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Conserved domains on  [gi|1063725293|ref|NP_001328241|]
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3'-5'-exoribonuclease family protein [Arabidopsis thaliana]

Protein Classification

exosome complex component MTR3( domain architecture ID 10183529)

exosome complex component MTR3 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_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 43-249 2.17e-106

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: 306.41  E-value: 2.17e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  43 CRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKAMVYSDVGRLNCNVSYTNFASP---TLGQGTDHKEYSSMLH 119
Cdd:cd11371     1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPgrrRHGQDSEERELSSLLH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 120 KALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGKSLMIDPVTEEEGCEDGS 199
Cdd:cd11371    81 QALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEASSGG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063725293 200 FMMTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLKQ 249
Cdd:cd11371   161 VMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
 
Name Accession Description Interval E-value
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 43-249 2.17e-106

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: 306.41  E-value: 2.17e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  43 CRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKAMVYSDVGRLNCNVSYTNFASP---TLGQGTDHKEYSSMLH 119
Cdd:cd11371     1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPgrrRHGQDSEERELSSLLH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 120 KALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGKSLMIDPVTEEEGCEDGS 199
Cdd:cd11371    81 QALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEASSGG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063725293 200 FMMTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLKQ 249
Cdd:cd11371   161 VMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 34-256 1.34e-46

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 155.56  E-value: 1.34e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESK-KAMVYSDVGRLNCNVSYTNFA-----SPtlgq 107
Cdd:PRK03983   15 RLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHpRHLQLPDRAVLRVRYNMAPFSvderkRP---- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 108 GTDHKEY--SSMLHKALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGKSLM 185
Cdd:PRK03983   91 GPDRRSIeiSKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIV 170

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063725293 186 IDPVTEEEGCEDGSFMMTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLKQSASASDE 256
Cdd:PRK03983  171 LDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIAE 241
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 42-166 1.36e-33

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: 118.08  E-value: 1.36e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  42 QCRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKaMVYSDVGRLNCNVSYTNFASPT---LGQGTDH-KEYSSM 117
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKE-DRDFAPGRLTVEYELAPFASGErpgEGRPSEReIEISRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1063725293 118 LHKALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGI 166
Cdd:pfam01138  80 IDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGI 128
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 34-244 8.20e-12

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: 63.28  E-value: 8.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVfgpreskKAMV---YSDV---GRLNCNVSYTNFASPTLGQ 107
Cdd:COG2123    23 RIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV-------KVEPgepFPDTpneGVLIVNAELLPLASPTFEP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 108 G-TDhkeyssmlhkalEGVIMM---------EtfPKtTVDVFALVLESGGS------DLSVL------ISCASL----AL 161
Cdd:COG2123    96 GpPD------------ENAIELarvvdrgirE--SK-AIDLEKLVIEPGKKvwmvfiDIYVLdydgnlFDASSLaavaAL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 162 ADAGIMMY--------------------DLITAVSVSCIGKSLMIDPVTEEEgcedgsfmmTCMPSRYEIT--------- 212
Cdd:COG2123   161 LTTKVPKVevgedgvvvdkgedtplpvnTLPVSVTMAKIGDYLVVDPTLEEE---------SVMDARITITtdedgniva 231

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1063725293 213 -QLTITGEWTTPNINEAMQLCLDASSKLGEIMR 244
Cdd:COG2123   232 mQKGGSGSFTEEEIDKAIDIALEKGKELRELLK 264
 
Name Accession Description Interval E-value
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 43-249 2.17e-106

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: 306.41  E-value: 2.17e-106
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  43 CRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKAMVYSDVGRLNCNVSYTNFASP---TLGQGTDHKEYSSMLH 119
Cdd:cd11371     1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKFAPFATPgrrRHGQDSEERELSSLLH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 120 KALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGKSLMIDPVTEEEGCEDGS 199
Cdd:cd11371    81 QALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEASSGG 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1063725293 200 FMMTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLKQ 249
Cdd:cd11371   161 VMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 34-256 1.34e-46

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 155.56  E-value: 1.34e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESK-KAMVYSDVGRLNCNVSYTNFA-----SPtlgq 107
Cdd:PRK03983   15 RLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHpRHLQLPDRAVLRVRYNMAPFSvderkRP---- 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 108 GTDHKEY--SSMLHKALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGKSLM 185
Cdd:PRK03983   91 GPDRRSIeiSKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGVIV 170

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063725293 186 IDPVTEEEGCEDGSFMMTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLKQSASASDE 256
Cdd:PRK03983  171 LDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKSKYGEIAE 241
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 44-248 4.73e-45

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: 150.56  E-value: 4.73e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  44 RPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESK-KAMVYSDVGRLNCNVSYTNFASP---TLGQGTDHKEYSSMLH 119
Cdd:cd11366     3 RPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHpRHLQLPDRAVIRVRYNMAPFSVDerkRPGPDRREIEISKVIK 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 120 KALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGKSLMIDPVTEEEGCEDGS 199
Cdd:cd11366    83 EALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGEAD 162

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1063725293 200 FMMTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLK 248
Cdd:cd11366   163 MPIAMMPNLGEITLLQLDGDLTPDEFKQAIELAKKGCKRIYELQKEALK 211
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 34-252 1.98e-39

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: 136.52  E-value: 1.98e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESK-KAMVYSDVGRLNCNVSYTNFAsptlgqGTDHK 112
Cdd:cd11370     3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRnRSQALHDRAVVNCEYSMATFS------TGERK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 113 ----------EYSSMLHKALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGK 182
Cdd:cd11370    77 rrgkgdrrstELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDS 156

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063725293 183 SLMIDPVTEEEgCEDGSFM-MTCMPSRYEITQLTITGEWTTPNINEAMQLCLDASSKLGEIMRDCLKQSAS 252
Cdd:cd11370   157 TPLLDLNYLEE-SGDLPDLtVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 42-166 1.36e-33

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: 118.08  E-value: 1.36e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  42 QCRPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKaMVYSDVGRLNCNVSYTNFASPT---LGQGTDH-KEYSSM 117
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKE-DRDFAPGRLTVEYELAPFASGErpgEGRPSEReIEISRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1063725293 118 LHKALEGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGI 166
Cdd:pfam01138  80 IDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGI 128
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 44-239 5.02e-28

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: 106.64  E-value: 5.02e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  44 RPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKAMVYSDVGRLNCNVSYTNFASPTLGQG---TDHKEYSSMLHK 120
Cdd:cd11358     2 RPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVGERRQGppgDEEMEISRLLER 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 121 ALEGVIMMETFPK---TTVDVFALVLESGGSDLSVLISCASLALADAGI-------------MMYDLITAVSVSCIGKS- 183
Cdd:cd11358    82 TIEASVILDKSTRkpsWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIprvfvdersppllLMKDLIVAVSVGGISDGv 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063725293 184 LMIDPVTEEEGCEDGSFMMTCMPSRyEITQLTITGEW--TTPNINEAMQLCLDASSKL 239
Cdd:cd11358   162 LLLDPTGEEEELADSTLTVAVDKSG-KLCLLSKVGGGslDTEEIKECLELAKKRSLHL 218
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 44-244 2.56e-26

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: 101.49  E-value: 2.56e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  44 RPALLQTGAVSSASGSAYAEFGNTKVIVSVFGPRESKKAMVYSDVGRLNCNVSytnfasPTLGQ-GTDHKEYSSMLHKAL 122
Cdd:cd11372     2 RPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVR------PKSGLpGVKEKLLELLLRSTL 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 123 EGVIMMETFPKTTVDVFALVLESGGSDLSVLISCASLALADAGIMMYDLITAVSVSCIGK-SLMIDPVTEEEgcEDGSFM 201
Cdd:cd11372    76 EPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDgEIILDPTAEEE--KEAKAV 153

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*.
gi 1063725293 202 MTC-MPSRYEITQLTI--TGEWTTPNINEAMQLCLDASSKLGEIMR 244
Cdd:cd11372   154 ATFaFDSGEEKNLVLSesEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 34-195 3.69e-16

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: 75.71  E-value: 3.69e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSV---FGPRESKKamvySDVGRLNCNVSYTNFASPTLGQGTD 110
Cdd:cd11367    19 RNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVkaeVGSPDPET----PNKGRLEFFVDCSPNASPEFEGRGG 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 111 HK---EYSSMLHKALEG--VIMMETF---PKTT-----VDVfaLVLESGGSdlsvLISCASL----ALADAGI------- 166
Cdd:cd11367    95 EElatELSSALERALKSgsAIDLSKLcivPGKQcwvlyVDV--LVLESGGN----LLDAISIavkaALFNTRIpkvevse 168

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*....
gi 1063725293 167 -----------------MMYDLITA---VSVSCIGKSLMIDPVTEEEGC 195
Cdd:cd11367   169 ddegtkeielsddpydvKRLDVSNVpliVTLSKIGNRHIVDATAEEEAC 217
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 34-244 8.20e-12

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: 63.28  E-value: 8.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVfgpreskKAMV---YSDV---GRLNCNVSYTNFASPTLGQ 107
Cdd:COG2123    23 RIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV-------KVEPgepFPDTpneGVLIVNAELLPLASPTFEP 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 108 G-TDhkeyssmlhkalEGVIMM---------EtfPKtTVDVFALVLESGGS------DLSVL------ISCASL----AL 161
Cdd:COG2123    96 GpPD------------ENAIELarvvdrgirE--SK-AIDLEKLVIEPGKKvwmvfiDIYVLdydgnlFDASSLaavaAL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 162 ADAGIMMY--------------------DLITAVSVSCIGKSLMIDPVTEEEgcedgsfmmTCMPSRYEIT--------- 212
Cdd:COG2123   161 LTTKVPKVevgedgvvvdkgedtplpvnTLPVSVTMAKIGDYLVVDPTLEEE---------SVMDARITITtdedgniva 231

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1063725293 213 -QLTITGEWTTPNINEAMQLCLDASSKLGEIMR 244
Cdd:COG2123   232 mQKGGSGSFTEEEIDKAIDIALEKGKELRELLK 264
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 34-242 9.36e-11

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: 60.31  E-value: 9.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVfgpreskKAMV---YSDV---GRLNCNVSYTNFASPTLGQ 107
Cdd:cd11365    17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV-------KLEVgepFPDTpneGVLIVNAELLPLASPTFEP 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 108 G---TDHKEYSSMLHKALEGVIMmetfpkttVDVFALVLESGGS------DLSV------LISCASL----ALADAGIMM 168
Cdd:cd11365    90 GppdENAIELARVVDRGIRESKA--------IDLEKLVIEPGKKvwvvfiDIYVldydgnLFDASALaavaALLNTKVPE 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 169 Y--------------------DLITAVSVSCIGKSLMIDPVTEEEGCEDGSFMMTcMPSRYEIT--QLTITGEWTTPNIN 226
Cdd:cd11365   162 YevdenevievlgeelplpvnTLPVSVTVAKIGGYIVVDPTLEEELVMDARITIT-IDEDGNIValQKGGGGSFTEDEID 240

                         250
                  ....*....|....*.
gi 1063725293 227 EAMQLCLDASSKLGEI 242
Cdd:cd11365   241 KAIDIALEKAAELREK 256
PRK04282 PRK04282
exosome complex protein Rrp42;
34-249 2.97e-10

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 59.12  E-value: 2.97e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSVfgpreskKAMV---YSDV---GRLNCNVSYTNFASPTLGQ 107
Cdd:PRK04282   25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV-------KLEIgepFPDTpneGVLIVNAELLPLASPTFEP 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 108 G-TDHK--EYSSMLHKALEGVIMmetfpkttVDVFALVLESGGS------DLSVL------ISCASL----ALADAGIMM 168
Cdd:PRK04282   98 GpPDENaiELARVVDRGIRESKA--------IDLEKLVIEPGKKvwvvfiDVYVLdhdgnlLDASMLaavaALLNTKVPA 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 169 Y--------------------DLITAVSVSCIGKSLMIDPVTEEEGCEDGSFMMTcMPSRYEIT--QLTITGEWTTPNIN 226
Cdd:PRK04282  170 VeegedgvvdklgedfplpvnDKPVTVTFAKIGNYLIVDPTLEEESVMDARITIT-TDEDGNIVaiQKSGIGSFTEEEVD 248

                         250       260
                  ....*....|....*....|...
gi 1063725293 227 EAMQLCLDASSKLGEIMRDCLKQ 249
Cdd:PRK04282  249 KAIDIALEKAKELREKLKEALGI 271
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 34-242 5.64e-08

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: 52.14  E-value: 5.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQtgaVSSASGSAYAEFGNTKVIVSVFG----PRESKKAMvysdvGRLNCNVSYTNFASPTLGQGt 109
Cdd:cd11368    18 RLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVSCeivePKPDRPNE-----GILFINVELSPMASPAFEPG- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 110 DHKEYSSMLHKALEGVImmetfpKTT--VDVFALVLESGGS------DLSVL------ISCASLAlADAGIMMY------ 169
Cdd:cd11368    89 RPSEEEVELSRLLERAL------RDSraVDTESLCIIAGEKvwsirvDVHVLnhdgnlIDAASLA-AIAALMHFrrpdvt 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293 170 ----DLI----------------TAVSVS-CI---GKSLMIDPVTEEEGCEDGSFMMTcMPSRYEITQLTITGEwTTPNI 225
Cdd:cd11368   162 vdgeEVTvhspeerepvplsihhIPICVTfAFfddGEIVVVDPTLLEEAVADGSLTVA-LNKHREICALSKSGG-APLSP 239

                         250
                  ....*....|....*..
gi 1063725293 226 NEAMQLCLDASSKLGEI 242
Cdd:cd11368   240 SQILRCVKIAAAKAKEL 256
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 34-73 2.06e-07

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: 50.63  E-value: 2.06e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSV 73
Cdd:cd11369    18 RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGI 57
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
34-73 9.84e-07

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 48.49  E-value: 9.84e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1063725293  34 RPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSV 73
Cdd:COG0689     2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTA 41
rph PRK00173
ribonuclease PH; Reviewed
 33-73 2.81e-06

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 47.03  E-value: 2.81e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1063725293  33 SRPDGRGFHQCRPALLQTGAVSSASGSAYAEFGNTKVIVSV 73
Cdd:PRK00173    1 MRPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTA 41
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 170-235 9.53e-04

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: 36.79  E-value: 9.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063725293 170 DLITAVSVSCIGKSLMIDPVTEEEGCEDGSFMMTCMPSRyEITQLTITGE--WTTPNINEAMQLCLDA 235
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTG-EIVALMKEGGagLTEDELLEALELAKEA 67
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 44-166 1.03e-03

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: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063725293  44 RPALLQTGAVSSASGSAYAEFGNTKVIVSV-FG-PRESKKAMVYSDVGRLNCNVSY------TNFASPTLGQGTDHKEYS 115
Cdd:cd11364     3 RPISCEVGLLPRTHGSALFTRGETQVLCTVtLGtLEDAQKIDSLGGEKSKRFMLHYnfppysVGETGRVGGPGRREIGHG 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063725293 116 SMLHKALEGVI-MMETFPkTTVDVFALVLESGGSDlSVLISCA-SLALADAGI 166
Cdd:cd11364    83 ALAERALLPVLpSPEDFP-YTIRVVSEVLESNGSS-SMASVCGgSLALMDAGV 133
 
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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