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IPR006225 is a Pseudouridine synthase, RluC/RluD.
<p>This entry represents the RluC/RluD subfamily of pseudouridine synthases. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases uracil-955, U-2504, and U-2580 in the case of RluC and uracil-1911, U-1915, and U-1917 in the case of RluD [[cite:PUB00032035]]. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [[cite:PUB00037409]]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different.</p> <p>Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an α+β structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are [[cite:PUB00045922], [cite:PUB00092579]]:</p> <ul><li>Pseudouridine synthase I, TruA.</li> <li>Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.</li> <li>Pseudouridine synthase RsuA. RluB, RluE and RluF are also part of this family.</li> <li>Pseudouridine synthase RluA. TruC, RluC and RluD belong to this family.</li> <li>Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific α+β subdomain.</li></ul>
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 | Pseudouridine synthesis | The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs. | ||
| Molecular function | RNA binding | Interacting selectively and non-covalently with an RNA molecule or a portion thereof. | ||
| Biological process | RNA modification | The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically. | ||
| Molecular function | Pseudouridine synthase activity | Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5. |
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | Pseudouridine synthase; TAIR: AT5G51140.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q0E0Y3|PUS7_ORYSJ RNA pseudouridine synthase 7; TrEMBL-Plants: tr|V7AZ29|V7AZ29_PHAVU Pseudouridine synthase; Found in the gene: LotjaGi1g1v0335700 | 12 | ||
| – | Pseudouridine synthase; TAIR: AT5G51140.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q0E0Y3|PUS7_ORYSJ RNA pseudouridine synthase 7; TrEMBL-Plants: tr|V7AZ29|V7AZ29_PHAVU Pseudouridine synthase; Found in the gene: LotjaGi1g1v0335700 | 12 | ||
| – | Pseudouridine synthase; TAIR: AT1G76050.2 Pseudouridine synthase family protein; Swiss-Prot: sp|Q3ECD0|PUS2_ARATH RNA pseudouridine synthase 2, chloroplastic; TrEMBL-Plants: tr|V7ARA7|V7ARA7_PHAVU Uncharacterized protein; Found in the gene: LotjaGi1g1v0431800 | 19 | ||
| – | Pseudouridine synthase; TAIR: AT1G76050.2 Pseudouridine synthase family protein; Swiss-Prot: sp|Q3ECD0|PUS2_ARATH RNA pseudouridine synthase 2, chloroplastic; TrEMBL-Plants: tr|V7ARA7|V7ARA7_PHAVU Uncharacterized protein; Found in the gene: LotjaGi1g1v0431800 | 19 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| cd02869 | CDD | 1 | 25.00 |