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Conserved domains on  [gi|398366099|ref|NP_011711|]
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exosome non-catalytic core subunit SKI6 [Saccharomyces cerevisiae S288C]

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

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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 1.34e-114

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: 327.58  E-value: 1.34e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  11 GLRLDGRRWNELRRFESSINTHPhAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERsKSS 90
Cdd:cd11370    1 GLRLDGRRPNELRRIRCRIGVFS-SADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVNCEYSMATFSTGER-KRR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  91 HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTP 170
Cdd:cd11370   79 GKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTP 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366099 171 LLDTNSLEENA-MSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQ 237
Cdd:cd11370  159 LLDLNYLEESGdLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 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 1.34e-114

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: 327.58  E-value: 1.34e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  11 GLRLDGRRWNELRRFESSINTHPhAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERsKSS 90
Cdd:cd11370    1 GLRLDGRRPNELRRIRCRIGVFS-SADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVNCEYSMATFSTGER-KRR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  91 HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTP 170
Cdd:cd11370   79 GKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTP 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366099 171 LLDTNSLEENA-MSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQ 237
Cdd:cd11370  159 LLDLNYLEESGdLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 10-234 3.01e-43

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 146.32  E-value: 3.01e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  10 EGLRLDGRRWNELRRFESSINThPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKS 89
Cdd:PRK03983  12 DGLRLDGRKPDELRPIKIEVGV-LKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKRP 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  90 ShkNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTT 169
Cdd:PRK03983  91 G--PDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGV 168

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398366099 170 PLLDTNSLEEN-AMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRK 234
Cdd:PRK03983 169 IVLDLNKEEDNyGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKS 234
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 21-152 6.91e-27

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: 100.74  E-value: 6.91e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099   21 ELRRFESSINTHPHAaDGSSYMEQGNNKIITLVKGPKEPRLKSqmDTSKALLNVSVNITKFSKFERsKSSHKNERRVLEI 100
Cdd:pfam01138   1 ELRPIEIETGVLSQA-DGSALVELGDTKVLATVTGPIEPKEDR--DFAPGRLTVEYELAPFASGER-PGEGRPSEREIEI 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 398366099  101 QTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGI 152
Cdd:pfam01138  77 SRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGI 128
 
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 1.34e-114

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: 327.58  E-value: 1.34e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  11 GLRLDGRRWNELRRFESSINTHPhAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERsKSS 90
Cdd:cd11370    1 GLRLDGRRPNELRRIRCRIGVFS-SADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVVNCEYSMATFSTGER-KRR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  91 HKNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTP 170
Cdd:cd11370   79 GKGDRRSTELSLAIRQTFEAVILTHLYPRSQIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLDSTP 158

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 398366099 171 LLDTNSLEENA-MSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRKHAQ 237
Cdd:cd11370  159 LLDLNYLEESGdLPDLTVAVLPKSDKVVLLQMESRLHLDRLEKVLELAIEGCKVIREIMDEVVREHTK 226
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 22-224 4.70e-46

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: 152.87  E-value: 4.70e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  22 LRRFESSINTHpHAADGSSYMEQGNNKIITLVKGPKEPRlKSQMDTSKALLNVSVNITKFSKFERSksSHKNERRVLEIQ 101
Cdd:cd11358    1 FRPVEIETGVL-NQADGSALVKLGNTKVICAVTGPIVEP-DKLERPDKGTLYVNVEISPGAVGERR--QGPPGDEEMEIS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 102 TSLVRMFEKNVML---NIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGI-------------SMFDYISGISVGL 165
Cdd:cd11358   77 RLLERTIEASVILdksTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIprvfvdersppllLMKDLIVAVSVGG 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 398366099 166 Y-DTTPLLDTNSLEEN-AMSTVTLgVVGKSEKLSLLLVEDKIPLD--RLENVLAIGIAGAHRV 224
Cdd:cd11358  157 IsDGVLLLDPTGEEEElADSTLTV-AVDKSGKLCLLSKVGGGSLDteEIKECLELAKKRSLHL 218
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 10-234 3.01e-43

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 146.32  E-value: 3.01e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  10 EGLRLDGRRWNELRRFESSINThPHAADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKS 89
Cdd:PRK03983  12 DGLRLDGRKPDELRPIKIEVGV-LKNADGSAYLEWGNNKIIAAVYGPREMHPRHLQLPDRAVLRVRYNMAPFSVDERKRP 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  90 ShkNERRVLEIQTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTT 169
Cdd:PRK03983  91 G--PDRRSIEISKVIREALEPAIMLELFPRTVIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAGCAVGKVDGV 168

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 398366099 170 PLLDTNSLEEN-AMSTVTLGVVGKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRK 234
Cdd:PRK03983 169 IVLDLNKEEDNyGEADMPVAIMPRLGEITLLQLDGNLTREEFLEALELAKKGIKRIYQLQREALKS 234
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 36-234 3.46e-38

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: 132.46  E-value: 3.46e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  36 ADGSSYMEQGNNKIITLVKGPKEPRLKSQMDTSKALLNVSVNITKFSKFERSKSShkNERRVLEIQTSLVRMFEKNVMLN 115
Cdd:cd11366   15 ADGSAYVEWGNNKIIAAVYGPREVHPRHLQLPDRAVIRVRYNMAPFSVDERKRPG--PDRREIEISKVIKEALEPAIILE 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 116 IYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLDTNSLEENAMST-VTLGVVGKSE 194
Cdd:cd11366   93 EFPRTAIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDGKIVLDLNKEEDNYGEAdMPIAMMPNLG 172

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 398366099 195 KLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRK 234
Cdd:cd11366  173 EITLLQLDGDLTPDEFKQAIELAKKGCKRIYELQKEALKR 212
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 34-234 2.29e-31

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: 114.59  E-value: 2.29e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  34 HAADGSSYMEQGNNKIITLVKGPKEPRlKSQMDTSKALLNVSVNITKFSKFERSKSSHKNERRVL--EIQTSLvrmfEKN 111
Cdd:cd11371   12 SQAKGSAYVELGNTKVICSVYGPRPIP-GRTEFSDRGRLNCEVKFAPFATPGRRRHGQDSEERELssLLHQAL----EPA 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 112 VMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLYDTTPLLD-TNSLEENAMSTVTLGVV 190
Cdd:cd11371   87 VRLEKYPKSQIDVFVTVLESDGSVLAAAITAASLALADAGIEMYDLVTACSAALIGDELLLDpTREEEEASSGGVMLAYM 166

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 398366099 191 GKSEKLSLLLVEDKIPLDRLENVLAIGIAGAHRVRDLMDEELRK 234
Cdd:cd11371  167 PSLNQVTQLWQSGEMDVDQLEEALDLCIDGCNRIHPVVRQALLE 210
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 21-152 6.91e-27

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: 100.74  E-value: 6.91e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099   21 ELRRFESSINTHPHAaDGSSYMEQGNNKIITLVKGPKEPRLKSqmDTSKALLNVSVNITKFSKFERsKSSHKNERRVLEI 100
Cdd:pfam01138   1 ELRPIEIETGVLSQA-DGSALVELGDTKVLATVTGPIEPKEDR--DFAPGRLTVEYELAPFASGER-PGEGRPSEREIEI 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 398366099  101 QTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGI 152
Cdd:pfam01138  77 SRLIDRALRPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGI 128
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 22-228 3.94e-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: 100.72  E-value: 3.94e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  22 LRRFESSINTHPHAaDGSSYMEQGNNKIITLVKGPKEPRLkSQMDTSKALLNVSVnitkfskfeRSKSSH-KNERRVLEi 100
Cdd:cd11372    1 LRPLSCELGLLSRA-DGSARFSQGDTSVLAAVYGPIEVKL-RKELPDRATLEVIV---------RPKSGLpGVKEKLLE- 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 101 qTSLVRMFEKNVMLNIYPRTVIDIEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL-YDTTPLLDTNSLEE 179
Cdd:cd11372   69 -LLLRSTLEPIILLHLHPRTLISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAItEDGEIILDPTAEEE 147

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 398366099 180 N-AMSTVTLgVVGKSEKLSLLLVEDKIPLDR--LENVLAIGIAGAHRVRDLM 228
Cdd:cd11372  148 KeAKAVATF-AFDSGEEKNLVLSESEGSFTEeeLFACLELAQAASAAIFDFY 198
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 156-220 3.91e-07

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: 46.03  E-value: 3.91e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 398366099  156 DYISGISVGLYDTTPLLDTNSLEENAM-STVTLGVVGKSEKLSLLLV-EDKIPLDRLENVLAIGIAG 220
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSdSDLTVAVAGTGEIVALMKEgGAGLTEDELLEALELAKEA 67
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 9-59 1.00e-03

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: 39.51  E-value: 1.00e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 398366099   9 PEGLRLDGRRWNELRRFESSINTHPHaADGSSYMEQGNNKIITLVK-GPKEP 59
Cdd:cd11365   13 EKGKRIDGRGLDEYRDIEIETGVIPK-AEGSALVKLGNTQVLAGVKlEVGEP 63
RNase_PH_PNPase_2 cd11364
Polyribonucleotide nucleotidyltransferase, repeat 2; Polyribonucleotide nucleotidyltransferase ...
 128-235 2.41e-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: 37.91  E-value: 2.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 128 VLEQDGGI-MGSlINGITLALIDAGISMFDYISGISVGLYdttplldTNSLEENAMSTVTLG-----------VVGKSEK 195
Cdd:cd11364  109 VLESNGSSsMAS-VCGGSLALMDAGVPIKAPVAGIAMGLI-------TEGIDDYRVLTDILGledhlgdmdfkVAGTRDG 180

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 398366099 196 LSLLLVEDKIPLDRLEnVLAIGIAGAHRVR----DLMDEELRKH 235
Cdd:cd11364  181 ITALQMDIKIPGITLE-IMREALQQAKEGRlhilDIMEKAISEP 223
rph PRK00173
ribonuclease PH; Reviewed
 119-178 3.01e-03

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 37.78  E-value: 3.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 119 RTVIDIE------IH----VLEQDGGIMGSLINGITLALIDA-----------GISMFDYISGISVGLYDTTPLLDTNSL 177
Cdd:PRK00173  99 RAVVDLKalgertITidcdVIQADGGTRTASITGAYVALADAlnklvargklkKNPLKDQVAAVSVGIVDGEPVLDLDYE 178


                 .
gi 398366099 178 E 178
Cdd:PRK00173 179 E 179
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 85-232 3.15e-03

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: 37.59  E-value: 3.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099  85 ERSKSSHKNERRVLEIQTSLVRMFEKNVMLN-IYPRTvIDIEIHVLEQDGGIMGSLINGITLALIDAGISMF-------- 155
Cdd:cd11362   66 QREASKGKQSGRTQEIQRLIGRSLRAAVDLEaLGERT-ITIDCDVLQADGGTRTASITGAYVALADAVDKLVekgvleen 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 398366099 156 ---DYISGISVGLYDTTPLLDTNsLEENAMSTVTLGVVGKSEKlslLLVE-----DKIPLDR--LENVLAIGIAGAHRVR 225
Cdd:cd11362  145 plkHFVAAVSVGIVDGEPLLDLD-YEEDSAADVDMNVVMTGSG---RFVEvqgtgEEAPFSRdeLNELLDLAEKGIQELI 220


                 ....*..
gi 398366099 226 DLMDEEL 232
Cdd:cd11362  221 ELQKEAL 227
 
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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