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Conserved domains on  [gi|25144570|ref|NP_741217|]
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Exosome complex component RRP45 [Caenorhabditis elegans]

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 1.55e-127

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: 369.16  E-value: 1.55e-127
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   6 VTNCEKAVILEALKIGKRFDFRSLEEFRDVKLVVGAEVGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPM 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  86 ANYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNV 165
Cdd:cd11368  81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 166 TLEPHHTLIYSEYEKAPVPLNIYHMPICTTIGLLDKGQIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTK 245
Cdd:cd11368 161 TVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPS 240

                       250
                ....*....|....*....
gi 25144570 246 QIERCVKLAMARAEALTAV 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 1.55e-127

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: 369.16  E-value: 1.55e-127
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   6 VTNCEKAVILEALKIGKRFDFRSLEEFRDVKLVVGAEVGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPM 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  86 ANYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNV 165
Cdd:cd11368  81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 166 TLEPHHTLIYSEYEKAPVPLNIYHMPICTTIGLLDKGQIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTK 245
Cdd:cd11368 161 TVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPS 240

                       250
                ....*....|....*....
gi 25144570 246 QIERCVKLAMARAEALTAV 264
Cdd:cd11368 241 QILRCVKIAAAKAKELTEL 259
PRK04282 PRK04282
exosome complex protein Rrp42;
14-261 2.01e-45

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 158.50  E-value: 2.01e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   14 ILEALKIGKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMANYA 89
Cdd:PRK04282  16 ILSLLKKGKRIDGRKLDEYRPIEIETGvikkAE-GSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPT 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   90 NEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVTLEP 169
Cdd:PRK04282  95 FEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGE 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  170 hHTLIYSEYEKAPVPLNiyHMPICTTIGLLdkGQIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQIER 249
Cdd:PRK04282 175 -DGVVDKLGEDFPLPVN--DKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDK 249

                        250
                 ....*....|..
gi 25144570  250 CVKLAMARAEAL 261
Cdd:PRK04282 250 AIDIALEKAKEL 261
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 11-261 6.89e-44

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: 154.19  E-value: 6.89e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  11 KAVILEALKIGKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMA 86
Cdd:COG2123  11 RDYILSLLKKGKRIDGRGLDEYRPIEIETGviekAE-GSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLA 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  87 NYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVT 166
Cdd:COG2123  90 SPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVE 169

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 167 LEPHHTLIYSEyEKAPVPLNiyHMPICTTIGLLDKgqIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQ 246
Cdd:COG2123 170 VGEDGVVVDKG-EDTPLPVN--TLPVSVTMAKIGD--YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEE 244

                       250
                ....*....|....*
gi 25144570 247 IERCVKLAMARAEAL 261
Cdd:COG2123 245 IDKAIDIALEKGKEL 259
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-163 7.74e-25

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: 98.82  E-value: 7.74e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570    31 EFRDVKL---VVGAEVGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMANYANEHD-RLGSKGMELIRLL 106
Cdd:pfam01138   1 ELRPIEIetgVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEgRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 25144570   107 ELIIRDSRCIDvealciraGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRP 163
Cdd:pfam01138  81 DRALRPSIPLE--------GYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
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 1.55e-127

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: 369.16  E-value: 1.55e-127
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   6 VTNCEKAVILEALKIGKRFDFRSLEEFRDVKLVVGAEVGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPM 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  86 ANYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNV 165
Cdd:cd11368  81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 166 TLEPHHTLIYSEYEKAPVPLNIYHMPICTTIGLLDKGQIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTK 245
Cdd:cd11368 161 TVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPS 240

                       250
                ....*....|....*....
gi 25144570 246 QIERCVKLAMARAEALTAV 264
Cdd:cd11368 241 QILRCVKIAAAKAKELTEL 259
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 18-262 3.52e-49

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: 168.12  E-value: 3.52e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  18 LKIGKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMANYANEHD 93
Cdd:cd11369  13 LAENVRPDGRELDEFRPTSVNVGsistAD-GSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDLPPLCSSKFRPG 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  94 RLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVTLEPhHTL 173
Cdd:cd11369  92 PPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTIDE-ETE 170

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 174 IYSEYEKAPVPLNIYHMPICTTIGLLDKGQIVViDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQIERCVKL 253
Cdd:cd11369 171 LVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLA-DPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQAQLQECIEL 249


                ....*....
gi 25144570 254 AMARAEALT 262
Cdd:cd11369 250 AKKRAKELQ 258
PRK04282 PRK04282
exosome complex protein Rrp42;
14-261 2.01e-45

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 158.50  E-value: 2.01e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   14 ILEALKIGKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMANYA 89
Cdd:PRK04282  16 ILSLLKKGKRIDGRKLDEYRPIEIETGvikkAE-GSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPT 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570   90 NEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVTLEP 169
Cdd:PRK04282  95 FEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGE 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  170 hHTLIYSEYEKAPVPLNiyHMPICTTIGLLdkGQIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQIER 249
Cdd:PRK04282 175 -DGVVDKLGEDFPLPVN--DKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEVDK 249

                        250
                 ....*....|..
gi 25144570  250 CVKLAMARAEAL 261
Cdd:PRK04282 250 AIDIALEKAKEL 261
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 11-261 1.86e-44

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: 155.45  E-value: 1.86e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  11 KAVILEALKIGKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMA 86
Cdd:cd11365   5 RDYILSLLEKGKRIDGRGLDEYRDIEIETGvipkAE-GSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLA 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  87 NYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVT 166
Cdd:cd11365  84 SPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEYE 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 167 LEPhhtLIYSEYEKAPVPLNIYHMPICTTIGLLDKgqIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQ 246
Cdd:cd11365 164 VDE---NEVIEVLGEELPLPVNTLPVSVTVAKIGG--YIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTEDE 238

                       250
                ....*....|....*
gi 25144570 247 IERCVKLAMARAEAL 261
Cdd:cd11365 239 IDKAIDIALEKAAEL 253
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 11-261 6.89e-44

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: 154.19  E-value: 6.89e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  11 KAVILEALKIGKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMA 86
Cdd:COG2123  11 RDYILSLLKKGKRIDGRGLDEYRPIEIETGviekAE-GSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLA 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  87 NYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVT 166
Cdd:COG2123  90 SPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVE 169

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 167 LEPHHTLIYSEyEKAPVPLNiyHMPICTTIGLLDKgqIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQ 246
Cdd:COG2123 170 VGEDGVVVDKG-EDTPLPVN--TLPVSVTMAKIGD--YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEE 244

                       250
                ....*....|....*
gi 25144570 247 IERCVKLAMARAEAL 261
Cdd:COG2123 245 IDKAIDIALEKGKEL 259
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-258 4.28e-40

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: 142.85  E-value: 4.28e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  32 FRDVKL---VVGAEVGTAICTIGNTKVMAAVSAEIAEPSS-MRPHKGVINIDVDLSPMANYANEHDRLGSKGMELIRLLE 107
Cdd:cd11358   1 FRPVEIetgVLNQADGSALVKLGNTKVICAVTGPIVEPDKlERPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 108 LIIRDSRCIDVEAlciraGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVTLEphhtliyseyEKAPVPLNI 187
Cdd:cd11358  81 RTIEASVILDKST-----RKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVD----------ERSPPLLLM 145

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 25144570 188 YHMPICTTIGLLDKGQIVViDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQIERCVKLAMARA 258
Cdd:cd11358 146 KDLIVAVSVGGISDGVLLL-DPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRS 215
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 10-271 1.36e-38

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: 140.42  E-value: 1.36e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  10 EKAVILEALKIGKRFDFRSLEEFRDVKL---VVGAEVGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMA 86
Cdd:cd11367   6 EKSYIIHGVEQNIRNDGRSRLDYRPIELetgVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNA 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  87 NYANEHDRLGSKGMELIRLLELIIRDSRCIDVEALCIRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRPNVT 166
Cdd:cd11367  86 SPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVE 165

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 167 LEP--HHTLIYsEYEKAPV---PLNIYHMPICTTIGLLdkGQIVVIDPTDKETACLDGSIVVACNKRREVCALHQSTNLI 241
Cdd:cd11367 166 VSEddEGTKEI-ELSDDPYdvkRLDVSNVPLIVTLSKI--GNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGGS 242

                       250       260       270
                ....*....|....*....|....*....|
gi 25144570 242 LSTKQIERCVKLAMARAEALTAVVSDVIKQ 271
Cdd:cd11367 243 LEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-163 7.74e-25

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: 98.82  E-value: 7.74e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570    31 EFRDVKL---VVGAEVGTAICTIGNTKVMAAVSAEIAEPSSMRPHKGVINIDVDLSPMANYANEHD-RLGSKGMELIRLL 106
Cdd:pfam01138   1 ELRPIEIetgVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEgRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 25144570   107 ELIIRDSRCIDvealciraGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHFRRP 163
Cdd:pfam01138  81 DRALRPSIPLE--------GYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 189-257 4.59e-13

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: 63.75  E-value: 4.59e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 25144570   189 HMPICTTIGLLDkGQIVViDPTDKETACLDGSIVVACNKRREVCALHQSTNLILSTKQIERCVKLAMAR 257
Cdd:pfam03725   1 DPVAAVTVGKID-GQLVV-DPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKEA 67
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 44-261 1.60e-10

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: 60.27  E-value: 1.60e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  44 GTAICTIGNTKVMAAVSAEI-AEPSSMRPHKGVIniDVDLSPMANYANEHDRLgskgmelirlLELIIRDSrcidVEALC 122
Cdd:cd11372  16 GSARFSQGDTSVLAAVYGPIeVKLRKELPDRATL--EVIVRPKSGLPGVKEKL----------LELLLRST----LEPII 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 123 IRAGKEIWKIRVDVRILDEDGSLLDCACLAAITALQHfrrpnvtlephhtliyseyekAPVPLNiyHMPICTTIGLLDKG 202
Cdd:cd11372  80 LLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLD---------------------AGVPMK--GLFAAVTCAITEDG 136

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 25144570 203 QIvVIDPTDKETACLDGSIVVA--CNKRREVCALHqsTNLILSTKQIERCVKLAMARAEAL 261
Cdd:cd11372 137 EI-ILDPTAEEEKEAKAVATFAfdSGEEKNLVLSE--SEGSFTEEELFACLELAQAASAAI 194
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 38-271 5.96e-05

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: 44.09  E-value: 5.96e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  38 VVGAEVGTAICTIGNTKVMAAVS----AEIAEPSSMRphkGVINIDVDLSPMAnyanEHDR----LGSKGMELIRLLEli 109
Cdd:cd11371  10 VVSQAKGSAYVELGNTKVICSVYgprpIPGRTEFSDR---GRLNCEVKFAPFA----TPGRrrhgQDSEERELSSLLH-- 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 110 irdsrcidvEAL--CIRAGKeIWKIRVDV--RILDEDGSLLDCACLAAITALQhfrrpnvtlephhtliyseyeKAPVPL 185
Cdd:cd11371  81 ---------QALepAVRLEK-YPKSQIDVfvTVLESDGSVLAAAITAASLALA---------------------DAGIEM 129

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570 186 niYHMPICTTIGLLdkGQIVVIDPTDKETACLDGSIVVACnkrreVCALHQSTNLI----LSTKQIERCVKLAMARAEAL 261
Cdd:cd11371 130 --YDLVTACSAALI--GDELLLDPTREEEEASSGGVMLAY-----MPSLNQVTQLWqsgeMDVDQLEEALDLCIDGCNRI 200

                       250
                ....*....|
gi 25144570 262 TAVVSDVIKQ 271
Cdd:cd11371 201 HPVVRQALLE 210
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 21-157 1.85e-04

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: 42.53  E-value: 1.85e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25144570  21 GKRFDFRSLEEFRDVK---LVVGAEVGTAICTIGNTKVMAAVS--AEIAEPSSMRPHKGVINIDVDlspMANYANEHDRL 95
Cdd:cd11370   1 GLRLDGRRPNELRRIRcriGVFSSADGSAYLEQGNTKVLAAVYgpHEPRNRSQALHDRAVVNCEYS---MATFSTGERKR 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 25144570  96 GSKGMELIRLLELIIRD--SRCIDVEaLCIRAgkeiwKIRVDVRILDEDGSLLdCACLAAIT-AL 157
Cdd:cd11370  78 RGKGDRRSTELSLAIRQtfEAVILTH-LYPRS-----QIDIYVQVLQADGGLL-AACINAATlAL 135
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 21-59 1.44e-03

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 40.00  E-value: 1.44e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 25144570   21 GKRFDFRSLEEFRDVKLVVG----AEvGTAICTIGNTKVMAAV 59
Cdd:PRK03983  13 GLRLDGRKPDELRPIKIEVGvlknAD-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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