Protein Domain : IPR020103

Type:  Domain Name:  Pseudouridine synthase, catalytic domain
Description:  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 alpha+beta 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 []:Pseudouridine synthase I, TruA.Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain.Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif.Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain.TruA from Escherichia colimodifies positions U-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA [].RsuA from E. coli catalyses formation of pseudouridine at position U-516 in 16S rRNA during assembly of the 30S ribosomal subunit []. 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.RluC and RluD are homologous enzymes which each convert three specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: bases U-955, U-2504, and U-2580 in the case of RluC and U-1911, U-1915, and U-1917 in the case of RluD []. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis []. 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. TruD modifies uracil-13 in tRNA, and belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life []. TruD is an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold. Short Name:  PsdUridine_synth_cat_dom
Paste the following link

1 Child Features

DB identifier Type Name
IPR006145 Domain Pseudouridine synthase, RsuA/RluB/C/D/E/F

7 Contains

DB identifier Type Name
IPR020097 Domain Pseudouridine synthase I, TruA, alpha/beta domain
IPR020095 Domain Pseudouridine synthase I, TruA, C-terminal
IPR011760 Domain Pseudouridine synthase, TruD, insertion domain
IPR020094 Domain Pseudouridine synthase I, TruA, N-terminal
IPR018496 Conserved_site Pseudouridine synthase, RsuA/RluB/E/F, conserved site
IPR006224 Conserved_site Pseudouridine synthase, RluC/RluD, conserved site
IPR020119 Conserved_site Pseudouridine synthase TruD, conserved site

1 Cross References

Identifier
SSF55120

4 Found Ins

DB identifier Type Name
IPR004802 Family tRNA pseudouridine synthase B family
IPR002501 Family Pseudouridine synthase II
IPR006225 Family Pseudouridine synthase, RluC/RluD
IPR005912 Family tRNA pseudouridine synthase, Pus10

4 GO Annotations

GO Term Gene Name
GO:0003723 IPR020103
GO:0009982 IPR020103
GO:0001522 IPR020103
GO:0009451 IPR020103

4 Ontology Annotations

GO Term Gene Name
GO:0003723 IPR020103
GO:0009982 IPR020103
GO:0001522 IPR020103
GO:0009451 IPR020103

0 Parent Features

3256 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
97541 D8RMK1 PAC:15411513 Selaginella moellendorffii 428  
78854 D8QUD6 PAC:15402293 Selaginella moellendorffii 268  
105100 D8RZ63 PAC:15412561 Selaginella moellendorffii 175  
107344 D8S3A7 PAC:15419977 Selaginella moellendorffii 421  
107717 D8S3A4 PAC:15422869 Selaginella moellendorffii 191  
417682 D8S387 PAC:15405370 Selaginella moellendorffii 148  
81986 D8QZK9 PAC:15412220 Selaginella moellendorffii 530  
111763 D8S9X0 PAC:15412764 Selaginella moellendorffii 428  
112010 D8S9W8 PAC:15410247 Selaginella moellendorffii 415  
117099 D8SHG0 PAC:15402614 Selaginella moellendorffii 289  
121195 D8SN49 PAC:15415500 Selaginella moellendorffii 355  
44317 D8SNZ9 PAC:15409736 Selaginella moellendorffii 363  
168290 D8R6E1 PAC:15420788 Selaginella moellendorffii 359  
124462 D8STK6 PAC:15403983 Selaginella moellendorffii 318  
75554 D8QNU2 PAC:15413626 Selaginella moellendorffii 447  
63437 D8QP88 PAC:15421957 Selaginella moellendorffii 403  
75008 D8QNX4 PAC:15409629 Selaginella moellendorffii 318  
76713 D8QTY7 PAC:15417914 Selaginella moellendorffii 327  
45172 D8SY63 PAC:15411322 Selaginella moellendorffii 251  
231248 D8RCZ2 PAC:15415295 Selaginella moellendorffii 300  
evm.TU.contig_29031.3 PAC:16429658 Carica papaya 200  
evm.model.supercontig_106.92 PAC:16405262 Carica papaya 402  
evm.model.supercontig_108.78 PAC:16405497 Carica papaya 542  
evm.model.supercontig_113.45 PAC:16406056 Carica papaya 371  
evm.model.supercontig_115.22 PAC:16406185 Carica papaya 392  
evm.model.supercontig_146.18 PAC:16409105 Carica papaya 354  
evm.model.supercontig_176.10 PAC:16411070 Carica papaya 258  
evm.model.supercontig_198.22 PAC:16412385 Carica papaya 484  
evm.model.supercontig_211.29 PAC:16413657 Carica papaya 156  
evm.model.supercontig_26.127 PAC:16415058 Carica papaya 371  

9 Publications

First Author Title Year Journal Volume Pages PubMed ID
            11953756
            10529181
            9585540
            10625422
            17466622
            15135053
            11779468
            15078091
            14659742