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Conserved domains on  [gi|73947485|ref|XP_852838|]
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exosome complex component RRP46 [Canis lupus familiaris]

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 ...
28-225 3.55e-97

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: 281.76  E-value: 3.55e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVL 107
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485 108 GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNSDGTLVLDPTAKQEKEARAVLTFALDS 187
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160
                       170       180       190
                ....*....|....*....|....*....|....*....
gi 73947485 188 VE-RKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYR 225
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 ...
28-225 3.55e-97

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: 281.76  E-value: 3.55e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVL 107
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485 108 GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNSDGTLVLDPTAKQEKEARAVLTFALDS 187
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160
                       170       180       190
                ....*....|....*....|....*....|....*....
gi 73947485 188 VE-RKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYR 225
Cdd:cd11372 161 GEeKNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
28-147 4.70e-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: 4.70e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485    28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEiFNKATLEVIL---------RPKIGLPGVAEKSRERLI 98
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRD-FAPGRLTVEYelapfasgeRPGEGRPSEREIEISRLI 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 73947485    99 RNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP 147
Cdd:pfam01138  81 DRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
28-185 1.22e-25

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223761 [Multi-domain]  Cd Length: 230  Bit Score: 100.05  E-value: 1.22e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRE----------RL 97
Cdd:COG0689  18 LRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKREadrgrtkeisRL 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  98 IRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNsDGTLVLDPTAKQEKEA 177
Cdd:COG0689  98 IGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIV-DGVIVLDLDYEEDSAA 176

                ....*...
gi 73947485 178 RAVLTFAL 185
Cdd:COG0689 177 EADMNVVM 184
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
28-234 2.01e-24

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 97.01  E-value: 2.01e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485   28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK----------VSKEIFNKATLEVILRPKiglPGVAEKSRE-- 95
Cdd:PRK03983  24 LRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHprhlqlpdraVLRVRYNMAPFSVDERKR---PGPDRRSIEis 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485   96 RLIRNTCEAVVLGTLHPRTSITVVLQVV-SDAGSLLACcLNAACMALVDAGVPMRALFCGVTCALnSDGTLVLDPTAKQE 174
Cdd:PRK03983 101 KVIREALEPAIMLELFPRTVIDVFIEVLqADAGTRVAG-ITAASLALADAGIPMRDLVAGCAVGK-VDGVIVLDLNKEED 178
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  175 KEARAVLTFALDSVERKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYRESLQRRYSK 234
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 ...
28-225 3.55e-97

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: 281.76  E-value: 3.55e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRERLIRNTCEAVVL 107
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485 108 GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNSDGTLVLDPTAKQEKEARAVLTFALDS 187
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160
                       170       180       190
                ....*....|....*....|....*....|....*....
gi 73947485 188 VE-RKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYR 225
Cdd:cd11372 161 GEeKNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
28-202 3.00e-48

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: 157.87  E-value: 3.00e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGL--------PGVAEKSRERLIR 99
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAvgerrqgpPGDEEMEISRLLE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485 100 NTCEAVVL---GTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP-------------MRALFCGVTCALNSDG 163
Cdd:cd11358  81 RTIEASVIldkSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPrvfvderspplllMKDLIVAVSVGGISDG 160
                       170       180       190
                ....*....|....*....|....*....|....*....
gi 73947485 164 TLVLDPTAKQEKEARAVLTFALDSvERKLLMSTTKGLYS 202
Cdd:cd11358 161 VLLLDPTGEEEELADSTLTVAVDK-SGKLCLLSKVGGGS 198
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
28-185 4.58e-34

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: 121.88  E-value: 4.58e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEI----------FNKATLEVILRPKIglPGVAEKSRE-- 95
Cdd:cd11370  12 LRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQAlhdravvnceYSMATFSTGERKRR--GKGDRRSTEls 89
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  96 RLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALnSDGTLVLDPTAKQEK 175
Cdd:cd11370  90 LAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGY-LDSTPLLDLNYLEES 168
                       170
                ....*....|
gi 73947485 176 EARAVLTFAL 185
Cdd:cd11370 169 GDLPDLTVAV 178
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
28-147 4.70e-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: 4.70e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485    28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEiFNKATLEVIL---------RPKIGLPGVAEKSRERLI 98
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRD-FAPGRLTVEYelapfasgeRPGEGRPSEREIEISRLI 80
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 73947485    99 RNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVP 147
Cdd:pfam01138  81 DRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
28-185 1.22e-25

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 223761 [Multi-domain]  Cd Length: 230  Bit Score: 100.05  E-value: 1.22e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILRPKIGLPGVAEKSRE----------RL 97
Cdd:COG0689  18 LRPIKITRGVLKHAEGSSLIEFGNTKVICTVSGPREPVPRFLRGTGKGWLTAEYGMLPRSTDERKKREadrgrtkeisRL 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  98 IRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNsDGTLVLDPTAKQEKEA 177
Cdd:COG0689  98 IGRALRAVIDLELLPESTIDIDCDVLQADGGTRTASITGASLALADAGIPLRDLVAAISVGIV-DGVIVLDLDYEEDSAA 176

                ....*...
gi 73947485 178 RAVLTFAL 185
Cdd:COG0689 177 EADMNVVM 184
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
28-232 8.25e-25

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: 97.40  E-value: 8.25e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK----------VSKEIFNKATLEVILRPKiglPGVAEKSRE-- 95
Cdd:cd11366   2 LRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHprhlqlpdraVIRVRYNMAPFSVDERKR---PGPDRREIEis 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  96 RLIRNTCEAVVLGTLHPRTSITVVLQVV-SDAGSLLACcLNAACMALVDAGVPMRALFCGVTcALNSDGTLVLDPTAKQE 174
Cdd:cd11366  79 KVIKEALEPAIILEEFPRTAIDVFVEVLqADAGTRVAG-LNAASLALADAGIPMRDLVAACA-AGKVDGKIVLDLNKEED 156
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 73947485 175 KEARAVLTFALDSVERKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYRESLQRRY 232
Cdd:cd11366 157 NYGEADMPIAMMPNLGEITLLQLDGDLTPDEFKQAIELAKKGCKRIYELQKEALKRKY 214
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
28-234 2.01e-24

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 97.01  E-value: 2.01e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485   28 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVK----------VSKEIFNKATLEVILRPKiglPGVAEKSRE-- 95
Cdd:PRK03983  24 LRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHprhlqlpdraVLRVRYNMAPFSVDERKR---PGPDRRSIEis 100
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485   96 RLIRNTCEAVVLGTLHPRTSITVVLQVV-SDAGSLLACcLNAACMALVDAGVPMRALFCGVTCALnSDGTLVLDPTAKQE 174
Cdd:PRK03983 101 KVIREALEPAIMLELFPRTVIDVFIEVLqADAGTRVAG-ITAASLALADAGIPMRDLVAGCAVGK-VDGVIVLDLNKEED 178
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  175 KEARAVLTFALDSVERKLLMSTTKGLYSAAELQQCLAAAQAASQHVFRFYRESLQRRYSK 234
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 ...
37-185 9.64e-20

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: 83.77  E-value: 9.64e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  37 LLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFNKATLEVILR--------PKIGLPGVAEKSRERLIRNTCEAVVLG 108
Cdd:cd11371  10 VVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKfapfatpgRRRHGQDSEERELSSLLHQALEPAVRL 89
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 73947485 109 TLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCALNsDGTLVLDPTAKQEKEARAVLTFAL 185
Cdd:cd11371  90 EKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALI-GDELLLDPTREEEEASSGGVMLAY 165
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
150-199 5.31e-07

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 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: 427466 [Multi-domain]  Cd Length: 67  Bit Score: 45.65  E-value: 5.31e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 73947485   150 ALFCGVTCALnSDGTLVLDPTAKQEKEARAVLTFALDSVERKLLMSTTKG 199
Cdd:pfam03725   1 DPVAAVTVGK-IDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGG 49
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
13-169 1.38e-06

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 48.74  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485   13 AESGTESGPRGPgCSLRHFACEQNLLSRPDGSASFLQGDTSVLAGV-YGPAEVK------VSKEIFNKATLEVILRP--- 82
Cdd:PLN00207 434 VEGGKRSDGRTP-DEIRPINSSCGLLPRAHGSALFTRGETQALAVVtLGDKQMAqridnlVDADEVKRFYLQYSFPPscv 512
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485   83 ----KIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLACCLNAACMALVDAGVPMRALFCGVTCA 158
Cdd:PLN00207 513 gevgRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAMG 592
                        170
                 ....*....|.
gi 73947485  159 lnsdgtLVLDP 169
Cdd:PLN00207 593 ------MVLDT 597
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
27-163 7.67e-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: 39.45  E-value: 7.67e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  27 SLRHFACEQNLLSRPDGSASFLQGDTSVLAGV-YGPAE--------VKVSKEIF-------NKATLEV-----ILRPKIG 85
Cdd:cd11364   1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVtLGTLEdaqkidslGGEKSKRFmlhynfpPYSVGETgrvggPGRREIG 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 73947485  86 LPGVAEKSRERLIRNTCEavvlgtlHPRTsITVVLQVVSDAGS--LLACClnAACMALVDAGVPMRALFCGVTCALNSDG 163
Cdd:cd11364  81 HGALAERALLPVLPSPED-------FPYT-IRVVSEVLESNGSssMASVC--GGSLALMDAGVPIKAPVAGIAMGLITEG 150
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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