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IPR006145 is a Pseudouridine synthase, RsuA/RluA-like.
<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> <p>This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit) and TruC [[cite:PUB00095796]].</p> <p>RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [[cite:PUB00018355], [cite:PUB00037953]]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site.</p> <p>RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine:</p> <ul><li>RluB modifies uracil-2605.</li> <li>RluC modifies uracil-955, U-2504, and U-2580.</li> <li>RluD modifies uracil-1911, U-1915, and U-1917.</li> <li>RluE modifies uracil-3457.</li> <li>RluF modifies uracil-2604, and to a lesser extent U-2605.</li></ul> <p>RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [[cite:PUB00032035], [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>
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 |
---|---|---|---|---|
– | PREDICTED: RNA pseudourine synthase 7-like [Cicer arietinum] gi|502133332|ref|XP_004501725.1| | 9 | ||
– | PREDICTED: RNA pseudourine synthase 3, mitochondrial-like isoform X1 [Cicer arietinum] gi|502172693|ref|XP_004515176.1| | 13 | ||
– | PREDICTED: RNA pseudourine synthase 3, mitochondrial-like [Glycine max] gi|356562211|ref|XP_003549365.1| | 7 | ||
– | PREDICTED: RNA pseudourine synthase 3, mitochondrial-like [Glycine max] gi|356562211|ref|XP_003549365.1| | 7 | ||
– | PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Glycine max] gi|356495831|ref|XP_003516775.1| | 7 | ||
– | PREDICTED: RNA pseudourine synthase 4, mitochondrial-like [Glycine max] gi|356495831|ref|XP_003516775.1| | 7 | ||
– | PREDICTED: RNA pseudourine synthase 2, chloroplastic-like [Cicer arietinum] gi|502131232|ref|XP_004500918.1| | 16 | ||
– | Pseudouridine synthase family protein isoform 2, partial [Theobroma cacao] gi|508726877|gb|EOY18774.1| | 22 | ||
– | Pseudouridine synthase family protein isoform 3 [Theobroma cacao] gi|508726878|gb|EOY18775.1| | 22 | ||
– | PREDICTED: RNA pseudourine synthase 5-like [Glycine max] gi|356576201|ref|XP_003556222.1| | 9 | ||
– | PREDICTED: RNA pseudourine synthase 5-like [Cicer arietinum] gi|502118549|ref|XP_004496322.1| | 9 | ||
– | 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 | ||
– | Pseudouridine synthase family protein; TAIR: AT3G19440.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q9LT72|PUS4_ARATH RNA pseudouridine synthase 4, mitochondrial; TrEMBL-Plants: tr|A0A0S3T6K0|A0A0S3T6K0_PHAAN Uncharacterized protein; Found in the gene: LotjaGi2g1v0461400 | 7 | ||
– | Pseudouridine synthase family protein; TAIR: AT1G78910.2 Pseudouridine synthase family protein; Swiss-Prot: sp|Q5XET6|PUS3_ARATH RNA pseudouridine synthase 3, mitochondrial; TrEMBL-Plants: tr|A0A151T0N6|A0A151T0N6_CAJCA Uncharacterized protein; Found in the gene: LotjaGi5g1v0039400 | 8 | ||
– | Pseudouridine synthase family protein; TAIR: AT1G78910.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q5XET6|PUS3_ARATH RNA pseudouridine synthase 3, mitochondrial; TrEMBL-Plants: tr|K7MNI8|K7MNI8_SOYBN Uncharacterized protein; Found in the gene: LotjaGi5g1v0039400 | 8 | ||
– | Pseudouridine synthase family protein; TAIR: AT1G78910.2 Pseudouridine synthase family protein; Swiss-Prot: sp|Q5XET6|PUS3_ARATH RNA pseudouridine synthase 3, mitochondrial; TrEMBL-Plants: tr|A0A151T0N6|A0A151T0N6_CAJCA Uncharacterized protein; Found in the gene: LotjaGi5g1v0039400 | 8 | ||
– | Pseudouridine synthase family protein; TAIR: AT1G78910.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q5XET6|PUS3_ARATH RNA pseudouridine synthase 3, mitochondrial; TrEMBL-Plants: tr|K7MNI8|K7MNI8_SOYBN Uncharacterized protein; Found in the gene: LotjaGi5g1v0039400 | 8 | ||
– | Pseudouridine synthase family protein; TAIR: AT1G56345.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q7XA65|PUS1_ARATH RNA pseudouridine synthase 1; TrEMBL-Plants: tr|A0A072VMN0|A0A072VMN0_MEDTR RNA pseudouridine synthase; Found in the gene: LotjaGi5g1v0229200 | 9 | ||
– | Pseudouridine synthase family protein; TAIR: AT1G56345.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q7XA65|PUS1_ARATH RNA pseudouridine synthase 1; TrEMBL-Plants: tr|A0A072VMN0|A0A072VMN0_MEDTR RNA pseudouridine synthase; Found in the gene: LotjaGi5g1v0229200 | 9 | ||
– | Ribosomal large subunit pseudouridine synthase B; TAIR: AT2G39140.1 pseudouridine synthase family protein; Swiss-Prot: sp|P35159|RLUB_BACSU Ribosomal large subunit pseudouridine synthase B; TrEMBL-Plants: tr|A0A151SE04|A0A151SE04_CAJCA Ribosomal large subunit pseudouridine synthase B; Found in the gene: LotjaGi5g1v0270600 | 25 | ||
– | Pseudouridine synthase; TAIR: AT3G52260.2 Pseudouridine synthase family protein; Swiss-Prot: sp|Q5M721|PUS5_ARATH RNA pseudouridine synthase 5; TrEMBL-Plants: tr|I1NHE4|I1NHE4_SOYBN Pseudouridine synthase; Found in the gene: LotjaGi5g1v0276400 | 12 | ||
– | Pseudouridine synthase family protein; TAIR: AT4G21770.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q9SVS0|PUS6_ARATH RNA pseudouridine synthase 6, chloroplastic; TrEMBL-Plants: tr|I1M124|I1M124_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0296200 | 15 | ||
– | Pseudouridine synthase family protein; TAIR: AT4G21770.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q9SVS0|PUS6_ARATH RNA pseudouridine synthase 6, chloroplastic; TrEMBL-Plants: tr|I1M124|I1M124_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0296200 | 15 | ||
– | Pseudouridine synthase family protein; TAIR: AT4G21770.1 Pseudouridine synthase family protein; Swiss-Prot: sp|Q9SVS0|PUS6_ARATH RNA pseudouridine synthase 6, chloroplastic; TrEMBL-Plants: tr|I1M124|I1M124_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0296200 | 15 |
A list of co-occurring predicted domains within the L. japonicus gene space:
Predicted domain | Source | Observations | Saturation (%) |
---|---|---|---|
mobidb-lite | MobiDBLite | 1 | 3.70 |