NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|9506689|ref|NP_061910|]
View 

exosome complex component RRP41 [Homo sapiens]

Protein Classification

RRP41/SKI6 family exosome complex component( domain architecture ID 10183526)

RRP41/SKI6 family exosome complex component is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 11-237 2.15e-137

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: 384.97  E-value: 2.15e-137
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   11 GYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRArALPDRALVNCQYSSATFSTGERKRRP 90
Cdd:cd11370   1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQ-ALHDRAVVNCEYSMATFSTGERKRRG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   91 HGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTAL 170
Cdd:cd11370  80 KGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTPL 159

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9506689  171 ADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVR 237
Cdd:cd11370 160 LDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226
 
Name Accession Description Interval E-value
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 11-237 2.15e-137

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: 384.97  E-value: 2.15e-137
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   11 GYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRArALPDRALVNCQYSSATFSTGERKRRP 90
Cdd:cd11370   1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQ-ALHDRAVVNCEYSMATFSTGERKRRG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   91 HGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTAL 170
Cdd:cd11370  80 KGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTPL 159

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9506689  171 ADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVR 237
Cdd:cd11370 160 LDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 1-227 3.41e-76

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 230.68  E-value: 3.41e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689     1 MAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRgSRARALPDRALVNCQYSSAT 80
Cdd:PRK03983   3 VEPPKLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMH-PRHLQLPDRAVLRVRYNMAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689    81 FSTGERKRrPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCAC 160
Cdd:PRK03983  82 FSVDERKR-PGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGC 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9506689   161 SAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTL 227
Cdd:PRK03983 161 AVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQL 227
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 21-152 1.27e-39

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: 133.49  E-value: 1.27e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689     21 ELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARAlpdRALVNCQYSSATFSTGERKRRPHGDRKSCEMG 100
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFA---PGRLTVEYELAPFASGERPGEGRPSEREIEIS 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 9506689    101 LQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIP 152
Cdd:pfam01138  78 RLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
13-177 1.54e-13

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 67.75  E-value: 1.54e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   13 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALA-------VvygPHEIRGSRaralpdRALVNCQYSSATFSTGE 85
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCtasveegV---PPFLKGSG------QGWVTAEYGMLPRATHT 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   86 RKRRPHGDRK----SCE----MGLQLRqtfeAAI-LTQLHPRsQIDIYVQVLQADGGTYAACVNAATLAVLDA------- 149
Cdd:COG0689  73 RNRREAARGKqsgrTQEiqrlIGRSLR----AVVdLKALGER-TITIDCDVLQADGGTRTASITGAFVALADAlnklvek 147

                       170       180       190
                ....*....|....*....|....*....|..
gi 9506689  150 ----GIPMRDFVCACSAGFVDGTALADLSHVE 177
Cdd:COG0689 148 gllkENPLKDQVAAVSVGIVDGEPVLDLDYEE 179
 
Name Accession Description Interval E-value
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 11-237 2.15e-137

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: 384.97  E-value: 2.15e-137
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   11 GYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRArALPDRALVNCQYSSATFSTGERKRRP 90
Cdd:cd11370   1 GLRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQ-ALHDRAVVNCEYSMATFSTGERKRRG 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   91 HGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTAL 170
Cdd:cd11370  80 KGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTPL 159

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9506689  171 ADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLLDRVVRQHVR 237
Cdd:cd11370 160 LDLNYLEESGDLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 1-227 3.41e-76

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 230.68  E-value: 3.41e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689     1 MAGLELLSDQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRgSRARALPDRALVNCQYSSAT 80
Cdd:PRK03983   3 VEPPKLILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMH-PRHLQLPDRAVLRVRYNMAP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689    81 FSTGERKRrPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCAC 160
Cdd:PRK03983  82 FSVDERKR-PGPDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGC 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9506689   161 SAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTL 227
Cdd:PRK03983 161 AVGKVDGVIVLDLNKEEDNYGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQL 227
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 21-227 3.00e-70

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: 214.50  E-value: 3.00e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   21 ELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRgSRARALPDRALVNCQYSSATFSTGERKRrPHGDRKSCEMG 100
Cdd:cd11366   1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVH-PRHLQLPDRAVIRVRYNMAPFSVDERKR-PGPDRREIEIS 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689  101 LQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAA 180
Cdd:cd11366  79 KVIKEALEPAIILEEFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNY 158

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 9506689  181 GGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTL 227
Cdd:cd11366 159 GEADMPIAMMPNLGEITLLQLDGDLTPDEFKQAIELAKKGCKRIYEL 205
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 22-228 1.12e-57

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: 182.38  E-value: 1.12e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARAlpDRALVNCQYSSATFSTgeRKRRPHG-DRKSCEMG 100
Cdd:cd11371   1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFS--DRGRLNCEVKFAPFAT--PGRRRHGqDSEERELS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689  101 LQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFVDGTALADLSHVEEAA 180
Cdd:cd11371  77 SLLHQALEPAVRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALIGDELLLDPTREEEEA 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
gi 9506689  181 GGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARDVHTLL 228
Cdd:cd11371 157 SSGGVMLAYMPSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVV 204
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 22-224 1.12e-56

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: 179.83  E-value: 1.12e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARalPDRALVNCQYSSATFSTGERkRRPHGDRKSCEMGL 101
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLER--PDKGTLYVNVEISPGAVGER-RQGPPGDEEMEISR 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689  102 QLRQTFEAAILTQL---HPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIP-------------MRDFVCACSAGFV 165
Cdd:cd11358  78 LLERTIEASVILDKstrKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPrvfvderspplllMKDLIVAVSVGGI 157

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9506689  166 -DGTALADLSHVEEAAGGPQLALALLPaSGQIALLEMDARLHED--HLERVLEAAAQAARDV 224
Cdd:cd11358 158 sDGVLLLDPTGEEEELADSTLTVAVDK-SGKLCLLSKVGGGSLDteEIKECLELAKKRSLHL 218
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 22-226 3.16e-44

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: 147.33  E-value: 3.16e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   22 LRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRgsRARALPDRALVNCQYSSATFSTGERKRrphgdrkscEMGL 101
Cdd:cd11372   1 LRPLSCELGLLSRADGSARFSQGDTSVLAAVYGPIEVK--LRKELPDRATLEVIVRPKSGLPGVKEK---------LLEL 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689  102 QLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV-DGTALADLSHVEEAA 180
Cdd:cd11372  70 LLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITeDGEIILDPTAEEEKE 149

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 9506689  181 GgpqLALAL--LPASGQIALLEMDAR--LHEDHLERVLEAAAQAARDVHT 226
Cdd:cd11372 150 A---KAVATfaFDSGEEKNLVLSESEgsFTEEELFACLELAQAASAAIFD 196
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 21-152 1.27e-39

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: 133.49  E-value: 1.27e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689     21 ELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARAlpdRALVNCQYSSATFSTGERKRRPHGDRKSCEMG 100
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFA---PGRLTVEYELAPFASGERPGEGRPSEREIEIS 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 9506689    101 LQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIP 152
Cdd:pfam01138  78 RLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
13-177 1.54e-13

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 67.75  E-value: 1.54e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   13 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALA-------VvygPHEIRGSRaralpdRALVNCQYSSATFSTGE 85
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLCtasveegV---PPFLKGSG------QGWVTAEYGMLPRATHT 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   86 RKRRPHGDRK----SCE----MGLQLRqtfeAAI-LTQLHPRsQIDIYVQVLQADGGTYAACVNAATLAVLDA------- 149
Cdd:COG0689  73 RNRREAARGKqsgrTQEiqrlIGRSLR----AVVdLKALGER-TITIDCDVLQADGGTRTASITGAFVALADAlnklvek 147

                       170       180       190
                ....*....|....*....|....*....|..
gi 9506689  150 ----GIPMRDFVCACSAGFVDGTALADLSHVE 177
Cdd:COG0689 148 gllkENPLKDQVAAVSVGIVDGEPVLDLDYEE 179
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 21-180 2.32e-13

Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA.


Pssm-ID: 206767 [Multi-domain]  Cd Length: 227  Bit Score: 67.25  E-value: 2.32e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   21 ELRKIQARMGVFAQADGSAYIEQGNTKALAVVYG----PHEIRGSRaralpdRALVNCQYSSATFSTGERKRRPHGDRK- 95
Cdd:cd11362   1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVeekvPPFLRGKG------KGWVTAEYSMLPRSTHERTQREASKGKq 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   96 ---SCE----MGLQLRqtfeAAI-LTQLHPRsQIDIYVQVLQADGGTYAACVNAATLAVLDA-----------GIPMRDF 156
Cdd:cd11362  75 sgrTQEiqrlIGRSLR----AAVdLEALGER-TITIDCDVLQADGGTRTASITGAYVALADAvdklvekgvleENPLKHF 149

                       170       180
                ....*....|....*....|....
gi 9506689  157 VCACSAGFVDGTALADLSHVEEAA 180
Cdd:cd11362 150 VAAVSVGIVDGEPLLDLDYEEDSA 173
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 155-220 2.26e-12

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: 60.28  E-value: 2.26e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9506689    155 DFVCACSAGFVDGTALADLSHVEEAAGGPQLALALLPASGQIALLEMD-ARLHEDHLERVLEAAAQA 220
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGgAGLTEDELLEALELAKEA 67
rph PRK00173
ribonuclease PH; Reviewed
 13-180 1.27e-11

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 62.43  E-value: 1.27e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689    13 RVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKAL---AVVYG-PHEIRGSRaralpdRALVNCQYSSATFSTGERKR 88
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLctaSVEEGvPRFLKGQG------QGWVTAEYGMLPRATHTRND 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689    89 RPHGDRK----SCEM----GLQLRqtfeAAI-LTQLHPRsQIDIYVQVLQADGGTYAACVNAATLAVLDA---------- 149
Cdd:PRK00173  76 REAAKGKqggrTQEIqrliGRSLR----AVVdLKALGER-TITIDCDVIQADGGTRTASITGAYVALADAlnklvargkl 150

                        170       180       190
                 ....*....|....*....|....*....|..
gi 9506689   150 -GIPMRDFVCACSAGFVDGTALADLSHVEEAA 180
Cdd:PRK00173 151 kKNPLKDQVAAVSVGIVDGEPVLDLDYEEDSA 182
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 11-223 2.25e-11

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 63.37  E-value: 2.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689    11 GYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVygpheIRGSRARALPDRALVNC--------QYSSATFS 82
Cdd:PLN00207 437 GKRSDGRTPDEIRPINSSCGLLPRAHGSALFTRGETQALAVV-----TLGDKQMAQRIDNLVDAdevkrfylQYSFPPSC 511

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689    83 TGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSA 162
Cdd:PLN00207 512 VGEVGRIGAPSRREIGHGMLAERALEPILPSEDDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPVKCPIAGIAM 591

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 9506689   163 GFV--------DGTA--LADLSHVEEAAGGPQLALAllPASGQIALLEMDARLHEDHLErVLEAAAQAARD 223
Cdd:PLN00207 592 GMVldteefggDGSPliLSDITGSEDASGDMDFKVA--GNEDGITAFQMDIKVGGITLP-IMERALLQAKD 659
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 4-52 1.79e-07

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: 50.68  E-value: 1.79e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 9506689    4 LELLSdQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVV 52
Cdd:cd11365   9 LSLLE-KGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGV 56
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 4-52 1.54e-06

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: 47.87  E-value: 1.54e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 9506689    4 LELLSdQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVV 52
Cdd:COG2123  15 LSLLK-KGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGV 62
PRK04282 PRK04282
exosome complex protein Rrp42;
4-52 3.00e-06

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 47.18  E-value: 3.00e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 9506689     4 LELLSdQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVV 52
Cdd:PRK04282  17 LSLLK-KGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGV 64
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 21-165 8.44e-06

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: 45.23  E-value: 8.44e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   21 ELRKIQARMGVFAQADGSAYIEQGNTKALAVV-YGPHEiRGSRARALPD----RALVncQYSSATFSTGERKR-RPHGDR 94
Cdd:cd11364   1 EIRPISCEVGLLPRTHGSALFTRGETQVLCTVtLGTLE-DAQKIDSLGGekskRFML--HYNFPPYSVGETGRvGGPGRR 77

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9506689   95 kscEMG---LQlrqtfEAAILTQLHPRSQ----IDIYVQVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV 165
Cdd:cd11364  78 ---EIGhgaLA-----ERALLPVLPSPEDfpytIRVVSEVLESNGSSSMASVCGGSLALMDAGVPIKAPVAGIAMGLI 147
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 10-52 3.72e-05

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: 43.67  E-value: 3.72e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 9506689   10 QGYRVDGRRAGELRKIQARmgvFAQADGSAYIEQGNTKALAVV 52
Cdd:cd11368  15 EGLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQV 54
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 9-50 5.40e-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: 40.23  E-value: 5.40e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 9506689    9 DQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALA 50
Cdd:cd11369  14 AENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLC 55
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 9-52 2.99e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 38.49  E-value: 2.99e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 9506689     9 DQGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVV 52
Cdd:PRK11824 311 EEGIRIDGRKLDEIRPISIEVGVLPRTHGSALFTRGETQALVVA 354
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 10-152 4.44e-03

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: 37.58  E-value: 4.44e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9506689   10 QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGphEIrGSRARALPDRALVNCQYS-SATFSTGERKR 88
Cdd:cd11367  16 QNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKA--EV-GSPDPETPNKGRLEFFVDcSPNASPEFEGR 92

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9506689   89 rpHGDRKSCEMGLQLRQTFEAAIL-----TQLHPRSQI-DIYVQ--VLQADGGTYAACVNAATLAVLDAGIP 152
Cdd:cd11367  93 --GGEELATELSSALERALKSGSAidlskLCIVPGKQCwVLYVDvlVLESGGNLLDAISIAVKAALFNTRIP 162
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH