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Conserved domains on  [gi|79314427|ref|NP_001030818|]
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Ribosomal protein S5 domain 2-like superfamily protein [Arabidopsis thaliana]

Protein Classification

exosome complex component RRP46( domain architecture ID 10183533)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 14-228 3.70e-84

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: 249.02  E-value: 3.70e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  14 LRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACFEVIWKPKSGQIGKVEKEYEMILKRTIQSICV 93
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  94 LTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAICCCLAENGYLVLDPNKLEEKKMTAFAYLVFPN 173
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 79314427 174 TTLSvlpegssvaegepvehGIITSITHGVMSVDDYFLCVENGRAATASLSAFFR 228
Cdd:cd11372 161 GEEK----------------NLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
 
Name Accession Description Interval E-value
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 14-228 3.70e-84

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: 249.02  E-value: 3.70e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  14 LRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACFEVIWKPKSGQIGKVEKEYEMILKRTIQSICV 93
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  94 LTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAICCCLAENGYLVLDPNKLEEKKMTAFAYLVFPN 173
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 79314427 174 TTLSvlpegssvaegepvehGIITSITHGVMSVDDYFLCVENGRAATASLSAFFR 228
Cdd:cd11372 161 GEEK----------------NLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 13-133 2.08e-31

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: 111.92  E-value: 2.08e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427    13 QLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKaGTKKNENAEKACFEVIWK---------PKSGQIGKVEKEYEMI 83
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPI-EPKEDRDFAPGRLTVEYElapfasgerPGEGRPSEREIEISRL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 79314427    84 LKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIP 133
Cdd:pfam01138  80 IDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 5-161 2.29e-26

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 102.40  E-value: 2.29e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427    5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPK-AGTKKNENAEKACFEVIWK--PKSGQ----IGKVE 77
Cdd:PRK03983  15 RLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPReMHPRHLQLPDRAVLRVRYNmaPFSVDerkrPGPDR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   78 KEYEM--ILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAICCCLAeNGYLVLDP 155
Cdd:PRK03983  95 RSIEIskVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIVLDL 173


                 ....*.
gi 79314427  156 NKLEEK 161
Cdd:PRK03983 174 NKEEDN 179
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 5-44 8.34e-06

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 46.15  E-value: 8.34e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAV 44
Cdd:COG1185 310 RIDGRKLDEIRPISCEVGVLPRTHGSALFTRGETQALVVA 349
 
Name Accession Description Interval E-value
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 14-228 3.70e-84

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: 249.02  E-value: 3.70e-84
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  14 LRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACFEVIWKPKSGQIGKVEKEYEMILKRTIQSICV 93
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIIL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  94 LTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAICCCLAENGYLVLDPNKLEEKKMTAFAYLVFPN 173
Cdd:cd11372  81 LHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDS 160

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*
gi 79314427 174 TTLSvlpegssvaegepvehGIITSITHGVMSVDDYFLCVENGRAATASLSAFFR 228
Cdd:cd11372 161 GEEK----------------NLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 14-187 1.26e-42

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: 143.62  E-value: 1.26e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  14 LRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACFEVIWKP--------KSGQIGKVEKEYEMILK 85
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEIspgavgerRQGPPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  86 RTIQSICVLTVN---PNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIP-------------MKHLAVAICCCLAENG 149
Cdd:cd11358  81 RTIEASVILDKStrkPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPrvfvderspplllMKDLIVAVSVGGISDG 160

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
gi 79314427 150 YLVLDPNKLEEKKMTAFAYLVFPN----TTLSVLPEGSSVAE 187
Cdd:cd11358 161 VLLLDPTGEEEELADSTLTVAVDKsgklCLLSKVGGGSLDTE 202
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 5-180 1.62e-35

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: 125.73  E-value: 1.62e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACF---EVIWKPKSG----QIGKVE 77
Cdd:cd11370   3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVvncEYSMATFSTgerkRRGKGD 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  78 K---EYEMILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLavaICCCLAenGYL--- 151
Cdd:cd11370  83 RrstELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDY---VCACSA--GYLdst 157

                       170       180       190
                ....*....|....*....|....*....|
gi 79314427 152 -VLDPNKLEEKkmtafayLVFPNTTLSVLP 180
Cdd:cd11370 158 pLLDLNYLEES-------GDLPDLTVAVLP 180
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 13-133 2.08e-31

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: 111.92  E-value: 2.08e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427    13 QLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKaGTKKNENAEKACFEVIWK---------PKSGQIGKVEKEYEMI 83
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPI-EPKEDRDFAPGRLTVEYElapfasgerPGEGRPSEREIEISRL 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 79314427    84 LKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIP 133
Cdd:pfam01138  80 IDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 5-161 2.29e-26

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 102.40  E-value: 2.29e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427    5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPK-AGTKKNENAEKACFEVIWK--PKSGQ----IGKVE 77
Cdd:PRK03983  15 RLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPReMHPRHLQLPDRAVLRVRYNmaPFSVDerkrPGPDR 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   78 KEYEM--ILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAICCCLAeNGYLVLDP 155
Cdd:PRK03983  95 RSIEIskVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKV-DGVIVLDL 173


                 ....*.
gi 79314427  156 NKLEEK 161
Cdd:PRK03983 174 NKEEDN 179
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 14-161 6.03e-24

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: 94.94  E-value: 6.03e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  14 LRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPKAGTKKNENAEKACF--EVIWKPKSGQIGKV------EKEYEMILK 85
Cdd:cd11371   1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLncEVKFAPFATPGRRRhgqdseERELSSLLH 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79314427  86 RTIQ-SICVLTVnPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAiCCCLAENGYLVLDPNKLEEK 161
Cdd:cd11371  81 QALEpAVRLEKY-PKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTA-CSAALIGDELLLDPTREEEE 155
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 13-161 2.35e-20

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: 85.85  E-value: 2.35e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  13 QLRPLACSRNILHRPHGSASWSQGDTKVLAAVYGPK-AGTKKNENAEKACFEVIWK--PKSGQIGKV------EKEYEMI 83
Cdd:cd11366   1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPReVHPRHLQLPDRAVIRVRYNmaPFSVDERKRpgpdrrEIEISKV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 79314427  84 LKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMKHLAVAICCCLAEnGYLVLDPNKLEEK 161
Cdd:cd11366  81 IKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVD-GKIVLDLNKEEDN 157
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 5-135 5.65e-12

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 64.92  E-value: 5.65e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427    5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAV-YGPKAGTKKNENAEKA------CFEVIWKPKS-GQIGKV 76
Cdd:PLN00207 439 RSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVVtLGDKQMAQRIDNLVDAdevkrfYLQYSFPPSCvGEVGRI 518

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79314427   77 ------EKEYEMILKRTIQSICVLTVNPNTTTSVIIQVVHDDGSLLPCAINAACAALVDAGIPMK 135
Cdd:PLN00207 519 gapsrrEIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVK 583
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 5-44 8.34e-06

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 46.15  E-value: 8.34e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAV 44
Cdd:COG1185 310 RIDGRKLDEIRPISCEVGVLPRTHGSALFTRGETQALVVA 349
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
5-44 8.57e-06

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 45.41  E-value: 8.57e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAV 44
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCTA 41
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 5-44 1.93e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 45.04  E-value: 1.93e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 79314427    5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAV 44
Cdd:PRK11824 315 RIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVA 354
rph PRK00173
ribonuclease PH; Reviewed
 5-41 2.10e-05

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 44.33  E-value: 2.10e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 79314427    5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVL 41
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVL 38
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 5-165 2.07e-04

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: 41.43  E-value: 2.07e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVygpKAGTKK------NE-----NAE-----KACFEviwkp 68
Cdd:cd11365  17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV---KLEVGEpfpdtpNEgvlivNAEllplaSPTFE----- 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  69 kSG-------QIGKVE----KEYEMIlkrTIQSICVLtvnPNTTTSVI---IQVVHDDGSLLPCAINAACAALVDAGIP- 133
Cdd:cd11365  89 -PGppdenaiELARVVdrgiRESKAI---DLEKLVIE---PGKKVWVVfidIYVLDYDGNLFDASALAAVAALLNTKVPe 161

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 79314427 134 --------------MKHLAV---AICCCLAE-NGYLVLDPNKLEEKKMTA 165
Cdd:cd11365 162 yevdenevievlgeELPLPVntlPVSVTVAKiGGYIVVDPTLEEELVMDA 211
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 5-165 2.87e-04

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: 41.00  E-value: 2.87e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVygpKA--GTKKNENAEKACFEV------IWKPK--SGQIG 74
Cdd:cd11369  18 RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGI---KAevATPAADTPDEGYLVPnvdlppLCSSKfrPGPPS 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427  75 kvekEYEMILKRTIQSICVLTVNPNTTTSVI------------IQVVHDDGSLLPCAINAACAALVDAGIP--------- 133
Cdd:cd11369  95 ----EEAQVLSSFLADILLNSNVLDLEQLCIvpgklawvlycdVYCLDYDGNLLDAALLALVAALKNLRLPavtideete 170

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
gi 79314427 134 -------------MKHLAVAICCCLAENGYLVLDPNKLEEKKMTA 165
Cdd:cd11369 171 lvvvnpeerrplnLKNLPVSTTFAVFDDKHLLADPTAEEELLASG 215
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 5-133 4.30e-04

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: 40.66  E-value: 4.30e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVygpKA--GTKKNENAEKA-------CFEVIWKPKSGQIG- 74
Cdd:cd11367  19 RNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGV---KAevGSPDPETPNKGrleffvdCSPNASPEFEGRGGe 95

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 79314427  75 KVEKEYEMILKRTIQSICV-----LTVNPNTTTSVI---IQVVHDDGSLLPCAINAACAALVDAGIP 133
Cdd:cd11367  96 ELATELSSALERALKSGSAidlskLCIVPGKQCWVLyvdVLVLESGGNLLDAISIAVKAALFNTRIP 162
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 5-44 9.55e-04

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: 39.40  E-value: 9.55e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 79314427   5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAV 44
Cdd:COG2123  23 RIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV 62
PRK04282 PRK04282
exosome complex protein Rrp42;
5-166 1.13e-03

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 39.09  E-value: 1.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427    5 REDGRTPNQLRPLACSRNILHRPHGSASWSQGDTKVLAAVygpKAGTKK------NE-----NAE-----KACFEViWKP 68
Cdd:PRK04282  25 RIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV---KLEIGEpfpdtpNEgvlivNAEllplaSPTFEP-GPP 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79314427   69 KSGQIgkvekEYEMILKRTIQSICV-----LTVNPNTTTSVI---IQVVHDDGSLLPCAINAACAALVDAGIP------- 133
Cdd:PRK04282 101 DENAI-----ELARVVDRGIRESKAidlekLVIEPGKKVWVVfidVYVLDHDGNLLDASMLAAVAALLNTKVPaveeged 175

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 79314427  134 -------------MKHLAVAicCCLAE-NGYLVLDPNKLEEKKMTAF 166
Cdd:PRK04282 176 gvvdklgedfplpVNDKPVT--VTFAKiGNYLIVDPTLEEESVMDAR 220
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 13-44 1.88e-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: 38.30  E-value: 1.88e-03
                        10        20        30
                ....*....|....*....|....*....|..
gi 79314427  13 QLRPLACSRNILHRPHGSASWSQGDTKVLAAV 44
Cdd:cd11364   1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTV 32
 
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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