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Conserved domains on  [gi|767970698|ref|XP_011541341|]
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pseudouridylate synthase RPUSD4, mitochondrial isoform X1 [Homo sapiens]

Protein Classification

pseudouridine synthase family protein( domain architecture ID 1007)

pseudouridine synthase family protein may catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PseudoU_synth super family cl00130
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
 28-136 3.44e-20

Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).


The actual alignment was detected with superfamily member cd02869:

Pssm-ID: 469624 [Multi-domain]  Cd Length: 185  Bit Score: 82.77  E-value: 3.44e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  28 SPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDWnrlapqkl 107
Cdd:cd02869   96 APLGRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLAS-IGHPIVGDPKYGGK-------- 166

                         90       100
                 ....*....|....*....|....*....
gi 767970698 108 svgtlkklglEQSKARYIPLHLHARQLIL 136
Cdd:cd02869  167 ----------ASDSPGLKRLALHAYRLSF 185
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 28-136 3.44e-20

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 82.77  E-value: 3.44e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  28 SPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDWnrlapqkl 107
Cdd:cd02869   96 APLGRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLAS-IGHPIVGDPKYGGK-------- 166

                         90       100
                 ....*....|....*....|....*....
gi 767970698 108 svgtlkklglEQSKARYIPLHLHARQLIL 136
Cdd:cd02869  167 ----------ASDSPGLKRLALHAYRLSF 185
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 32-162 5.27e-18

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 77.87  E-value: 5.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  32 RMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDWNRLAPQKLSvgt 111
Cdd:COG0564  107 RDPKDRKKMAVVDEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAH-IGHPIVGDPLYGGDRSNRLLGLD--- 182

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 767970698 112 lkklgleqskaryiPLHLHARQLILPALGSGkEELNLVCKLPRFFVHSLHR 162
Cdd:COG0564  183 --------------RQALHAYRLGFPHPVTG-EPLEFEAPLPEDFQALLEK 218
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 16-164 2.07e-16

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 75.05  E-value: 2.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698   16 AQGQQQHHKMTLSPSYRMDDGK--MVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGD 93
Cdd:TIGR00005 163 VHGQFDSGGGTVDAPLGRVPNNrgLMAVHPSSEGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQY-LGHPLAGD 241

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767970698   94 HKYSDwnrlaPQKLSVGTLKKLGLEqskaRYIplhLHARQLILPALGSGkEELNLVCKLPRFFVHSLHRLR 164
Cdd:TIGR00005 242 PLYGN-----KPVPGNNLNGLLNFD----RQA---LHAYELGFIHPATG-EILEFEAPLPADLVLLLEALR 299
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
 42-132 4.53e-09

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 54.28  E-value: 4.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  42 RRSRNAQVAVTQYQVLS-----------STLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDW--NRLAPQKLS 108
Cdd:PRK11112 117 REDKAPQPAVTHYRGLAtvempvatgryPTTRYSLVELEPKTGRKHQLRRHMAH-LRHPIIGDTKHGDLrqNRSLAEHFG 195

                         90       100       110
                 ....*....|....*....|....*....|
gi 767970698 109 VGtlkKLGLEQSKARYI------PLHLHAR 132
Cdd:PRK11112 196 CS---RLMLHASELSLThpftgePLTITAG 222
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 30-83 1.69e-06

RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 45.47  E-value: 1.69e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767970698   30 SYRMDDGKMVKVRRSrNAQVAVTQYQVLSSTLSS--ALVELQPITGIKHQLRVHLS 83
Cdd:pfam00849  96 KKEKNKSPFRKEEEL-GGKKAVTHLKVLKSGSKGdySLLELELVTGRKHQIRAHLA 150
 
Name Accession Description Interval E-value
PseudoU_synth_RluA_like cd02869
Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and ...
 28-136 3.44e-20

Pseudouridine synthase, RluA family; This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.


Pssm-ID: 211346 [Multi-domain]  Cd Length: 185  Bit Score: 82.77  E-value: 3.44e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  28 SPSYRMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDWnrlapqkl 107
Cdd:cd02869   96 APLGRKKRKKRARVVVSEDGKPAITHYKVLERFGNVTLVELQLETGRTHQIRVHLAS-IGHPIVGDPKYGGK-------- 166

                         90       100
                 ....*....|....*....|....*....
gi 767970698 108 svgtlkklglEQSKARYIPLHLHARQLIL 136
Cdd:cd02869  167 ----------ASDSPGLKRLALHAYRLSF 185
RluA COG0564
Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and ...
 32-162 5.27e-18

Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]; Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440330 [Multi-domain]  Cd Length: 218  Bit Score: 77.87  E-value: 5.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  32 RMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDWNRLAPQKLSvgt 111
Cdd:COG0564  107 RDPKDRKKMAVVDEDGKPAVTHYRVLERFGGYSLVEVRLETGRTHQIRVHLAH-IGHPIVGDPLYGGDRSNRLLGLD--- 182

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 767970698 112 lkklgleqskaryiPLHLHARQLILPALGSGkEELNLVCKLPRFFVHSLHR 162
Cdd:COG0564  183 --------------RQALHAYRLGFPHPVTG-EPLEFEAPLPEDFQALLEK 218
rluA_subfam TIGR00005
pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine ...
 16-164 2.07e-16

pseudouridine synthase, RluA family; In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 161659 [Multi-domain]  Cd Length: 299  Bit Score: 75.05  E-value: 2.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698   16 AQGQQQHHKMTLSPSYRMDDGK--MVKVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFgLDCPILGD 93
Cdd:TIGR00005 163 VHGQFDSGGGTVDAPLGRVPNNrgLMAVHPSSEGKPAVTHFRVLERFGNASLVECELETGRTHQIRVHLQY-LGHPLAGD 241

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767970698   94 HKYSDwnrlaPQKLSVGTLKKLGLEqskaRYIplhLHARQLILPALGSGkEELNLVCKLPRFFVHSLHRLR 164
Cdd:TIGR00005 242 PLYGN-----KPVPGNNLNGLLNFD----RQA---LHAYELGFIHPATG-EILEFEAPLPADLVLLLEALR 299
PRK11112 PRK11112
tRNA pseudouridine synthase C; Provisional
 42-132 4.53e-09

tRNA pseudouridine synthase C; Provisional


Pssm-ID: 182971 [Multi-domain]  Cd Length: 257  Bit Score: 54.28  E-value: 4.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  42 RRSRNAQVAVTQYQVLS-----------STLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSDW--NRLAPQKLS 108
Cdd:PRK11112 117 REDKAPQPAVTHYRGLAtvempvatgryPTTRYSLVELEPKTGRKHQLRRHMAH-LRHPIIGDTKHGDLrqNRSLAEHFG 195

                         90       100       110
                 ....*....|....*....|....*....|
gi 767970698 109 VGtlkKLGLEQSKARYI------PLHLHAR 132
Cdd:PRK11112 196 CS---RLMLHASELSLThpftgePLTITAG 222
PseudoU_synth_TruC cd02563
tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific ...
 1-98 6.31e-08

tRNA pseudouridine isomerase C; Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.


Pssm-ID: 211333 [Multi-domain]  Cd Length: 223  Bit Score: 50.41  E-value: 6.31e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698   1 MPSAGVVDIPIVEKeaqgqqqhhkmtlspsyrMDDGKMVKVRRSRNAQVAVTQYQVLSSTLSSA-----------LVELQ 69
Cdd:cd02563   93 VPESGTIDYPLSEE------------------LDKLADKFASDDKAPQAATTHYRLLAVEELPVvvgkyptsrysLVELT 154

                         90       100
                 ....*....|....*....|....*....
gi 767970698  70 PITGIKHQLRVHLSFgLDCPILGDHKYSD 98
Cdd:cd02563  155 PHTGRKHQLRRHLAH-IRHPIIGDTTHGD 182
PRK10158 PRK10158
bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;
50-141 2.03e-07

bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA;


Pssm-ID: 236659 [Multi-domain]  Cd Length: 219  Bit Score: 49.22  E-value: 2.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  50 AVTQYQVLS-STLSSALVELQPITGIKHQLRVHLsFGLDCPILGDHKYSDwnrlapqklsvgtlkklglEQSKARYIPLH 128
Cdd:PRK10158 135 AQTEYEVVEyAADNTARVVLKPITGRSHQLRVHM-LALGHPILGDRFYAS-------------------PEARAMAPRLL 194

                         90
                 ....*....|....*
gi 767970698 129 LHARQLIL--PALGS 141
Cdd:PRK10158 195 LHAEMLTIthPAYGN 209
PSRA_1 cd02558
Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial ...
 37-96 8.05e-07

Pseudouridine synthase, a subgroup of the RluA family; This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.


Pssm-ID: 211332 [Multi-domain]  Cd Length: 246  Bit Score: 47.65  E-value: 8.05e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767970698  37 KMVKVRRSRNAQV------AVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSfGLDCPILGDHKY 96
Cdd:cd02558  141 RIVKGRGFFQAREvegepnAETRIELLARRGGWGLYRLSPHTGKTHQLRVHMA-ALGVPILNDPFY 205
PseudoU_synth_2 pfam00849
RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA ...
 30-83 1.69e-06

RNA pseudouridylate synthase; Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA.


Pssm-ID: 459961 [Multi-domain]  Cd Length: 151  Bit Score: 45.47  E-value: 1.69e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767970698   30 SYRMDDGKMVKVRRSrNAQVAVTQYQVLSSTLSS--ALVELQPITGIKHQLRVHLS 83
Cdd:pfam00849  96 KKEKNKSPFRKEEEL-GGKKAVTHLKVLKSGSKGdySLLELELVTGRKHQIRAHLA 150
PseudoU_synth_ScRIB2 cd02557
Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, ...
 50-98 4.83e-04

Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2; Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.


Pssm-ID: 211331 [Multi-domain]  Cd Length: 213  Bit Score: 39.15  E-value: 4.83e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 767970698  50 AVTQYQVLSS--TLSSALVELQPITGIKHQLRVHLSFgLDCPILGDHKYSD 98
Cdd:cd02557  138 ARTIFKRLSYngDLNTSVVLCKPITGRTHQIRVHLQY-LGHPIVNDPIYNN 187
PRK11025 PRK11025
23S rRNA pseudouridine(955/2504/2580) synthase RluC;
17-164 7.20e-03

23S rRNA pseudouridine(955/2504/2580) synthase RluC;


Pssm-ID: 182909 [Multi-domain]  Cd Length: 317  Bit Score: 36.25  E-value: 7.20e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767970698  17 QGQQQHH-KMTLSPSYR--MDDGKMVkVRRSRNAQVAVTQYQVLSSTLSSALVELQPITGIKHQLRVHLSFGlDCPILGD 93
Cdd:PRK11025 181 RGQWQSHvKVVQAPLLKniLQSGERI-VRVSQEGKPSETRFKVEERYAFATLVRASPVTGRTHQIRVHTQYA-GHPIAFD 258

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767970698  94 HKYSDwnRLAPQKLSvgtlkKLGLEQskaryipLHLHARQLILPALGSGkEELNLVCKLPRFFVHSLHRLR 164
Cdd:PRK11025 259 DRYGD--REFDQQLT-----GTGLNR-------LFLHAAALKFTHPGTG-EVMRIEAPLDEQLKRCLQKLR 314
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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