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Conserved domains on  [gi|6320486|ref|NP_010566|]
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exosome non-catalytic core subunit RRP45 [Saccharomyces cerevisiae S288C]

Protein Classification

exosome complex component RRP45( domain architecture ID 10183520)

exosome complex component RRP45 is a component of the exosome that plays an important role in RNA turnover, 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

CATH:  3.30.230.70
Gene Ontology:  GO:0006396|GO:0000178|GO:0061629|GO:0003723|GO:0035925|GO:0000175
PubMed:  16829983|17174896

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 7-278 2.99e-143

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: 403.83  E-value: 2.99e-143
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    7 ISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPM 86
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   87 AGSQFENGNiTGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPD 166
Cdd:cd11368  81 ASPAFEPGR-PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPD 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  167 ITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNpqdteenikgetNSEISIIDATLKEELLRDGVLTVTLNKNREVV 246
Cdd:cd11368 160 VTVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFD------------DGEIVVVDPTLLEEAVADGSLTVALNKHREIC 227

                       250       260       270
                ....*....|....*....|....*....|..
gi 6320486  247 QVSKAGGLPMDALTLMKCCHEAYSIIEKITDQ 278
Cdd:cd11368 228 ALSKSGGAPLSPSQILRCVKIAAAKAKELTEL 259
 
Name Accession Description Interval E-value
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 7-278 2.99e-143

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: 403.83  E-value: 2.99e-143
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    7 ISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPM 86
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   87 AGSQFENGNiTGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPD 166
Cdd:cd11368  81 ASPAFEPGR-PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPD 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  167 ITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNpqdteenikgetNSEISIIDATLKEELLRDGVLTVTLNKNREVV 246
Cdd:cd11368 160 VTVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFD------------DGEIVVVDPTLLEEAVADGSLTVALNKHREIC 227

                       250       260       270
                ....*....|....*....|....*....|..
gi 6320486  247 QVSKAGGLPMDALTLMKCCHEAYSIIEKITDQ 278
Cdd:cd11368 228 ALSKSGGAPLSPSQILRCVKIAAAKAKELTEL 259
PRK04282 PRK04282
exosome complex protein Rrp42;
15-285 9.42e-55

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 178.92  E-value: 9.42e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    15 ILEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQF 91
Cdd:PRK04282  16 ILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPTF 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    92 ENGNiTGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHG 171
Cdd:PRK04282  96 EPGP-PDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGE 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   172 EQIIvhpVNEREPVPLGILHIPICVTFsffnpqdteenikGETNSEIsIIDATLKEELLRDGVLTVTLNKNREVVQVSKA 251
Cdd:PRK04282 175 DGVV---DKLGEDFPLPVNDKPVTVTF-------------AKIGNYL-IVDPTLEEESVMDARITITTDEDGNIVAIQKS 237

                        250       260       270
                 ....*....|....*....|....*....|....
gi 6320486   252 GGLPMDALTLMKCCHEAYSIIEKITDQILQLLKE 285
Cdd:PRK04282 238 GIGSFTEEEVDKAIDIALEKAKELREKLKEALGI 271
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 32-165 8.94e-30

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: 109.60  E-value: 8.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486     32 QFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRII 108
Cdd:pfam01138   1 ELRPIEIETGvlsQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6320486    109 EKSVRRSGALDveglcivaGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKP 165
Cdd:pfam01138  81 DRALRPSIPLE--------GYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
Name Accession Description Interval E-value
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 7-278 2.99e-143

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: 403.83  E-value: 2.99e-143
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    7 ISASESKFILEALRQNYRLDGRSFDQFRDVEITFGKEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPM 86
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   87 AGSQFENGNiTGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPD 166
Cdd:cd11368  81 ASPAFEPGR-PSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPD 159

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  167 ITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFNpqdteenikgetNSEISIIDATLKEELLRDGVLTVTLNKNREVV 246
Cdd:cd11368 160 VTVDGEEVTVHSPEEREPVPLSIHHIPICVTFAFFD------------DGEIVVVDPTLLEEAVADGSLTVALNKHREIC 227

                       250       260       270
                ....*....|....*....|....*....|..
gi 6320486  247 QVSKAGGLPMDALTLMKCCHEAYSIIEKITDQ 278
Cdd:cd11368 228 ALSKSGGAPLSPSQILRCVKIAAAKAKELTEL 259
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 33-275 5.10e-63

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: 198.32  E-value: 5.10e-63
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   33 FRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPY-EDRPFEGLFVISTEISPMAGSQFEnGNITGEDEVLCSRII 108
Cdd:cd11358   1 FRPVEIETGvlnQADGSALVKLGNTKVICAVTGPIVEPDkLERPDKGTLYVNVEISPGAVGERR-QGPPGDEEMEISRLL 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  109 EKSVRRSGALDveglcIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHgeqiivhpvnEREPVPLG 188
Cdd:cd11358  80 ERTIEASVILD-----KSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVD----------ERSPPLLL 144

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  189 ILHIPICVTFSFFnpqdteenikgetNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEA 268
Cdd:cd11358 145 MKDLIVAVSVGGI-------------SDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELA 211


                ....*..
gi 6320486  269 YSIIEKI 275
Cdd:cd11358 212 KKRSLHL 218
PRK04282 PRK04282
exosome complex protein Rrp42;
15-285 9.42e-55

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 178.92  E-value: 9.42e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    15 ILEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQF 91
Cdd:PRK04282  16 ILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPTF 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    92 ENGNiTGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHG 171
Cdd:PRK04282  96 EPGP-PDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGE 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   172 EQIIvhpVNEREPVPLGILHIPICVTFsffnpqdteenikGETNSEIsIIDATLKEELLRDGVLTVTLNKNREVVQVSKA 251
Cdd:PRK04282 175 DGVV---DKLGEDFPLPVNDKPVTVTF-------------AKIGNYL-IVDPTLEEESVMDARITITTDEDGNIVAIQKS 237

                        250       260       270
                 ....*....|....*....|....*....|....
gi 6320486   252 GGLPMDALTLMKCCHEAYSIIEKITDQILQLLKE 285
Cdd:PRK04282 238 GIGSFTEEEVDKAIDIALEKAKELREKLKEALGI 271
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 15-275 3.85e-54

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: 177.02  E-value: 3.85e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   15 ILEALRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQF 91
Cdd:cd11365   8 ILSLLEKGKRIDGRGLDEYRDIEIETGvipKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASPTF 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   92 ENGNiTGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHG 171
Cdd:cd11365  88 EPGP-PDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEYEVDE 166

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  172 EQIIvhpVNEREPVPLGILHIPICVTFsffnpqdteenikGETNSEIsIIDATLKEELLRDGVLTVTLNKNREVVQVSKA 251
Cdd:cd11365 167 NEVI---EVLGEELPLPVNTLPVSVTV-------------AKIGGYI-VVDPTLEEELVMDARITITIDEDGNIVALQKG 229

                       250       260
                ....*....|....*....|....
gi 6320486  252 GGLPMDALTLMKCCHEAYSIIEKI 275
Cdd:cd11365 230 GGGSFTEDEIDKAIDIALEKAAEL 253
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 19-279 1.18e-50

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: 168.12  E-value: 1.18e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   19 LRQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGN 95
Cdd:cd11369  13 LAENVRPDGRELDEFRPTSVNVGsisTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDLPPLCSSKFRPGP 92

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   96 ITGEDEVLCSRIiEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITVHGEQII 175
Cdd:cd11369  93 PSEEAQVLSSFL-ADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTIDEETEL 171

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  176 VhPVNEREPVPLGILHIPICVTFSFFnpqdteenikgetNSEISIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLP 255
Cdd:cd11369 172 V-VVNPEERRPLNLKNLPVSTTFAVF-------------DDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGSP 237

                       250       260
                ....*....|....*....|....
gi 6320486  256 MDALTLMKCCHEAYSIIEKITDQI 279
Cdd:cd11369 238 LSQAQLQECIELAKKRAKELQKLI 261
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 7-285 9.49e-34

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: 124.25  E-value: 9.49e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    7 ISASESKFILEALRQNYRLDGRSFDQFRDVEItfgkEFGDVS-------VKMGNTKVHCRISCQIAQPYEDRPFEGLFVI 79
Cdd:cd11367   2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIEL----ETGVLSntngsarVRLGNTDVLVGVKAEVGSPDPETPNKGRLEF 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486   80 STEISPMAGSQFENGNitGEDEVL-CSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAG 158
Cdd:cd11367  78 FVDCSPNASPEFEGRG--GEELATeLSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAA 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486  159 LMHFKKPDITV----HGEQIIVHPVNEREPVPLGILHIPICVTFSffnpqdteeniKGETNseiSIIDATLKEELLRDGV 234
Cdd:cd11367 156 LFNTRIPKVEVseddEGTKEIELSDDPYDVKRLDVSNVPLIVTLS-----------KIGNR---HIVDATAEEEACSSAR 221

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|.
gi 6320486  235 LTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYSIIEKITDQILQLLKE 285
Cdd:cd11367 222 LLVAVNAKGRICGVQKSGGGSLEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 32-165 8.94e-30

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: 109.60  E-value: 8.94e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486     32 QFRDVEITFG---KEFGDVSVKMGNTKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRII 108
Cdd:pfam01138   1 ELRPIEIETGvlsQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRPSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 6320486    109 EKSVRRSGALDveglcivaGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKP 165
Cdd:pfam01138  81 DRALRPSIPLE--------GYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 191-271 1.87e-09

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: 52.96  E-value: 1.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6320486    191 HIPICVTFSFFNPQdteenikgetnseiSIIDATLKEELLRDGVLTVTLNKNREVVQVSKAGGLPMDALTLMKCCHEAYS 270
Cdd:pfam03725   1 DPVAAVTVGKIDGQ--------------LVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKE 66


                  .
gi 6320486    271 I 271
Cdd:pfam03725  67 A 67
rph PRK00173
ribonuclease PH; Reviewed
 24-63 4.24e-03

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 37.78  E-value: 4.24e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 6320486    24 RLDGRSFDQFRDVEITFGkeF-----GDVSVKMGNTKVHCRISCQ 63
Cdd:PRK00173   2 RPDGRAADQLRPVTITRN--FtkhaeGSVLVEFGDTKVLCTASVE 44
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 7-56 5.53e-03

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 37.69  E-value: 5.53e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 6320486     7 ISASESKFILEalrQNYRLDGRSFDQFRDVEITFG---KEFGDVSVKMGNTKV 56
Cdd:PRK03983   1 LQVEPPKLILE---DGLRLDGRKPDELRPIKIEVGvlkNADGSAYLEWGNNKI 50
 
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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