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Conserved domains on  [gi|334185300|ref|NP_001189874|]
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ribonuclease PH45A [Arabidopsis thaliana]

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 ...
 11-272 5.95e-139

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: 393.05  E-value: 5.95e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  11 LTVNESKFVESALQSELRVDGRGLYDYRKLTIKFGKEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPM 90
Cdd:cd11368    1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  91 ADPSFEPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDC 170
Cdd:cd11368   81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 171 TVGGdnsQDVIIHPPEEREPLPLIIHHLPIAFTFGFFNKGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGV 250
Cdd:cd11368  161 TVDG---EEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPL 237

                        250       260
                 ....*....|....*....|..
gi 334185300 251 NQSVILHCLRLASSRASATTKI 272
Cdd:cd11368  238 SPSQILRCVKIAAAKAKELTEL 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 ...
 11-272 5.95e-139

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: 393.05  E-value: 5.95e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  11 LTVNESKFVESALQSELRVDGRGLYDYRKLTIKFGKEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPM 90
Cdd:cd11368    1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  91 ADPSFEPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDC 170
Cdd:cd11368   81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 171 TVGGdnsQDVIIHPPEEREPLPLIIHHLPIAFTFGFFNKGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGV 250
Cdd:cd11368  161 TVDG---EEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPL 237

                        250       260
                 ....*....|....*....|..
gi 334185300 251 NQSVILHCLRLASSRASATTKI 272
Cdd:cd11368  238 SPSQILRCVKIAAAKAKELTEL 259
PRK04282 PRK04282
exosome complex protein Rrp42;
19-278 3.37e-77

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 236.70  E-value: 3.37e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  19 VESALQSELRVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPMADPSF 95
Cdd:PRK04282  16 ILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPTF 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  96 EPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGGD 175
Cdd:PRK04282  96 EPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGED 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 176 NSQDViihppeEREPLPLIIHHLPIAFTFGFFnkGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVI 255
Cdd:PRK04282 176 GVVDK------LGEDFPLPVNDKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEV 247

                        250       260
                 ....*....|....*....|...
gi 334185300 256 LHCLRLASSRASATTKIIRDAVE 278
Cdd:PRK04282 248 DKAIDIALEKAKELREKLKEALG 270
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 28-278 4.58e-76

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: 233.54  E-value: 4.58e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  28 RVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPMADPSFEPGHPGESA 104
Cdd:COG2123   23 RIDGRGLDEYRPIEIETGvieKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASPTFEPGPPDENA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 105 VELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGGDNsqdvIIHP 184
Cdd:COG2123  103 IELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEVGEDG----VVVD 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 185 PEEREPLPliIHHLPIAFTFGFFnkGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVILHCLRLASS 264
Cdd:COG2123  179 KGEDTPLP--VNTLPVSVTMAKI--GDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEEIDKAIDIALE 254

                        250
                 ....*....|....
gi 334185300 265 RAsattKIIRDAVE 278
Cdd:COG2123  255 KG----KELRELLK 264
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 36-152 3.67e-24

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: 94.97  E-value: 3.67e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300   36 DYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQlVQPYKDRP-SEGSFSIFTEFSPMADPSFE-PGHPGESAVELGRI 110
Cdd:pfam01138   1 ELRPIEIETGvlsQADGSALVELGDTKVLATVTGP-IEPKEDRDfAPGRLTVEYELAPFASGERPgEGRPSEREIEISRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 334185300  111 IDRALRESRAvdteslcvLAGKLVWSVRIDLHILDNGGNLVD 152
Cdd:pfam01138  80 IDRALRPSIP--------LEGYPRWTIRIDVTVLSSDGSLLD 113
 
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 ...
 11-272 5.95e-139

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: 393.05  E-value: 5.95e-139
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  11 LTVNESKFVESALQSELRVDGRGLYDYRKLTIKFGKEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPM 90
Cdd:cd11368    1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVELSPM 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  91 ADPSFEPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDC 170
Cdd:cd11368   81 ASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDV 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 171 TVGGdnsQDVIIHPPEEREPLPLIIHHLPIAFTFGFFNKGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGV 250
Cdd:cd11368  161 TVDG---EEVTVHSPEEREPVPLSIHHIPICVTFAFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPL 237

                        250       260
                 ....*....|....*....|..
gi 334185300 251 NQSVILHCLRLASSRASATTKI 272
Cdd:cd11368  238 SPSQILRCVKIAAAKAKELTEL 259
PRK04282 PRK04282
exosome complex protein Rrp42;
19-278 3.37e-77

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 236.70  E-value: 3.37e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  19 VESALQSELRVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPMADPSF 95
Cdd:PRK04282  16 ILSLLKKGKRIDGRKLDEYRPIEIETGvikKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASPTF 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  96 EPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGGD 175
Cdd:PRK04282  96 EPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAVEEGED 175

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 176 NSQDViihppeEREPLPLIIHHLPIAFTFGFFnkGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVI 255
Cdd:PRK04282 176 GVVDK------LGEDFPLPVNDKPVTVTFAKI--GNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFTEEEV 247

                        250       260
                 ....*....|....*....|...
gi 334185300 256 LHCLRLASSRASATTKIIRDAVE 278
Cdd:PRK04282 248 DKAIDIALEKAKELREKLKEALG 270
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 28-278 4.58e-76

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: 233.54  E-value: 4.58e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  28 RVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPMADPSFEPGHPGESA 104
Cdd:COG2123   23 RIDGRGLDEYRPIEIETGvieKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASPTFEPGPPDENA 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 105 VELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGGDNsqdvIIHP 184
Cdd:COG2123  103 IELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEVGEDG----VVVD 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 185 PEEREPLPliIHHLPIAFTFGFFnkGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVILHCLRLASS 264
Cdd:COG2123  179 KGEDTPLP--VNTLPVSVTMAKI--GDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEEIDKAIDIALE 254

                        250
                 ....*....|....
gi 334185300 265 RAsattKIIRDAVE 278
Cdd:COG2123  255 KG----KELRELLK 264
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 21-267 3.03e-70

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: 218.24  E-value: 3.03e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  21 SALQSELRVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPMADPSFEP 97
Cdd:cd11365   10 SLLEKGKRIDGRGLDEYRDIEIETGvipKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASPTFEP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  98 GHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGGDNS 177
Cdd:cd11365   90 GPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEYEVDENEV 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 178 QDViihppeEREPLPLIIHHLPIAFTFGffnK-GSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVIL 256
Cdd:cd11365  170 IEV------LGEELPLPVNTLPVSVTVA---KiGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTEDEID 240

                        250
                 ....*....|.
gi 334185300 257 HCLRLASSRAS 267
Cdd:cd11365  241 KAIDIALEKAA 251
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 17-273 1.83e-53

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: 175.44  E-value: 1.83e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  17 KFVESALQSELRVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEFSPMADP 93
Cdd:cd11369    7 EYYRRFLAENVRPDGRELDEFRPTSVNVGsisTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDLPPLCSS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  94 SFEPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVg 173
Cdd:cd11369   87 KFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTI- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 174 gDNSQDVIIHPPEEREPLPLIihHLPIAFTFGFFNKGSILVmDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQS 253
Cdd:cd11369  166 -DEETELVVVNPEERRPLNLK--NLPVSTTFAVFDDKHLLA-DPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQA 241

                        250       260
                 ....*....|....*....|
gi 334185300 254 VILHCLRLASSRASATTKII 273
Cdd:cd11369  242 QLQECIELAKKRAKELQKLI 261
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 11-279 6.39e-44

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: 151.21  E-value: 6.39e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  11 LTVNESKFVESALQSELRVDGRGLYDYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKDRPSEGSFSIFTEF 87
Cdd:cd11367    2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGvlsNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  88 SPMADPSFEPGHPGESAVELGRIIDRALRESRAVDTESLCVLAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRR 167
Cdd:cd11367   82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 168 PDCTV-GGDNSQDVIIHPPEEREPLPLIIHHLPIAFTFGFFnkGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPG 246
Cdd:cd11367  162 PKVEVsEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKI--GNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSG 239

                        250       260       270
                 ....*....|....*....|....*....|...
gi 334185300 247 EEGVNQSVILHCLRLASSRASATTKIIRDAVEA 279
Cdd:cd11367  240 GGSLEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 37-267 3.24e-39

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: 137.07  E-value: 3.24e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300  37 YRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQLVQPYKD-RPSEGSFSIFTEFSPMADPSFEPGHPGESAVELGRIID 112
Cdd:cd11358    1 FRPVEIETGvlnQADGSALVKLGNTKVICAVTGPIVEPDKLeRPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300 113 RALRESRAVDTEslcvlAGKLVWSVRIDLHILDNGGNLVDAANVAALAALMTFRRPDCTVGgdnsqdviihppeEREPLP 192
Cdd:cd11358   81 RTIEASVILDKS-----TRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVD-------------ERSPPL 142

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334185300 193 LIIHHLPIAFTFGFFNkGSILVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVILHCLRLASSRAS 267
Cdd:cd11358  143 LLMKDLIVAVSVGGIS-DGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSL 216
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 36-152 3.67e-24

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: 94.97  E-value: 3.67e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334185300   36 DYRKLTIKFG---KEYGSSQVQLGQTHVMAFVTAQlVQPYKDRP-SEGSFSIFTEFSPMADPSFE-PGHPGESAVELGRI 110
Cdd:pfam01138   1 ELRPIEIETGvlsQADGSALVELGDTKVLATVTGP-IEPKEDRDfAPGRLTVEYELAPFASGERPgEGRPSEREIEISRL 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 334185300  111 IDRALRESRAvdteslcvLAGKLVWSVRIDLHILDNGGNLVD 152
Cdd:pfam01138  80 IDRALRPSIP--------LEGYPRWTIRIDVTVLSSDGSLLD 113
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 197-265 7.19e-15

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: 67.99  E-value: 7.19e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334185300  197 HLPIAFTFGFFNKGsiLVMDPTYVEEAVMCGRMTVTVNANGDICAIQKPGEEGVNQSVILHCLRLASSR 265
Cdd:pfam03725   1 DPVAAVTVGKIDGQ--LVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKEA 67
 
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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