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Conserved domains on  [gi|1002237474|ref|XP_015622944|]
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exosome complex component RRP45A isoform X1 [Oryza sativa Japonica Group]

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 ...
 9-269 4.96e-137

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: 393.82  E-value: 4.96e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474   9 PTVNEREFIERALQSDLRVDGRRPFDFRRLKILFGREDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPM 88
Cdd:cd11368     1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  89 ADPAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPEC 168
Cdd:cd11368    81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 169 TVGGEDgqqVTVHDPEVRDPLPLTIHHLPIAVTFAYFGEGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGV 248
Cdd:cd11368   161 TVDGEE---VTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPL 237

                         250       260
                  ....*....|....*....|.
gi 1002237474 249 MSSVIMQCLRIASVKAADITS 269
Cdd:cd11368   238 SPSQILRCVKIAAAKAKELTE 258
 
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 ...
 9-269 4.96e-137

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: 393.82  E-value: 4.96e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474   9 PTVNEREFIERALQSDLRVDGRRPFDFRRLKILFGREDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPM 88
Cdd:cd11368     1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  89 ADPAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPEC 168
Cdd:cd11368    81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 169 TVGGEDgqqVTVHDPEVRDPLPLTIHHLPIAVTFAYFGEGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGV 248
Cdd:cd11368   161 TVDGEE---VTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPL 237

                         250       260
                  ....*....|....*....|.
gi 1002237474 249 MSSVIMQCLRIASVKAADITS 269
Cdd:cd11368   238 SPSQILRCVKIAAAKAKELTE 258
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 14-272 6.71e-81

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: 250.87  E-value: 6.71e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  14 REFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPMAD 90
Cdd:COG2123    11 RDYILSLLKKGKRIDGRGLDEYRPIEIETGvieKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLAS 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  91 PAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPECTV 170
Cdd:COG2123    91 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEV 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 171 gGEDGQQVtvhDPEVRDPLPLTihHLPIAVTFAYFgeGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKaGGEGVMS 250
Cdd:COG2123   171 -GEDGVVV---DKGEDTPLPVN--TLPVSVTMAKI--GDYLVVDPTLEEESVMDARITITTDEDGNIVAMQK-GGSGSFT 241

                         250       260
                  ....*....|....*....|...
gi 1002237474 251 -SVIMQCLRIASVKAADITSKIK 272
Cdd:COG2123   242 eEEIDKAIDIALEKGKELRELLK 264
PRK04282 PRK04282
exosome complex protein Rrp42;
14-277 1.49e-79

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 247.48  E-value: 1.49e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  14 REFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPMAD 90
Cdd:PRK04282   13 KDYILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLAS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  91 PAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPECTV 170
Cdd:PRK04282   93 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 171 GGEDGQQVTvhdpevRDPLPLTIHHLPIAVTFAYFgeGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGVMS 250
Cdd:PRK04282  173 GEDGVVDKL------GEDFPLPVNDKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTE 244

                         250       260
                  ....*....|....*....|....*..
gi 1002237474 251 SVIMQCLRIASVKAADITSKIKNEVNS 277
Cdd:PRK04282  245 EEVDKAIDIALEKAKELREKLKEALGI 271
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 34-150 1.53e-22

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: 92.66  E-value: 1.53e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  34 DFRRLKILFG---REDGSAEVQLGDTRVMGYATAQlVQPYKDRPN-EGTLAIFTEFSPMADPAFE-PGRPGESAIELGRV 108
Cdd:pfam01138   1 ELRPIEIETGvlsQADGSALVELGDTKVLATVTGP-IEPKEDRDFaPGRLTVEYELAPFASGERPgEGRPSEREIEISRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1002237474 109 VDRGLRESRAVDmeslcvvaGKHVWSVRVDLHILDNGGNLID 150
Cdd:pfam01138  80 IDRALRPSIPLE--------GYPRWTIRIDVTVLSSDGSLLD 113
 
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 ...
 9-269 4.96e-137

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: 393.82  E-value: 4.96e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474   9 PTVNEREFIERALQSDLRVDGRRPFDFRRLKILFGREDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPM 88
Cdd:cd11368     1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  89 ADPAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPEC 168
Cdd:cd11368    81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 169 TVGGEDgqqVTVHDPEVRDPLPLTIHHLPIAVTFAYFGEGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGV 248
Cdd:cd11368   161 TVDGEE---VTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPL 237

                         250       260
                  ....*....|....*....|.
gi 1002237474 249 MSSVIMQCLRIASVKAADITS 269
Cdd:cd11368   238 SPSQILRCVKIAAAKAKELTE 258
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 14-272 6.71e-81

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: 250.87  E-value: 6.71e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  14 REFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPMAD 90
Cdd:COG2123    11 RDYILSLLKKGKRIDGRGLDEYRPIEIETGvieKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLAS 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  91 PAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPECTV 170
Cdd:COG2123    91 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEV 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 171 gGEDGQQVtvhDPEVRDPLPLTihHLPIAVTFAYFgeGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKaGGEGVMS 250
Cdd:COG2123   171 -GEDGVVV---DKGEDTPLPVN--TLPVSVTMAKI--GDYLVVDPTLEEESVMDARITITTDEDGNIVAMQK-GGSGSFT 241

                         250       260
                  ....*....|....*....|...
gi 1002237474 251 -SVIMQCLRIASVKAADITSKIK 272
Cdd:COG2123   242 eEEIDKAIDIALEKGKELRELLK 264
PRK04282 PRK04282
exosome complex protein Rrp42;
14-277 1.49e-79

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 247.48  E-value: 1.49e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  14 REFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPMAD 90
Cdd:PRK04282   13 KDYILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLAS 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  91 PAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPECTV 170
Cdd:PRK04282   93 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEE 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 171 GGEDGQQVTvhdpevRDPLPLTIHHLPIAVTFAYFgeGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGVMS 250
Cdd:PRK04282  173 GEDGVVDKL------GEDFPLPVNDKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTE 244

                         250       260
                  ....*....|....*....|....*..
gi 1002237474 251 SVIMQCLRIASVKAADITSKIKNEVNS 277
Cdd:PRK04282  245 EEVDKAIDIALEKAKELREKLKEALGI 271
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 14-270 3.24e-76

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: 238.27  E-value: 3.24e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  14 REFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPMAD 90
Cdd:cd11365     5 RDYILSLLEKGKRIDGRGLDEYRDIEIETGvipKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLAS 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  91 PAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPECtv 170
Cdd:cd11365    85 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEY-- 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 171 ggEDGQQVTVHDPEVRDPLPLTihHLPIAVTFAYFgeGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGVMS 250
Cdd:cd11365   163 --EVDENEVIEVLGEELPLPVN--TLPVSVTVAKI--GGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTE 236

                         250       260
                  ....*....|....*....|
gi 1002237474 251 SVIMQCLRIASVKAADITSK 270
Cdd:cd11365   237 DEIDKAIDIALEKAAELREK 256
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 13-261 1.91e-50

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: 172.01  E-value: 1.91e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  13 EREFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAIFTEFSPMA 89
Cdd:cd11367     6 EKSYIIHGVEQNIRNDGRSRLDYRPIELETGvlsNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNA 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  90 DPAFEpGRPGES-AIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPEC 168
Cdd:cd11367    86 SPEFE-GRGGEElATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKV 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 169 TVGGEDGQQVTVH---DPEvrDPLPLTIHHLPIAVTFAYFgeGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGG 245
Cdd:cd11367   165 EVSEDDEGTKEIElsdDPY--DVKRLDVSNVPLIVTLSKI--GNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGG 240

                         250
                  ....*....|....*.
gi 1002237474 246 EGVMSSVIMQCLRIAS 261
Cdd:cd11367   241 GSLEPESIIEMIETAK 256
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 5-271 4.90e-48

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: 165.42  E-value: 4.90e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474   5 QRWHPtvneREFIERALQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMGYATAQLVQPYKDRPNEGTLAI 81
Cdd:cd11369     1 KKLHP----LEYYRRFLAENVRPDGRELDEFRPTSVNVGsisTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVP 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  82 FTEFSPMADPAFEPGRPGESAIELGRVVDRGLRESRAVDMESLCVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALS 161
Cdd:cd11369    77 NVDLPPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALK 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 162 TFRRPECTVGGEDGQQVTvhDPEvrDPLPLTIHHLPIAVTFAYFgEGNIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQ 241
Cdd:cd11369   157 NLRLPAVTIDEETELVVV--NPE--ERRPLNLKNLPVSTTFAVF-DDKHLLADPTAEEELLASGLVTVVVDENGELCSVH 231

                         250       260       270
                  ....*....|....*....|....*....|
gi 1002237474 242 KAGGEGVMSSVIMQCLRIASVKAADITSKI 271
Cdd:cd11369   232 KPGGSPLSQAQLQECIELAKKRAKELQKLI 261
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 35-267 1.01e-41

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: 147.47  E-value: 1.01e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  35 FRRLKI---LFGREDGSAEVQLGDTRVMGYATAQLVQPYKD-RPNEGTLAIFTEFSPMADPAFEPGRPGESAIELGRVVD 110
Cdd:cd11358     1 FRPVEIetgVLNQADGSALVKLGNTKVICAVTGPIVEPDKLeRPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474 111 RGLRESRAVDmeslcVVAGKHVWSVRVDLHILDNGGNLIDAANIAALAALSTFRRPECTVGGedgqqvtvhdpevRDPLP 190
Cdd:cd11358    81 RTIEASVILD-----KSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDE-------------RSPPL 142

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002237474 191 LTIHHLPIAVTFAYFGEGnIMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGVMSSVIMQCLRIASVKAADI 267
Cdd:cd11358   143 LLMKDLIVAVSVGGISDG-VLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 34-150 1.53e-22

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: 92.66  E-value: 1.53e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  34 DFRRLKILFG---REDGSAEVQLGDTRVMGYATAQlVQPYKDRPN-EGTLAIFTEFSPMADPAFE-PGRPGESAIELGRV 108
Cdd:pfam01138   1 ELRPIEIETGvlsQADGSALVELGDTKVLATVTGP-IEPKEDRDFaPGRLTVEYELAPFASGERPgEGRPSEREIEISRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1002237474 109 VDRGLRESRAVDmeslcvvaGKHVWSVRVDLHILDNGGNLID 150
Cdd:pfam01138  80 IDRALRPSIPLE--------GYPRWTIRIDVTVLSSDGSLLD 113
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 195-260 1.42e-14

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: 67.99  E-value: 1.42e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002237474 195 HLPIAVTFAYFGEGniMVIDPTYKEEAVMGGRMTATINSNGDVCSIQKAGGEGVMSSVIMQCLRIA 260
Cdd:pfam03725   1 DPVAAVTVGKIDGQ--LVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELA 64
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 25-59 1.54e-05

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: 46.00  E-value: 1.54e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1002237474  25 LRVDGRRPFDFRRLKI---LFGREDGSAEVQLGDTRVM 59
Cdd:cd11370     2 LRLDGRRPNELRRIRCrigVFSSADGSAYLEQGNTKVL 39
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 21-114 1.81e-03

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 40.00  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002237474  21 LQSDLRVDGRRPFDFRRLKILFG---REDGSAEVQLGDTRVMG--YATAQLVQPYKDRPNEGTLAIFTEFSPMAdpAFEP 95
Cdd:PRK03983   10 LEDGLRLDGRKPDELRPIKIEVGvlkNADGSAYLEWGNNKIIAavYGPREMHPRHLQLPDRAVLRVRYNMAPFS--VDER 87

                          90       100
                  ....*....|....*....|.
gi 1002237474  96 GRPGES--AIELGRVVDRGLR 114
Cdd:PRK03983   88 KRPGPDrrSIEISKVIREALE 108
 
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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