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Conserved domains on  [gi|254692991|ref|NP_081424|]
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exosome complex component RRP43 isoform 2 [Mus musculus]

Protein Classification

exosome complex component RRP43( domain architecture ID 10183523)

exosome complex component RRP43 similar to Saccharomyces cerevisiae exosome RRP43 subunit which is involved in pre-rRNA processing and found both in the nucleus and in the cytoplasm.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 6-266 4.81e-163

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: 452.78  E-value: 4.81e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991   6 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDL 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  86 PPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11369   81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:cd11369  161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLL 266
Cdd:cd11369  241 AQLQECIELAKKRAKELQKLI 261
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 6-266 4.81e-163

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: 452.78  E-value: 4.81e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991   6 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDL 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  86 PPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11369   81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:cd11369  161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLL 266
Cdd:cd11369  241 AQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
12-272 4.67e-81

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 245.17  E-value: 4.67e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 91
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  92 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:PRK04282  94 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:PRK04282 168 PAVEEGEDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTE 244

                        250       260
                 ....*....|....*....|....*..
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLLDEVIQS 272
Cdd:PRK04282 245 EEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 12-267 3.43e-77

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: 235.08  E-value: 3.43e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 91
Cdd:COG2123   12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASP 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  92 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:COG2123   92 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:COG2123  166 PKVEVGEDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTE 242

                        250       260
                 ....*....|....*....|..
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLLD 267
Cdd:COG2123  243 EEIDKAIDIALEKGKELRELLK 264
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 2.50e-31

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 113.07  E-value: 2.50e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991   31 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRF-RTGPPGEEAQVTSQFI 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERpGEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 254692991  110 ADVVdnsqvikkEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 166
Cdd:pfam01138  81 DRAL--------RPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 6-266 4.81e-163

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: 452.78  E-value: 4.81e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991   6 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDL 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  86 PPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11369   81 PPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:cd11369  161 PAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQ 240

                        250       260
                 ....*....|....*....|.
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLL 266
Cdd:cd11369  241 AQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
12-272 4.67e-81

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 245.17  E-value: 4.67e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 91
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  92 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:PRK04282  94 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:PRK04282 168 PAVEEGEDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTE 244

                        250       260
                 ....*....|....*....|....*..
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLLDEVIQS 272
Cdd:PRK04282 245 EEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 12-267 3.43e-77

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: 235.08  E-value: 3.43e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 91
Cdd:COG2123   12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASP 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  92 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:COG2123   92 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKV 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:COG2123  166 PKVEVGEDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTE 242

                        250       260
                 ....*....|....*....|..
gi 254692991 246 AKLQDCMSRAVTRHKEVSKLLD 267
Cdd:COG2123  243 EEIDKAIDIALEKGKELRELLK 264
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-262 5.40e-77

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: 232.99  E-value: 5.40e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  32 FRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVD-APDRGYVVPNVDLPPLCSSRFRTGPPGEEAQVTSQFIA 110
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLeRPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 111 DVVDNSQVIKKedlciSPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETalaevnlkkKSYLNVR 190
Cdd:cd11358   81 RTIEASVILDK-----STRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDERS---------PPLLLMK 146

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 254692991 191 TNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEV 262
Cdd:cd11358  147 DLIVAVSVGGISDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 12-265 9.11e-77

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: 233.65  E-value: 9.11e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSS 91
Cdd:cd11365    6 DYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASP 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  92 RFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQL 165
Cdd:cd11365   86 TFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKV 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 166 PEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDTlLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTG 245
Cdd:cd11365  160 PEYEVDENE--VIEVLGEELPLPVNTLPVSVTVAKIGGY-IVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTE 236

                        250       260
                 ....*....|....*....|
gi 254692991 246 AKLQDCMSRAVTRHKEVSKL 265
Cdd:cd11365  237 DEIDKAIDIALEKAAELREK 256
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 18-265 1.55e-57

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: 184.65  E-value: 1.55e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  18 LKENCRPDGRELGEFRATTVNIGsisTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGP 97
Cdd:cd11368   13 LKEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPMASPAFEPGR 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  98 PGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEEtala 177
Cdd:cd11368   90 PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGE---- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 178 EVNLKKKSY-----LNVRTNPVATSFAVFDD-TLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDC 251
Cdd:cd11368  166 EVTVHSPEErepvpLSIHHIPICVTFAFFDDgEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPSQILRC 245

                        250
                 ....*....|....
gi 254692991 252 MSRAVTRHKEVSKL 265
Cdd:cd11368  246 VKIAAAKAKELTEL 259
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 18-270 2.09e-53

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: 174.32  E-value: 2.09e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  18 LKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGP 97
Cdd:cd11367   14 VEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDCSPNASPEFEGRG 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  98 PGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETA-L 176
Cdd:cd11367   94 GEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVEVSEDDEgT 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 177 AEVNLKKK----SYLNVRTNPVATSFAVFDDTlLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCM 252
Cdd:cd11367  174 KEIELSDDpydvKRLDVSNVPLIVTLSKIGNR-HIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGGSLEPESIIEMI 252

                        250
                 ....*....|....*...
gi 254692991 253 SRAVTRHKEVSKLLDEVI 270
Cdd:cd11367  253 ETAKEVGKKLNAALDKAL 270
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 2.50e-31

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 113.07  E-value: 2.50e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991   31 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRF-RTGPPGEEAQVTSQFI 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERpGEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 254692991  110 ADVVdnsqvikkEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 166
Cdd:pfam01138  81 DRAL--------RPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 193-255 2.42e-16

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: 71.45  E-value: 2.42e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 254692991  193 PVATSFAVFDDTLlIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCMSRA 255
Cdd:pfam03725   3 VAAVTVGKIDGQL-VVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELA 64
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 33-257 1.90e-07

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: 50.26  E-value: 1.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  33 RATTVNIGSISTADGSALVKLGNTTVICGVKAefaapPVDA------PDRGYVvpNVDLPPlcssrfRTGPPGEEAQVTS 106
Cdd:cd11372    2 RPLSCELGLLSRADGSARFSQGDTSVLAAVYG-----PIEVklrkelPDRATL--EVIVRP------KSGLPGVKEKLLE 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 107 QFIADVVDNsqVIKKED---LCISpgklawvlycdLIC--LDYDGNILDACTFALLAALKNvqlpevtineetalAEVNL 181
Cdd:cd11372   69 LLLRSTLEP--IILLHLhprTLIS-----------VVLqvLQDDGSLLACAINAACLALLD--------------AGVPM 121

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 254692991 182 KkksylnvrTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTD--EDGKLCCLHKPGgsGLTGAKLQDCMSRAVT 257
Cdd:cd11372  122 K--------GLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDsgEEKNLVLSESEG--SFTEEELFACLELAQA 189
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 17-62 1.83e-06

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 47.71  E-value: 1.83e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 254692991  17 FLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGV 62
Cdd:PRK03983   9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV 54
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
23-60 3.66e-06

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 46.95  E-value: 3.66e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 254692991  23 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVIC 60
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLC 39
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 23-63 4.82e-06

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: 46.38  E-value: 4.82e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 254692991  23 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVK 63
Cdd:cd11370    3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY 43
rph PRK00173
ribonuclease PH; Reviewed
 23-70 6.46e-06

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 46.26  E-value: 6.46e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 254692991  23 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPP 70
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPR 49
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 32-224 3.43e-05

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: 43.71  E-value: 3.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  32 FRATTVNIGSISTADGSALVKLGNTTVICGV--------KAEFAappvdapDRGYVVPNVDLPPLCSSRFRTGPPGEEAQ 103
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVygprpipgRTEFS-------DRGRLNCEVKFAPFATPGRRRHGQDSEER 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991 104 VTSQFIADVVD---------NSQVikkeDLCISpgklawvlycdliCLDYDGNILDACTFALLAALKNVQLPEVTIneet 174
Cdd:cd11371   74 ELSSLLHQALEpavrlekypKSQI----DVFVT-------------VLESDGSVLAAAITAASLALADAGIEMYDL---- 132

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 254692991 175 alaevnlkkksylnvrtnpVATSFAVFDDTLLIVDPTGEEEHLSTGTLTV 224
Cdd:cd11371  133 -------------------VTACSAALIGDELLLDPTREEEEASSGGVML 163
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 31-97 1.02e-03

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: 39.24  E-value: 1.02e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254692991  31 EFRATTVNIGSISTADGSALVKLGNTTVICGV--KAEFAAPPVDAPDRGYVVPNVDLPPLC-SSRFRTGP 97
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAVygPREVHPRHLQLPDRAVIRVRYNMAPFSvDERKRPGP 70
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 31-70 3.65e-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: 37.98  E-value: 3.65e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 254692991  31 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPP 70
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPP 40
 
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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