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Conserved domains on  [gi|1227483608|pdb|5VZJ|D]
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Chain D, Exosome complex component RRP46

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 ...
 6-212 1.46e-75

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: 226.68  E-value: 1.46e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        6 QAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCY 85
Cdd:cd11372   5 SCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIILLHLH 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       86 PRQLCQITCQILESGEdeaefslRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsDIIVDPTAEQLKISLSVHTL 165
Cdd:cd11372  85 PRTLISVVLQVLQDDG-------SLLACAINAACLALLDAGVPMKGLFAAVTCAITEDG-EIILDPTAEEEKEAKAVATF 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
5VZJ_D      166 ALEFVNGgkvvKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIR 212
Cdd:cd11372 157 AFDSGEE----KNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 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 ...
 6-212 1.46e-75

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: 226.68  E-value: 1.46e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        6 QAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCY 85
Cdd:cd11372   5 SCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIILLHLH 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       86 PRQLCQITCQILESGEdeaefslRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsDIIVDPTAEQLKISLSVHTL 165
Cdd:cd11372  85 PRTLISVVLQVLQDDG-------SLLACAINAACLALLDAGVPMKGLFAAVTCAITEDG-EIILDPTAEEEKEAKAVATF 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
5VZJ_D      166 ALEFVNGgkvvKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIR 212
Cdd:cd11372 157 AFDSGEE----KNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 4-127 2.43e-15

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: 69.93  E-value: 2.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D          4 SVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPK-ARQELPTQLALEIIV-------RPAKGVATTREKVLEDKLRAV 75
Cdd:pfam01138   4 PIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKeDRDFAPGRLTVEYELapfasgeRPGEGRPSEREIEISRLIDRA 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
5VZJ_D         76 LTPLITRHCYPRQLCQITCQILESGEDeaefslrELSCCINAAFLALVDAGI 127
Cdd:pfam01138  84 LRPSIPLEGYPRWTIRIDVTVLSSDGS-------LLDAAINAASLALADAGI 128
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 5-214 3.85e-11

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 60.80  E-value: 3.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D         5 VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQ-ELPTQLALEIIVRPA-------KGVATTREKVLEDKL-RAV 75
Cdd:PRK03983  27 IKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHlQLPDRAVLRVRYNMApfsvderKRPGPDRRSIEISKViREA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        76 LTPLITRHCYPRQLCQITCQILesgedEAEFSLRelSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsdIIVDPTAEQ 155
Cdd:PRK03983 107 LEPAIMLELFPRTVIDVFIEVL-----QADAGTR--VAGITAASLALADAGIPMRDLVAGCAVGKVDGV--IVLDLNKEE 177

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
5VZJ_D       156 LKISLSVHTLALeFVNGGKVVknvlLLDSNGDFNEDQLFSLLELGEQKCQElVTNIRRI 214
Cdd:PRK03983 178 DNYGEADMPVAI-MPRLGEIT----LLQLDGNLTREEFLEALELAKKGIKR-IYQLQRE 230
 
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 ...
 6-212 1.46e-75

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: 226.68  E-value: 1.46e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        6 QAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVATTREKVLEDKLRAVLTPLITRHCY 85
Cdd:cd11372   5 SCELGLLSRADGSARFSQGDTSVLAAVYGPIEVKLRKELPDRATLEVIVRPKSGLPGVKEKLLELLLRSTLEPIILLHLH 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       86 PRQLCQITCQILESGEdeaefslRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsDIIVDPTAEQLKISLSVHTL 165
Cdd:cd11372  85 PRTLISVVLQVLQDDG-------SLLACAINAACLALLDAGVPMKGLFAAVTCAITEDG-EIILDPTAEEEKEAKAVATF 156

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
5VZJ_D      166 ALEFVNGgkvvKNVLLLDSNGDFNEDQLFSLLELGEQKCQELVTNIR 212
Cdd:cd11372 157 AFDSGEE----KNLVLSESEGSFTEEELFACLELAQAASAAIFDFYR 199
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 4-218 1.19e-18

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: 81.05  E-value: 1.19e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        4 SVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLAL---EI-------IVRPAKGVATTREKVLEDKLR 73
Cdd:cd11370  14 RIRCRIGVFSSADGSAYLEQGNTKVLAAVYGPHEPRNRSQALHDRAVvncEYsmatfstGERKRRGKGDRRSTELSLAIR 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       74 AVLTPLITRHCYPRQLCQITCQILESgeDEAefslrELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSdiIVDPTA 153
Cdd:cd11370  94 QTFEAVILTHLYPRSQIDIYVQVLQA--DGG-----LLAACINAATLALIDAGIPMKDYVCACSAGYLDSTP--LLDLNY 164

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
5VZJ_D      154 EQLKISLSVHTLALeFVNGGKVVknVLLLDSngDFNEDQLFSLLELGEQKCQELVTNIRRIIQDN 218
Cdd:cd11370 165 LEESGDLPDLTVAV-LPKSDKVV--LLQMES--RLHLDRLEKVLELAIEGCKVIREIMDEVVREH 224
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 5-207 7.10e-18

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: 78.91  E-value: 7.10e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        5 VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVRPAKGVA--------TTREKVLEDKLR--- 73
Cdd:cd11358   4 VEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLERPDKGTLYVNVEISPGAVgerrqgppGDEEMEISRLLErti 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       74 --AVLTPLITRHcyPRQLCQITCQILESGEdeaefSLRElsCCINAAFLALVDAGIALNSM-CASIPIAIIKD------- 143
Cdd:cd11358  84 eaSVILDKSTRK--PSWVLYVDIQVLSRDG-----GLLD--ACWNAAIAALKDAGIPRVFVdERSPPLLLMKDlivavsv 154

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
5VZJ_D      144 ----TSDIIVDPTAEQLKISLSVHTLAlefVNGGKVVKNVLLLDSNGDFnEDQLFSLLELGEQKCQEL 207
Cdd:cd11358 155 ggisDGVLLLDPTGEEEELADSTLTVA---VDKSGKLCLLSKVGGGSLD-TEEIKECLELAKKRSLHL 218
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 10-212 7.09e-16

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: 73.37  E-value: 7.09e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       10 GILDHVDGSSEFVSQDTKVICSVTGPIEPKARQELPTQLALEIIVR--------PAKGVATTREKVLEDKLRAVLTPLIT 81
Cdd:cd11371   9 GVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDRGRLNCEVKfapfatpgRRRHGQDSEERELSSLLHQALEPAVR 88

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       82 RHCYPRQLCQITCQILESGEDeaefslrELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsdIIVDPTAEQLKISLS 161
Cdd:cd11371  89 LEKYPKSQIDVFVTVLESDGS-------VLAAAITAASLALADAGIEMYDLVTACSAALIGDE--LLLDPTREEEEASSG 159

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
5VZJ_D      162 VHTLALeFVNGGKVVKnvllLDSNGDFNEDQLFSLLELGEQKCQELVTNIR 212
Cdd:cd11371 160 GVMLAY-MPSLNQVTQ----LWQSGEMDVDQLEEALDLCIDGCNRIHPVVR 205
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 4-127 2.43e-15

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: 69.93  E-value: 2.43e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D          4 SVQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPK-ARQELPTQLALEIIV-------RPAKGVATTREKVLEDKLRAV 75
Cdd:pfam01138   4 PIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKeDRDFAPGRLTVEYELapfasgeRPGEGRPSEREIEISRLIDRA 83

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
5VZJ_D         76 LTPLITRHCYPRQLCQITCQILESGEDeaefslrELSCCINAAFLALVDAGI 127
Cdd:pfam01138  84 LRPSIPLEGYPRWTIRIDVTVLSSDGS-------LLDAAINAASLALADAGI 128
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 5-208 3.17e-12

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: 63.51  E-value: 3.17e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        5 VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQ-ELPTQLALEIIVRPA-------KGVATT-REKVLEDKLRAV 75
Cdd:cd11366   5 IKIEVGVLKNADGSAYVEWGNNKIIAAVYGPREVHPRHlQLPDRAVIRVRYNMApfsvderKRPGPDrREIEISKVIKEA 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D       76 LTPLITRHCYPRQLCQITCQILesgedEAEFSLRelSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsdIIVDPTAEQ 155
Cdd:cd11366  85 LEPAIILEEFPRTAIDVFVEVL-----QADAGTR--VAGLNAASLALADAGIPMRDLVAACAAGKVDGK--IVLDLNKEE 155

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|...
5VZJ_D      156 LKISLSVHTLALeFVNGGKVVknvlLLDSNGDFNEDQLFSLLELGEQKCQELV 208
Cdd:cd11366 156 DNYGEADMPIAM-MPNLGEIT----LLQLDGDLTPDEFKQAIELAKKGCKRIY 203
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 5-214 3.85e-11

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 60.80  E-value: 3.85e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D         5 VQAEIGILDHVDGSSEFVSQDTKVICSVTGPIEPKARQ-ELPTQLALEIIVRPA-------KGVATTREKVLEDKL-RAV 75
Cdd:PRK03983  27 IKIEVGVLKNADGSAYLEWGNNKIIAAVYGPREMHPRHlQLPDRAVLRVRYNMApfsvderKRPGPDRRSIEISKViREA 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        76 LTPLITRHCYPRQLCQITCQILesgedEAEFSLRelSCCINAAFLALVDAGIALNSMCASIPIAIIKDTsdIIVDPTAEQ 155
Cdd:PRK03983 107 LEPAIMLELFPRTVIDVFIEVL-----QADAGTR--VAGITAASLALADAGIPMRDLVAGCAVGKVDGV--IVLDLNKEE 177

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
5VZJ_D       156 LKISLSVHTLALeFVNGGKVVknvlLLDSNGDFNEDQLFSLLELGEQKCQElVTNIRRI 214
Cdd:PRK03983 178 DNYGEADMPVAI-MPRLGEIT----LLQLDGNLTREEFLEALELAKKGIKR-IYQLQRE 230
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 134-203 3.70e-06

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: 43.33  E-value: 3.70e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D        134 ASIPIAIIKDTsdIIVDPTAEQLKISLSVHTLAlefVNGGKVVKNVLLLDsNGDFNEDQLFSLLELGEQK 203
Cdd:pfam03725   4 AAVTVGKIDGQ--LVVDPTLEEESLSDSDLTVA---VAGTGEIVALMKEG-GAGLTEDELLEALELAKEA 67
RNase_PH_PNPase_1 cd11363
Polyribonucleotide nucleotidyltransferase, repeat 1; Polyribonucleotide nucleotidyltransferase ...
 115-215 2.09e-03

Polyribonucleotide nucleotidyltransferase, repeat 1; 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. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E.


Pssm-ID: 206768 [Multi-domain]  Cd Length: 229  Bit Score: 38.27  E-value: 2.09e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_D      115 INAAFLALVDAGIALNSMCASIPIAIIKDtsDIIVDPTAEQLKISlsvhTLALEfVNGGKvvKNVLLLDSNGDF-NEDQL 193
Cdd:cd11363 127 INGASAALSLSDIPFNGPVGAVRVGRIDG--EFVVNPTREELEES----DLDLV-VAGTK--DAVLMVEAGAKEvSEEDM 197

                        90       100
                ....*....|....*....|..
5VZJ_D      194 FSLLELGEQKCQELVTNIRRII 215
Cdd:cd11363 198 LEAIKFGHEAIQQLIAAQEELA 219
 
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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