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Conserved domains on  [gi|557878601|ref|NP_001273630|]
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RNA 3'-terminal phosphate cyclase-like protein isoform c [Homo sapiens]

Protein Classification

RNA 3'-terminal phosphate cyclase-like family protein( domain architecture ID 1005057)

RNA 3'-terminal phosphate cyclase-like protein (RCL) plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1, and A2 that are required for proper maturation of the 18S RNA

EC:  6.5.1.4
Gene Ontology:  GO:0004521|GO:0006396
PubMed:  28132487

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
18S_RNA_Rcl1p super family cl29293
18S rRNA biogenesis protein RCL1; Members of this strictly eukaryotic protein family are not ...
 7-185 7.99e-97

18S rRNA biogenesis protein RCL1; Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only.


The actual alignment was detected with superfamily member TIGR03400:

Pssm-ID: 274564 [Multi-domain]  Cd Length: 360  Bit Score: 284.89  E-value: 7.99e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601    7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPqgqGAAVLP 86
Cdd:TIGR03400 186 GVAYSTRVSPSLANRMIDAARGVLNNLLPDVYITTDVWKGKNSGKSPGYGLSLVAETTNGCIISAEAVSSP---GEPSLP 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601   87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQDVSKVLLGPLSPYTIEFLRHLKSFFQIMFKIETkpcGEELKG 166
Cdd:TIGR03400 263 EDLGKRAAYLLLEEIYKGGCVDSTHQPLALLLMALGQEDVSKLRLGKLSEYTVEFLRDIKEFFGVTFKLKD---DKSDNG 339

                         170
                  ....*....|....*....
gi 557878601  167 GDKVLMTCVGIGFSNLSKT 185
Cdd:TIGR03400 340 SGKVLLTCVGIGYTNVSKK 358
 
Name Accession Description Interval E-value
18S_RNA_Rcl1p TIGR03400
18S rRNA biogenesis protein RCL1; Members of this strictly eukaryotic protein family are not ...
 7-185 7.99e-97

18S rRNA biogenesis protein RCL1; Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only.


Pssm-ID: 274564 [Multi-domain]  Cd Length: 360  Bit Score: 284.89  E-value: 7.99e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601    7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPqgqGAAVLP 86
Cdd:TIGR03400 186 GVAYSTRVSPSLANRMIDAARGVLNNLLPDVYITTDVWKGKNSGKSPGYGLSLVAETTNGCIISAEAVSSP---GEPSLP 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601   87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQDVSKVLLGPLSPYTIEFLRHLKSFFQIMFKIETkpcGEELKG 166
Cdd:TIGR03400 263 EDLGKRAAYLLLEEIYKGGCVDSTHQPLALLLMALGQEDVSKLRLGKLSEYTVEFLRDIKEFFGVTFKLKD---DKSDNG 339

                         170
                  ....*....|....*....
gi 557878601  167 GDKVLMTCVGIGFSNLSKT 185
Cdd:TIGR03400 340 SGKVLLTCVGIGYTNVSKK 358
RNA_Cyclase_Class_I cd00875
RNA 3' phosphate cyclase domain (class I) This subfamily of cyclase-like proteins are encoded ...
 7-157 7.26e-78

RNA 3' phosphate cyclase domain (class I) This subfamily of cyclase-like proteins are encoded in eukaryotic genomes. They lack a conserved catalytic histidine residue required for cyclase activity, so probably do not function as cyclases. They are believed to play a role in ribosomal RNA processing and assembly.


Pssm-ID: 238447 [Multi-domain]  Cd Length: 341  Bit Score: 235.67  E-value: 7.26e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601   7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPQGQGAavLP 86
Cdd:cd00875  190 GVAYSTRVSPSIANRMIDAARGVLNPFIPDVYIYTDVRKGDNSGKSPGFGISLVAETTTGVLYSAENVSPAGGESE--VP 267

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557878601  87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQDV-SKVLLGPLSPYT--IEFLRHLKSFFQIMFKIET 157
Cdd:cd00875  268 EDLGRECAYQLLEEISRGGCVDSYQQPLALLLMALGSEDVgRLRLGGPLIDEEfkIHLLRDLKEFFGIMFKIDD 341
RTC pfam01137
RNA 3'-terminal phosphate cyclase; RNA cyclases are a family of RNA-modifying enzymes that are ...
 7-155 2.18e-45

RNA 3'-terminal phosphate cyclase; RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organizms. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids.


Pssm-ID: 460079 [Multi-domain]  Cd Length: 324  Bit Score: 151.89  E-value: 2.18e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601    7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPqgqgaAVLP 86
Cdd:pfam01137 182 GIAYVARLPPSIANRMVAAAAGLLLRFLPDVYIITDVEKGEESGKGGGGGIVLVAETTEGCILGASALGER-----GKPA 256

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557878601   87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQdVSKVLLGPLSPYTIEFLRHLKSFFQIMFKI 155
Cdd:pfam01137 257 EDVGEEAAEELLEELESGGCVDEHLQDQLILFMALAGG-ESVFRTGPLTLHTITNIRVIEQFLGVKFKI 324
PRK04204 PRK04204
RNA 3'-terminal phosphate cyclase;
19-156 6.67e-03

RNA 3'-terminal phosphate cyclase;


Pssm-ID: 235255 [Multi-domain]  Cd Length: 343  Bit Score: 36.34  E-value: 6.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601  19 ANRIVDSARSIL--NKFIPDIYIYTDhmkGVNSGKSPGFGLSLVAETTSGTFLSAELasnpqgqGAAVLP-EDLGRNCAR 95
Cdd:PRK04204 202 AERQAKAAAELLalSLGLIEIEINVE---ELSRGLGPGSGIVLWAESEHITEGFDAL-------GERGKPaEVVGEEAAE 271

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557878601  96 LLLEEIYRGGCVDStnqSLA---LLLMTLGQQdVSKVLLGPLSPYTIEFLRHLKSFFQIMFKIE 156
Cdd:PRK04204 272 ELLRYLASGAAVDE---HLAdqlILPMALAGG-EGSFTVAELTSHLLTNIWVVEKFLPVKFEVE 331
 
Name Accession Description Interval E-value
18S_RNA_Rcl1p TIGR03400
18S rRNA biogenesis protein RCL1; Members of this strictly eukaryotic protein family are not ...
 7-185 7.99e-97

18S rRNA biogenesis protein RCL1; Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only.


Pssm-ID: 274564 [Multi-domain]  Cd Length: 360  Bit Score: 284.89  E-value: 7.99e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601    7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPqgqGAAVLP 86
Cdd:TIGR03400 186 GVAYSTRVSPSLANRMIDAARGVLNNLLPDVYITTDVWKGKNSGKSPGYGLSLVAETTNGCIISAEAVSSP---GEPSLP 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601   87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQDVSKVLLGPLSPYTIEFLRHLKSFFQIMFKIETkpcGEELKG 166
Cdd:TIGR03400 263 EDLGKRAAYLLLEEIYKGGCVDSTHQPLALLLMALGQEDVSKLRLGKLSEYTVEFLRDIKEFFGVTFKLKD---DKSDNG 339

                         170
                  ....*....|....*....
gi 557878601  167 GDKVLMTCVGIGFSNLSKT 185
Cdd:TIGR03400 340 SGKVLLTCVGIGYTNVSKK 358
RNA_Cyclase_Class_I cd00875
RNA 3' phosphate cyclase domain (class I) This subfamily of cyclase-like proteins are encoded ...
 7-157 7.26e-78

RNA 3' phosphate cyclase domain (class I) This subfamily of cyclase-like proteins are encoded in eukaryotic genomes. They lack a conserved catalytic histidine residue required for cyclase activity, so probably do not function as cyclases. They are believed to play a role in ribosomal RNA processing and assembly.


Pssm-ID: 238447 [Multi-domain]  Cd Length: 341  Bit Score: 235.67  E-value: 7.26e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601   7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPQGQGAavLP 86
Cdd:cd00875  190 GVAYSTRVSPSIANRMIDAARGVLNPFIPDVYIYTDVRKGDNSGKSPGFGISLVAETTTGVLYSAENVSPAGGESE--VP 267

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557878601  87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQDV-SKVLLGPLSPYT--IEFLRHLKSFFQIMFKIET 157
Cdd:cd00875  268 EDLGRECAYQLLEEISRGGCVDSYQQPLALLLMALGSEDVgRLRLGGPLIDEEfkIHLLRDLKEFFGIMFKIDD 341
RTC pfam01137
RNA 3'-terminal phosphate cyclase; RNA cyclases are a family of RNA-modifying enzymes that are ...
 7-155 2.18e-45

RNA 3'-terminal phosphate cyclase; RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organizms. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids.


Pssm-ID: 460079 [Multi-domain]  Cd Length: 324  Bit Score: 151.89  E-value: 2.18e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601    7 GCRYSVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNPqgqgaAVLP 86
Cdd:pfam01137 182 GIAYVARLPPSIANRMVAAAAGLLLRFLPDVYIITDVEKGEESGKGGGGGIVLVAETTEGCILGASALGER-----GKPA 256

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557878601   87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQdVSKVLLGPLSPYTIEFLRHLKSFFQIMFKI 155
Cdd:pfam01137 257 EDVGEEAAEELLEELESGGCVDEHLQDQLILFMALAGG-ESVFRTGPLTLHTITNIRVIEQFLGVKFKI 324
RTC_insert pfam05189
RNA 3'-terminal phosphate cyclase (RTC), insert domain; RNA cyclases are a family of ...
 10-102 3.14e-35

RNA 3'-terminal phosphate cyclase (RTC), insert domain; RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organizms. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids.


Pssm-ID: 461577 [Multi-domain]  Cd Length: 102  Bit Score: 119.20  E-value: 3.14e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601   10 YSVRVSPQMANRIVDSARSILNKFIPDIYIYTD-HMKGVNSGKSPGFGLSLVAETTSGTFLSAElASNPQGqgaaVLPED 88
Cdd:pfam05189  14 YVAGLPPHVAERMAEAAREVLNKLLPDVYIYIDvVVEGRDSGKGPGSGIVLVAETTTGCILGAD-ALGERG----VPAED 88

                          90
                  ....*....|....
gi 557878601   89 LGRNCARLLLEEIY 102
Cdd:pfam05189  89 VGEEAAEELLEEIA 102
RNA_Cyclase cd00295
RNA 3' phosphate cyclase domain - RNA phosphate cyclases are enzymes that catalyze the ...
 11-155 4.60e-24

RNA 3' phosphate cyclase domain - RNA phosphate cyclases are enzymes that catalyze the ATP-dependent conversion of 3'-phosphate at the end of RNA into 2', 3'-cyclic phosphodiester bond. The enzymes are conserved in eucaryotes, bacteria and archaea. The exact biological role of this enzyme is unknown, but it has been proposed that it is likely to function in cellular RNA metabolism and processing. RNA phosphate cyclase has been characterized in human (with at least three isozymes), and E. coli, and it seems to be taxonomically widespread. The crystal structure of RNA phospate cyclase shows that it consists of two domains. The larger domain contains three repeats of a fold originally identified in the bacterial translation initiation factor IF3.


Pssm-ID: 238183 [Multi-domain]  Cd Length: 338  Bit Score: 96.27  E-value: 4.60e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601  11 SVRVSPQMANRIVDSARSILNKFIPDIYIYTDHMKGVNSGKSPGFGLSLVAETTSGTFLSAELASNpqgqgAAVLPEDLG 90
Cdd:cd00295  195 GTRVPPAFAEREIASAAGSFNLFEPDIFILPDDQRGDECGNGPGNSISLEAESEKGCSEAAEHCGE-----AGESAEDVA 269

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 557878601  91 RNCARLLLEEIYRGGCVDSTNQSLALLLMTLGQQDVSKVLLGPL--SPYTIEFLRHLKSFFQIMFKI 155
Cdd:cd00295  270 AFCAKELKEVIASGAAVDEYLADQLLLGMALAGEAGEFIVAGPLchLLQLTNFARDVEAFFNCEFRF 336
RNA_Cyclase_Class_II cd00874
RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze ...
 10-156 1.04e-05

RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine residue is found in all members of this subfamily.


Pssm-ID: 238446 [Multi-domain]  Cd Length: 326  Bit Score: 44.52  E-value: 1.04e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601  10 YSVRVSPQMANRIVDSARSILNKfIPDIYI---YTDHmkgvnSGKSPGFGLSLVAETTSGTFLSAELasnpqGQgAAVLP 86
Cdd:cd00874  190 HAANLPPHVAERQAEAAAALLRK-ALGLQIeiePEDQ-----SALGPGSGIVLWAEYEHSRLGFSAL-----GK-KGVPA 257

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 557878601  87 EDLGRNCARLLLEEIYRGGCVDSTNQSLALLLMTLGqqDVSKVLLGPLSPYT---IEFLRHlksFFQIMFKIE 156
Cdd:cd00874  258 EKVGEEAAEELLAYLSSGAAVDEHLADQLIPFMALA--GGSEFRTGELTLHLqtnIWVIEK---FLGVKFRIE 325
PRK04204 PRK04204
RNA 3'-terminal phosphate cyclase;
19-156 6.67e-03

RNA 3'-terminal phosphate cyclase;


Pssm-ID: 235255 [Multi-domain]  Cd Length: 343  Bit Score: 36.34  E-value: 6.67e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878601  19 ANRIVDSARSIL--NKFIPDIYIYTDhmkGVNSGKSPGFGLSLVAETTSGTFLSAELasnpqgqGAAVLP-EDLGRNCAR 95
Cdd:PRK04204 202 AERQAKAAAELLalSLGLIEIEINVE---ELSRGLGPGSGIVLWAESEHITEGFDAL-------GERGKPaEVVGEEAAE 271

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557878601  96 LLLEEIYRGGCVDStnqSLA---LLLMTLGQQdVSKVLLGPLSPYTIEFLRHLKSFFQIMFKIE 156
Cdd:PRK04204 272 ELLRYLASGAAVDE---HLAdqlILPMALAGG-EGSFTVAELTSHLLTNIWVVEKFLPVKFEVE 331
 
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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