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Conserved domains on  [gi|70794772|ref|NP_001020577|]
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exosome complex component RRP45 [Rattus norvegicus]

Protein Classification

exosome complex component RRP45( domain architecture ID 10183520)

exosome complex component RRP45 is a component of the exosome that plays an important role in RNA turnover, maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts

CATH:  3.30.230.70
Gene Ontology:  GO:0006396|GO:0000178|GO:0061629|GO:0003723|GO:0035925|GO:0000175
PubMed:  16829983|17174896

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 6-264 7.53e-159

RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


:

Pssm-ID: 206773 [Multi-domain]  Cd Length: 259  Bit Score: 448.52  E-value: 7.53e-159
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   6 LSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQM 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  86 AAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDV 165
Cdd:cd11368  81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 166 SVQGEEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKD 245
Cdd:cd11368 161 TVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPS 240

                       250
                ....*....|....*....
gi 70794772 246 QVFRCSKIAGVKVAEITEL 264
Cdd:cd11368 241 QILRCVKIAAAKAKELTEL 259
 
Name Accession Description Interval E-value
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 6-264 7.53e-159

RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206773 [Multi-domain]  Cd Length: 259  Bit Score: 448.52  E-value: 7.53e-159
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   6 LSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQM 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  86 AAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDV 165
Cdd:cd11368  81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 166 SVQGEEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKD 245
Cdd:cd11368 161 TVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPS 240

                       250
                ....*....|....*....
gi 70794772 246 QVFRCSKIAGVKVAEITEL 264
Cdd:cd11368 241 QILRCVKIAAAKAKELTEL 259
PRK04282 PRK04282
exosome complex protein Rrp42;
1-271 3.78e-53

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 178.92  E-value: 3.78e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772    1 MKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILF 77
Cdd:PRK04282   3 SNQEIIPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   78 FNLELSQMAAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVAL 157
Cdd:PRK04282  83 VNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAAL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  158 CHFRRPDVSVQGEEVTLytpEERDPVPLSIHHMPICVSFAFFqqGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS 237
Cdd:PRK04282 163 LNTKVPAVEEGEDGVVD---KLGEDFPLPVNDKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKS 237

                        250       260       270
                 ....*....|....*....|....*....|....
gi 70794772  238 GGIMLLKDQVFRCSKIAGVKVAEITELIQKALEN 271
Cdd:PRK04282 238 GIGSFTEEEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 1-265 5.88e-52

Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441726 [Multi-domain]  Cd Length: 264  Bit Score: 175.38  E-value: 5.88e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   1 MKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISfgTDY-----GCCIVELGKTRVLGQVSCELVSPKLNRATEGI 75
Cdd:COG2123   1 MSSPIIPEIKRDYILSLLKKGKRIDGRGLDEYRPIEIE--TGViekaeGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  76 LFFNLELSQMAAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIV 155
Cdd:COG2123  79 LIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVA 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 156 ALCHFRRPDVSVQGEEVTLyTPEERDPVPlsIHHMPICVSFAFFqqGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQ 235
Cdd:COG2123 159 ALLTTKVPKVEVGEDGVVV-DKGEDTPLP--VNTLPVSVTMAKI--GDYLVVDPTLEEESVMDARITITTDEDGNIVAMQ 233

                       250       260       270
                ....*....|....*....|....*....|
gi 70794772 236 SSGGIMLLKDQVFRCSKIAGVKVAEITELI 265
Cdd:COG2123 234 KGGSGSFTEEEIDKAIDIALEKGKELRELL 263
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-144 1.45e-23

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 95.35  E-value: 1.45e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772    31 DYRNIRISFGTD---YGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAAPAFE-PGRQSDLLVKLNRLL 106
Cdd:pfam01138   1 ELRPIEIETGVLsqaDGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPgEGRPSEREIEISRLI 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 70794772   107 ERCLRNSKCIDteslcvvaGEKVWQIRVDLHLLNHDGN 144
Cdd:pfam01138  81 DRALRPSIPLE--------GYPRWTIRIDVTVLSSDGS 110
 
Name Accession Description Interval E-value
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 6-264 7.53e-159

RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206773 [Multi-domain]  Cd Length: 259  Bit Score: 448.52  E-value: 7.53e-159
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   6 LSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQM 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  86 AAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDV 165
Cdd:cd11368  81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 166 SVQGEEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKD 245
Cdd:cd11368 161 TVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPS 240

                       250
                ....*....|....*....
gi 70794772 246 QVFRCSKIAGVKVAEITEL 264
Cdd:cd11368 241 QILRCVKIAAAKAKELTEL 259
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-261 2.29e-59

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites.


Pssm-ID: 206766 [Multi-domain]  Cd Length: 218  Bit Score: 193.31  E-value: 2.29e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  32 YRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSP-KLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLLE 107
Cdd:cd11358   1 FRPVEIETGvlnQADGSALVKLGNTKVICAVTGPIVEPdKLERPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 108 RCLRNSKCIDTeslcvVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQgeevtlytpeERDPVPLSI 187
Cdd:cd11358  81 RTIEASVILDK-----STRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVD----------ERSPPLLLM 145

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 70794772 188 HHMPICVSFAFFQQGTyLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVFRCSKIAGVKVAEI 261
Cdd:cd11358 146 KDLIVAVSVGGISDGV-LLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
PRK04282 PRK04282
exosome complex protein Rrp42;
1-271 3.78e-53

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 178.92  E-value: 3.78e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772    1 MKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILF 77
Cdd:PRK04282   3 SNQEIIPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLI 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   78 FNLELSQMAAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVAL 157
Cdd:PRK04282  83 VNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAAL 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  158 CHFRRPDVSVQGEEVTLytpEERDPVPLSIHHMPICVSFAFFqqGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSS 237
Cdd:PRK04282 163 LNTKVPAVEEGEDGVVD---KLGEDFPLPVNDKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKS 237

                        250       260       270
                 ....*....|....*....|....*....|....
gi 70794772  238 GGIMLLKDQVFRCSKIAGVKVAEITELIQKALEN 271
Cdd:PRK04282 238 GIGSFTEEEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 1-265 5.88e-52

Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 441726 [Multi-domain]  Cd Length: 264  Bit Score: 175.38  E-value: 5.88e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   1 MKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISfgTDY-----GCCIVELGKTRVLGQVSCELVSPKLNRATEGI 75
Cdd:COG2123   1 MSSPIIPEIKRDYILSLLKKGKRIDGRGLDEYRPIEIE--TGViekaeGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  76 LFFNLELSQMAAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIV 155
Cdd:COG2123  79 LIVNAELLPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVA 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 156 ALCHFRRPDVSVQGEEVTLyTPEERDPVPlsIHHMPICVSFAFFqqGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQ 235
Cdd:COG2123 159 ALLTTKVPKVEVGEDGVVV-DKGEDTPLP--VNTLPVSVTMAKI--GDYLVVDPTLEEESVMDARITITTDEDGNIVAMQ 233

                       250       260       270
                ....*....|....*....|....*....|
gi 70794772 236 SSGGIMLLKDQVFRCSKIAGVKVAEITELI 265
Cdd:COG2123 234 KGGSGSFTEEEIDKAIDIALEKGKELRELL 263
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 11-264 6.60e-51

RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA.


Pssm-ID: 206770 [Multi-domain]  Cd Length: 256  Bit Score: 172.40  E-value: 6.60e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  11 RRFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAA 87
Cdd:cd11365   5 RDYILSLLEKGKRIDGRGLDEYRDIEIETGvipKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLAS 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  88 PAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSV 167
Cdd:cd11365  85 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEYEV 164

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 168 QGEEVTLYTPEERdpvPLSIHHMPICVSFAffQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQV 247
Cdd:cd11365 165 DENEVIEVLGEEL---PLPVNTLPVSVTVA--KIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTEDEI 239

                       250
                ....*....|....*..
gi 70794772 248 FRCSKIAGVKVAEITEL 264
Cdd:cd11365 240 DKAIDIALEKAAELREK 256
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 11-265 9.50e-46

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 159.26  E-value: 9.50e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  11 RRFLlraiEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAA 87
Cdd:cd11369  10 RRFL----AENVRPDGRELDEFRPTSVNVGsisTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDLPPLCS 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  88 PAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSV 167
Cdd:cd11369  86 SKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTI 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 168 QgEEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGtYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQV 247
Cdd:cd11369 166 D-EETELVVVNPEERRPLNLKNLPVSTTFAVFDDK-HLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQAQL 243

                       250
                ....*....|....*...
gi 70794772 248 FRCSKIAGVKVAEITELI 265
Cdd:cd11369 244 QECIELAKKRAKELQKLI 261
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 6-271 7.26e-36

RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206772 [Multi-domain]  Cd Length: 272  Bit Score: 133.10  E-value: 7.26e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772   6 LSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFG---TDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLEL 82
Cdd:cd11367   2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGvlsNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772  83 SQMAAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRR 162
Cdd:cd11367  82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772 163 PDVSVQGEEVTLYTPE-ERDPV---PLSIHHMPICVSFAffQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSG 238
Cdd:cd11367 162 PKVEVSEDDEGTKEIElSDDPYdvkRLDVSNVPLIVTLS--KIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSG 239

                       250       260       270
                ....*....|....*....|....*....|...
gi 70794772 239 GIMLLKDQVFRCSKIAGVKVAEITELIQKALEN 271
Cdd:cd11367 240 GGSLEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-144 1.45e-23

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 95.35  E-value: 1.45e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 70794772    31 DYRNIRISFGTD---YGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELSQMAAPAFE-PGRQSDLLVKLNRLL 106
Cdd:pfam01138   1 ELRPIEIETGVLsqaDGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPgEGRPSEREIEISRLI 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 70794772   107 ERCLRNSKCIDteslcvvaGEKVWQIRVDLHLLNHDGN 144
Cdd:pfam01138  81 DRALRPSIPLE--------GYPRWTIRIDVTVLSSDGS 110
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 189-254 2.02e-16

3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 427466 [Multi-domain]  Cd Length: 67  Bit Score: 73.38  E-value: 2.02e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 70794772   189 HMPICVSFAFFqqGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGIMLLKDQVFRCSKIA 254
Cdd:pfam03725   1 DPVAAVTVGKI--DGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELA 64
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 18-59 6.87e-03

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 38.08  E-value: 6.87e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 70794772   18 IEEKKRLDGRQTYDYRNIRISFGT----DyGCCIVELGKTRVLGQV 59
Cdd:PRK03983  10 LEDGLRLDGRKPDELRPIKIEVGVlknaD-GSAYLEWGNNKIIAAV 54
 
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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