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Conserved domains on  [gi|1407938512|pdb|6D6Q|D]
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Chain D, Exosome complex component RRP46

Protein Classification

exosome complex component RRP46( domain architecture ID 10183533)

exosome complex component RRP46 is a subunit of the eukaryotic exosome and a member of the RNase_PH family, named after the bacterial ribonuclease PH, a 3'-5' exoribonuclease.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 30-227 4.03e-99

RRP46 subunit of eukaryotic exosome; The RRP46 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: 206777 [Multi-domain]  Cd Length: 199  Bit Score: 286.77  E-value: 4.03e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVL 109
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D      110 GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDS 189
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160

                       170       180       190
                ....*....|....*....|....*....|....*....
6D6Q_D      190 VE-RKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYR 227
Cdd:cd11372 161 GEeKNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
 
Name Accession Description Interval E-value
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 30-227 4.03e-99

RRP46 subunit of eukaryotic exosome; The RRP46 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: 206777 [Multi-domain]  Cd Length: 199  Bit Score: 286.77  E-value: 4.03e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVL 109
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D      110 GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDS 189
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160

                       170       180       190
                ....*....|....*....|....*....|....*....
6D6Q_D      190 VE-RKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYR 227
Cdd:cd11372 161 GEeKNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 30-149 5.16e-27

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: 100.74  E-value: 5.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D         30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEiFNKATLEVIL---------RPKIGLPGVAEKSRERLI 100
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRD-FAPGRLTVEYelapfasgeRPGEGRPSEREIEISRLI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
6D6Q_D        101 RNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP 149
Cdd:pfam01138  81 DRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 30-236 4.87e-25

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 98.55  E-value: 4.87e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D        30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK----------VSKEIFNKATLEVILRPKiglPGVAEKSRE-- 97
Cdd:PRK03983  24 LRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHprhlqlpdraVLRVRYNMAPFSVDERKR---PGPDRRSIEis 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D        98 RLIRNTCEAVVLGTLHPRTSITVVLQVV-SDAGSLLACcLNAACMALVDAGVPMRALFCGVACALdSDGTLVLDPTSKQE 176
Cdd:PRK03983 101 KVIREALEPAIMLELFPRTVIDVFIEVLqADAGTRVAG-ITAASLALADAGIPMRDLVAGCAVGK-VDGVIVLDLNKEED 178

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       177 KEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSK 236
Cdd:PRK03983 179 NYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGE 238
 
Name Accession Description Interval E-value
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 30-227 4.03e-99

RRP46 subunit of eukaryotic exosome; The RRP46 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: 206777 [Multi-domain]  Cd Length: 199  Bit Score: 286.77  E-value: 4.03e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVL 109
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D      110 GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEARAVLTFALDS 189
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160

                       170       180       190
                ....*....|....*....|....*....|....*....
6D6Q_D      190 VE-RKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYR 227
Cdd:cd11372 161 GEeKNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 30-207 7.63e-50

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: 162.11  E-value: 7.63e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL--------PGVAEKSRERLIR 101
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAvgerrqgpPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D      102 NTCEAVVL---GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP-------------MRALFCGVACALDSDG 165
Cdd:cd11358  81 RTIEASVIldkSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPrvfvderspplllMKDLIVAVSVGGISDG 160

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
6D6Q_D      166 TLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTE 207
Cdd:cd11358 161 VLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTE 202
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 30-187 1.78e-33

RRP41 subunit of eukaryotic exosome; The RRP41 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: 206775 [Multi-domain]  Cd Length: 226  Bit Score: 120.34  E-value: 1.78e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEI----------FNKATLEVILRPKIglPGVAEKSRE-- 97
Cdd:cd11370  12 LRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQAlhdravvnceYSMATFSTGERKRR--GKGDRRSTEls 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       98 RLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALdSDGTLVLDPTSKQEK 177
Cdd:cd11370  90 LAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGY-LDSTPLLDLNYLEES 168

                       170
                ....*....|
6D6Q_D      178 EARAVLTFAL 187
Cdd:cd11370 169 GDLPDLTVAV 178
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 30-149 5.16e-27

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: 100.74  E-value: 5.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D         30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEiFNKATLEVIL---------RPKIGLPGVAEKSRERLI 100
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRD-FAPGRLTVEYelapfasgeRPGEGRPSEREIEISRLI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
6D6Q_D        101 RNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP 149
Cdd:pfam01138  81 DRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 30-234 9.57e-26

RRP41 subunit of archaeal exosome; The RRP41 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.


Pssm-ID: 206771 [Multi-domain]  Cd Length: 214  Bit Score: 99.72  E-value: 9.57e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK----------VSKEIFNKATLEVILRPKiglPGVAEKSRE-- 97
Cdd:cd11366   2 LRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHprhlqlpdraVIRVRYNMAPFSVDERKR---PGPDRREIEis 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       98 RLIRNTCEAVVLGTLHPRTSITVVLQVV-SDAGSLLACcLNAACMALVDAGVPMRALFCGVAcALDSDGTLVLDPTSKQE 176
Cdd:cd11366  79 KVIKEALEPAIILEEFPRTAIDVFVEVLqADAGTRVAG-LNAASLALADAGIPMRDLVAACA-AGKVDGKIVLDLNKEED 156

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
6D6Q_D      177 KEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRY 234
Cdd:cd11366 157 NYGEADMPIAMMPNLGEITLLQLDGDLTPDEFKQAIELAKKGCKRIYELQKEALKRKY 214
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 30-236 4.87e-25

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 98.55  E-value: 4.87e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D        30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK----------VSKEIFNKATLEVILRPKiglPGVAEKSRE-- 97
Cdd:PRK03983  24 LRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHprhlqlpdraVLRVRYNMAPFSVDERKR---PGPDRRSIEis 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D        98 RLIRNTCEAVVLGTLHPRTSITVVLQVV-SDAGSLLACcLNAACMALVDAGVPMRALFCGVACALdSDGTLVLDPTSKQE 176
Cdd:PRK03983 101 KVIREALEPAIMLELFPRTVIDVFIEVLqADAGTRVAG-ITAASLALADAGIPMRDLVAGCAVGK-VDGVIVLDLNKEED 178

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       177 KEARAVLTFALDSVERKLLMSSTKGLYSDTELQQCLAAAQAASQHVFRFYRESLQRRYSK 236
Cdd:PRK03983 179 NYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGE 238
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 39-187 4.31e-19

MTR3 subunit of eukaryotic exosome; The MTR3 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: 206776 [Multi-domain]  Cd Length: 210  Bit Score: 82.23  E-value: 4.31e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       39 LLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR--------PKIGLPGVAEKSRERLIRNTCEAVVLG 110
Cdd:cd11371  10 VVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKfapfatpgRRRHGQDSEERELSSLLHQALEPAVRL 89

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
6D6Q_D      111 TLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACALDsDGTLVLDPTSKQEKEARAVLTFAL 187
Cdd:cd11371  90 EKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALI-GDELLLDPTREEEEASSGGVMLAY 165
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 15-171 4.81e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 50.28  E-value: 4.81e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D        15 AENGTGSSPRGPgCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGV-YGPAEVK------VSKEIFNKATLEVILRP--- 84
Cdd:PLN00207 434 VEGGKRSDGRTP-DEIRPINSSCGLLPRAHGSALFTRGETQALAVVtLGDKQMAqridnlVDADEVKRFYLQYSFPPscv 512

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D        85 ----KIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVACA 160
Cdd:PLN00207 513 gevgRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMG 592

                        170
                 ....*....|.
6D6Q_D       161 ldsdgtLVLDP 171
Cdd:PLN00207 593 ------MVLDT 597
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 152-201 4.00e-06

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: 43.33  E-value: 4.00e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
6D6Q_D        152 ALFCGVACALdSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKG 201
Cdd:pfam03725   1 DPVAAVTVGK-IDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGG 49
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 29-165 1.36e-04

Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase (PNPase) 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. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E.


Pssm-ID: 206769 [Multi-domain]  Cd Length: 223  Bit Score: 41.76  E-value: 1.36e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       29 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGV-YGPAE--------VKVSKEIF-------NKATLEV-----ILRPKIG 87
Cdd:cd11364   1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVtLGTLEdaqkidslGGEKSKRFmlhynfpPYSVGETgrvggPGRREIG 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6D6Q_D       88 LPGVAEKSRERLIRNTCEavvlgtlHPRTsITVVLQVVSDAGS--LLACClnAACMALVDAGVPMRALFCGVACALDSDG 165
Cdd:cd11364  81 HGALAERALLPVLPSPED-------FPYT-IRVVSEVLESNGSssMASVC--GGSLALMDAGVPIKAPVAGIAMGLITEG 150
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 138-166 5.48e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 37.72  E-value: 5.48e-03
                         10        20
                 ....*....|....*....|....*....
6D6Q_D       138 AACMALVDAGVPMRALFCGVACALDSDGT 166
Cdd:PRK11824 445 GSSLALMDAGVPIKAPVAGIAMGLIKEGD 473
 
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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