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Conserved domains on  [gi|189083688|ref|NP_055819|]
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exosome complex component RRP42 [Homo sapiens]

Protein Classification

exosome complex component RRP42( domain architecture ID 10183516)

exosome complex component RRP42 is essential for the development of female gametophytes and plays an important role in mesophyll cell morphogenesis.

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 6-276 4.20e-168

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: 466.69  E-value: 4.20e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   6 LSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDC 85
Cdd:cd11367    2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  86 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 165
Cdd:cd11367   82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 166 PRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 245
Cdd:cd11367  162 PKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGG 241

                        250       260       270
                 ....*....|....*....|....*....|.
gi 189083688 246 SLDPESIFEMMETGKRVGKVLHASLQSVVHK 276
Cdd:cd11367  242 SLEPESIIEMIETAKEVGKKLNAALDKALKE 272
 
Name Accession Description Interval E-value
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 6-276 4.20e-168

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: 466.69  E-value: 4.20e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   6 LSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDC 85
Cdd:cd11367    2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  86 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 165
Cdd:cd11367   82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 166 PRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 245
Cdd:cd11367  162 PKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGG 241

                        250       260       270
                 ....*....|....*....|....*....|.
gi 189083688 246 SLDPESIFEMMETGKRVGKVLHASLQSVVHK 276
Cdd:cd11367  242 SLEPESIIEMIETAKEVGKKLNAALDKALKE 272
PRK04282 PRK04282
exosome complex protein Rrp42;
6-274 7.68e-61

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 193.94  E-value: 7.68e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   6 LSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDC 85
Cdd:PRK04282   8 IPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAEL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  86 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 165
Cdd:PRK04282  88 LPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 166 PRVRvlEDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 245
Cdd:PRK04282 168 PAVE--EGEDGVVDKLGEDFP-----LPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG 240

                        250       260
                 ....*....|....*....|....*....
gi 189083688 246 SLDPESIFEMMETGKRVGKVLHASLQSVV 274
Cdd:PRK04282 241 SFTEEEVDKAIDIALEKAKELREKLKEAL 269
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 1-267 5.46e-60

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: 191.55  E-value: 5.46e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   1 MASVTLSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLE 80
Cdd:COG2123    1 MSSPIIPEIKRDYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  81 ffvdCSAS----ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAV 156
Cdd:COG2123   81 ----VNAEllplASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAA 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 157 KAALFNTRIPRVRVleDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVV 236
Cdd:COG2123  157 VAALLTTKVPKVEV--GEDGVVVDKGEDTP-----LPVNTLPVSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNI 229

                        250       260       270
                 ....*....|....*....|....*....|.
gi 189083688 237 TCMRKVGKGSLDPESIFEMMETGKRVGKVLH 267
Cdd:COG2123  230 VAMQKGGSGSFTEEEIDKAIDIALEKGKELR 260
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 4.07e-29

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: 107.68  E-value: 4.07e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   31 DYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGG-DDLGTEIANTL 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRpSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 189083688  110 YRIFnnKSSVDLktlcisPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIP 166
Cdd:pfam01138  81 DRAL--RPSIPL------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
Name Accession Description Interval E-value
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 6-276 4.20e-168

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: 466.69  E-value: 4.20e-168
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   6 LSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDC 85
Cdd:cd11367    2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  86 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 165
Cdd:cd11367   82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 166 PRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 245
Cdd:cd11367  162 PKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGG 241

                        250       260       270
                 ....*....|....*....|....*....|.
gi 189083688 246 SLDPESIFEMMETGKRVGKVLHASLQSVVHK 276
Cdd:cd11367  242 SLEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-266 2.25e-64

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: 201.40  E-value: 2.25e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  32 YRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTP-KLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLY 110
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPdKLERPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 111 RIFNNKSSVDlktlcISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEdeegskdielsddpYDCI 190
Cdd:cd11358   81 RTIEASVILD-----KSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDE--------------RSPP 141

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 189083688 191 RLSVENVPCIVTLCKI-GYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVL 266
Cdd:cd11358  142 LLLMKDLIVAVSVGGIsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
PRK04282 PRK04282
exosome complex protein Rrp42;
6-274 7.68e-61

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 193.94  E-value: 7.68e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   6 LSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDC 85
Cdd:PRK04282   8 IPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAEL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  86 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 165
Cdd:PRK04282  88 LPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 166 PRVRvlEDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 245
Cdd:PRK04282 168 PAVE--EGEDGVVDKLGEDFP-----LPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG 240

                        250       260
                 ....*....|....*....|....*....
gi 189083688 246 SLDPESIFEMMETGKRVGKVLHASLQSVV 274
Cdd:PRK04282 241 SFTEEEVDKAIDIALEKAKELREKLKEAL 269
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 1-267 5.46e-60

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: 191.55  E-value: 5.46e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   1 MASVTLSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLE 80
Cdd:COG2123    1 MSSPIIPEIKRDYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  81 ffvdCSAS----ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAV 156
Cdd:COG2123   81 ----VNAEllplASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAA 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 157 KAALFNTRIPRVRVleDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVV 236
Cdd:COG2123  157 VAALLTTKVPKVEV--GEDGVVVDKGEDTP-----LPVNTLPVSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNI 229

                        250       260       270
                 ....*....|....*....|....*....|.
gi 189083688 237 TCMRKVGKGSLDPESIFEMMETGKRVGKVLH 267
Cdd:COG2123  230 VAMQKGGSGSFTEEEIDKAIDIALEKGKELR 260
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 13-267 7.56e-60

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: 190.89  E-value: 7.56e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  13 YIVHGVQEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPE 92
Cdd:cd11365    7 YILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLASPT 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  93 FEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVle 172
Cdd:cd11365   87 FEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEYEV-- 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 173 DEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESI 252
Cdd:cd11365  165 DENEVIEVLGEELP-----LPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFTEDEI 239

                        250
                 ....*....|....*
gi 189083688 253 FEMMETGKRVGKVLH 267
Cdd:cd11365  240 DKAIDIALEKAAELR 254
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 6-268 8.70e-49

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: 162.70  E-value: 8.70e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   6 LSEAEKVYIVHGVQEDLRVDGRGCEDYRCVEVEtdvVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDC 85
Cdd:cd11368    1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKIT---FGLEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVEL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  86 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 165
Cdd:cd11368   78 SPMASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRR 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 166 PRVRVledeEGSKDIELSDDPYDCIRLSVENVPCIVT--LCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVG 243
Cdd:cd11368  158 PDVTV----DGEEVTVHSPEEREPVPLSIHHIPICVTfaFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSG 233

                        250       260
                 ....*....|....*....|....*
gi 189083688 244 KGSLDPESIFEMMETGKRVGKVLHA 268
Cdd:cd11368  234 GAPLSPSQILRCVKIAAAKAKELTE 258
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 19-261 1.71e-46

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: 156.95  E-value: 1.71e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  19 QEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVD----CSASATPefe 94
Cdd:cd11369   14 AENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDlpplCSSKFRP--- 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  95 GRGGDD---LGTEIANtlyrIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVl 171
Cdd:cd11369   91 GPPSEEaqvLSSFLAD----ILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTI- 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 172 eDEEGSKDIELSDDPydcIRLSVENVPCIVTLCKIGYRHV-VDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPE 250
Cdd:cd11369  166 -DEETELVVVNPEER---RPLNLKNLPVSTTFAVFDDKHLlADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQA 241

                        250
                 ....*....|.
gi 189083688 251 SIFEMMETGKR 261
Cdd:cd11369  242 QLQECIELAKK 252
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 4.07e-29

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: 107.68  E-value: 4.07e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688   31 DYRCVEVETDVVSNTSGSARVKLGHTDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGG-DDLGTEIANTL 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRpSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 189083688  110 YRIFnnKSSVDLktlcisPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIP 166
Cdd:pfam01138  81 DRAL--RPSIPL------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 196-261 6.68e-14

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: 65.29  E-value: 6.68e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 189083688  196 NVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKR 261
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKE 66
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 37-272 1.41e-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: 44.86  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  37 VETDVVSNTSGSARVKLGHTDILVGVkaeMGtPKlekPNEGYLEFF----VDCSAS----ATPEFEGRGGDDLGTEIANT 108
Cdd:cd11371    6 LKTGVVSQAKGSAYVELGNTKVICSV---YG-PR---PIPGRTEFSdrgrLNCEVKfapfATPGRRRHGQDSEERELSSL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 109 LYRIFNnkSSVDLKTLcisPREhcwVLYVDVLLLECGGNLFDAISIAVKAALfntriprvrvledeeGSKDIELsddpYD 188
Cdd:cd11371   79 LHQALE--PAVRLEKY---PKS---QIDVFVTVLESDGSVLAAAITAASLAL---------------ADAGIEM----YD 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688 189 CIrlsvenVPCivTLCKIGYRHVVDATLQEEACSLASLLVSV-TSKGVVTCMrkVGKGSLDPESIFEMMETG----KRVG 263
Cdd:cd11371  132 LV------TAC--SAALIGDELLLDPTREEEEASSGGVMLAYmPSLNQVTQL--WQSGEMDVDQLEEALDLCidgcNRIH 201


                 ....*....
gi 189083688 264 KVLHASLQS 272
Cdd:cd11371  202 PVVRQALLE 210
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 19-79 1.46e-05

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 45.40  E-value: 1.46e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 189083688  19 QEDLRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVKA--EMGTPKLEKPNEGYL 79
Cdd:PRK03983  11 EDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAVYGprEMHPRHLQLPDRAVL 73
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 22-113 5.99e-03

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: 37.14  E-value: 5.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 189083688  22 LRVDGRGCEDYRCVEVETDVVSNTSGSARVKLGHTDILVGVK--AEMGTPKLEKPNEGylefFVDCSASATP--EFEGR- 96
Cdd:cd11370    2 LRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYgpHEPRNRSQALHDRA----VVNCEYSMATfsTGERKr 77

                         90
                 ....*....|....*....
gi 189083688  97 --GGDDLGTEIANTLYRIF 113
Cdd:cd11370   78 rgKGDRRSTELSLAIRQTF 96
 
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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