to an increased spontaneous mutation frequency. Isopentenylated A-37 is modified by methylthiolation at position 2 leading to the formation of 2-methylthio-N6-(dimethylallyl)adenosine, either by MiaB alone or in concert with a separate methylase yet to be discovered [[cite:PUB00009727]]. MiaB contains two 4Fe-4S clusters which are labile under oxidizing conditions [[cite:PUB00009728], [cite:PUB00083447]]. One cluster is coordinated with three cysteines and an exchangeable S-adenosyl-L-methionine, the other is thought to be the sulfur donor. The second cluster has a polysulfide group bound to it, which is methylated in the first reaction step. Concurrently, the SAM-[4Fe-4S] cluster forms the 5'-dAdo radical, which abstracts a hydrogen atom from the substrate, which is then methylthiolated by the methylated polysulfide group [[cite:PUB00017717], [cite:PUB00083446], [cite:PUB00083448]]. Additionally, the sequence is homologous to the biotin synthetase, BioB, which utilises both an iron-sulfur cluster and S-adenosym methionine (SAM) to generate a radical which is responsible for initiating the insertion of sulfur into the substrate [[cite:PUB00009729]]. It is reasonable to surmise that the methyl group of SAM becomes the methyl group of the product, but this has not been shown, and the possibility of a separate methylase exists. These enzymes contain a TRAM domain [[cite:PUB00009729]] which is believed to be responsible for binding to tRNAs. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterised and shown to complement the E. coli MiaB enzyme [[cite:PUB00017717]].</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
| GO term | Namespace | Name | Definition | Relationships |
|---|---|---|---|---|
| Biological process | TRNA modification | The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically. | ||
| Molecular function | Transferase activity | Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. | ||
| Molecular function | 4 iron, 4 sulfur cluster binding | Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; TAIR: AT4G36390.1 Methylthiotransferase; Swiss-Prot: sp|Q8H0V1|CK5P1_ARATH CDK5RAP1-like protein; TrEMBL-Plants: tr|G7KGB3|G7KGB3_MEDTR Radical SAM methylthiotransferase, MiaB/RimO family protein; Found in the gene: LotjaGi2g1v0385400 | 28 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| cd01335 | CDD | 1 | 100.00 |