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Conserved domains on  [gi|28573444|ref|NP_725517|]
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Rrp42 [Drosophila melanogaster]

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 ...
 5-278 5.16e-133

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: 378.09  E-value: 5.16e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   5 ALSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVD 84
Cdd:cd11367   1 KLSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  85 CSANATPEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTK 164
Cdd:cd11367  81 CSPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTR 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 165 LPRVTATMLDAGITDLIISDNPYDCTRIGIETVPLLVTVCKIGDYVLVDPSAEEEVCSTVSMVVSVsmrNGQAFLSGTHL 244
Cdd:cd11367 161 IPKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAV---NAKGRICGVQK 237

                       250       260       270
                ....*....|....*....|....*....|....
gi 28573444 245 TGGGAMHRDTMRNCLELGLAIGEHLDRLLTKMLN 278
Cdd:cd11367 238 SGGGSLEPESIIEMIETAKEVGKKLNAALDKALK 271
 
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 ...
 5-278 5.16e-133

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: 378.09  E-value: 5.16e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   5 ALSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVD 84
Cdd:cd11367   1 KLSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  85 CSANATPEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTK 164
Cdd:cd11367  81 CSPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTR 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 165 LPRVTATMLDAGITDLIISDNPYDCTRIGIETVPLLVTVCKIGDYVLVDPSAEEEVCSTVSMVVSVsmrNGQAFLSGTHL 244
Cdd:cd11367 161 IPKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAV---NAKGRICGVQK 237

                       250       260       270
                ....*....|....*....|....*....|....
gi 28573444 245 TGGGAMHRDTMRNCLELGLAIGEHLDRLLTKMLN 278
Cdd:cd11367 238 SGGGSLEPESIIEMIETAKEVGKKLNAALDKALK 271
PRK04282 PRK04282
exosome complex protein Rrp42;
6-220 2.01e-46

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 156.96  E-value: 2.01e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444    6 LSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVDC 85
Cdd:PRK04282   8 IPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAEL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   86 SANATPEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKL 165
Cdd:PRK04282  88 LPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 28573444  166 PRVTatmldagITDLIISDNPYDCTRIGIETVPLLVTVCKIGDYVLVDPSAEEEV 220
Cdd:PRK04282 168 PAVE-------EGEDGVVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEES 215
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 1-221 1.31e-44

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: 152.26  E-value: 1.31e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   1 MAYVALSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLE 80
Cdd:COG2123   1 MSSPIIPEIKRDYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  81 ffvdCSAN----ATPEFEGrGGSDlaqelilslQNAYE----------SPLAFNYRTLCLIPGQQCWKLYIDILILECGG 146
Cdd:COG2123  81 ----VNAEllplASPTFEP-GPPD---------ENAIElarvvdrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDG 146

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28573444 147 NLHDAVSLAAKAALFNTKLPRVTatMLDAGItdlIISDNPYdcTRIGIETVPLLVTVCKIGDYVLVDPSAEEEVC 221
Cdd:COG2123 147 NLFDASSLAAVAALLTTKVPKVE--VGEDGV---VVDKGED--TPLPVNTLPVSVTMAKIGDYLVVDPTLEEESV 214
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 1.51e-27

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: 103.44  E-value: 1.51e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444    31 DYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVDCSANATPEFEGRGG-SDLAQELILSL 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRpSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 28573444   110 QNAYESplafnyrtLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKLP 166
Cdd:pfam01138  81 DRALRP--------SIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 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 ...
 5-278 5.16e-133

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: 378.09  E-value: 5.16e-133
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   5 ALSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVD 84
Cdd:cd11367   1 KLSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVD 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  85 CSANATPEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTK 164
Cdd:cd11367  81 CSPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTR 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 165 LPRVTATMLDAGITDLIISDNPYDCTRIGIETVPLLVTVCKIGDYVLVDPSAEEEVCSTVSMVVSVsmrNGQAFLSGTHL 244
Cdd:cd11367 161 IPKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAV---NAKGRICGVQK 237

                       250       260       270
                ....*....|....*....|....*....|....
gi 28573444 245 TGGGAMHRDTMRNCLELGLAIGEHLDRLLTKMLN 278
Cdd:cd11367 238 SGGGSLEPESIIEMIETAKEVGKKLNAALDKALK 271
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 11-220 2.02e-47

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: 159.30  E-value: 2.02e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  11 KTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVDCSANAT 90
Cdd:cd11365   5 RDYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLAS 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  91 PEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKLPRVta 170
Cdd:cd11365  85 PTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEY-- 162

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 28573444 171 tmldaGITDLIISDNPYDCTRIGIETVPLLVTVCKIGDYVLVDPSAEEEV 220
Cdd:cd11365 163 -----EVDENEVIEVLGEELPLPVNTLPVSVTVAKIGGYIVVDPTLEEEL 207
PRK04282 PRK04282
exosome complex protein Rrp42;
6-220 2.01e-46

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 156.96  E-value: 2.01e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444    6 LSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVDC 85
Cdd:PRK04282   8 IPEIKKDYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAEL 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   86 SANATPEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKL 165
Cdd:PRK04282  88 LPLASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKV 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 28573444  166 PRVTatmldagITDLIISDNPYDCTRIGIETVPLLVTVCKIGDYVLVDPSAEEEV 220
Cdd:PRK04282 168 PAVE-------EGEDGVVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEES 215
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 1-221 1.31e-44

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: 152.26  E-value: 1.31e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   1 MAYVALSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLE 80
Cdd:COG2123   1 MSSPIIPEIKRDYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLI 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  81 ffvdCSAN----ATPEFEGrGGSDlaqelilslQNAYE----------SPLAFNYRTLCLIPGQQCWKLYIDILILECGG 146
Cdd:COG2123  81 ----VNAEllplASPTFEP-GPPD---------ENAIElarvvdrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDG 146

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 28573444 147 NLHDAVSLAAKAALFNTKLPRVTatMLDAGItdlIISDNPYdcTRIGIETVPLLVTVCKIGDYVLVDPSAEEEVC 221
Cdd:COG2123 147 NLFDASSLAAVAALLTTKVPKVE--VGEDGV---VVDKGED--TPLPVNTLPVSVTMAKIGDYLVVDPTLEEESV 214
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-269 1.42e-36

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: 130.14  E-value: 1.42e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  32 YRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLT-PEFGKLEFFVDCSANATPEFEGRGGSDLAQELILSLQ 110
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLErPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 111 NAYEsplafNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKLPRVTAtmldagitdliisdNPYDCT 190
Cdd:cd11358  81 RTIE-----ASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFV--------------DERSPP 141

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 191 RIGIETVPLLVTVCKIGDYV-LVDPSAEEEVCSTVSMVVSVSMRNGqafLSGTHLTGGGAMHRDTMRNCLELGLAIGEHL 269
Cdd:cd11358 142 LLLMKDLIVAVSVGGISDGVlLLDPTGEEEELADSTLTVAVDKSGK---LCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 11-261 1.07e-34

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: 126.13  E-value: 1.07e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  11 KTYILHGVeddfRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVD----CS 86
Cdd:cd11369  10 RRFLAENV----RPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDlpplCS 85

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  87 ANATPefeGRGgSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKLP 166
Cdd:cd11369  86 SKFRP---GPP-SEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLP 161

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 167 RVTATmldagITDLIISDNPYDCTRIGIETVPLLVTVCKI-GDYVLVDPSAEEEVcSTVSMVVSVSMRNGQafLSGTHLT 245
Cdd:cd11369 162 AVTID-----EETELVVVNPEERRPLNLKNLPVSTTFAVFdDKHLLADPTAEEEL-LASGLVTVVVDENGE--LCSVHKP 233

                       250
                ....*....|....*.
gi 28573444 246 GGGAMHRDTMRNCLEL 261
Cdd:cd11369 234 GGSPLSQAQLQECIEL 249
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 6-272 2.74e-31

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: 117.24  E-value: 2.74e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   6 LSEAEKTYILHGVEDDFRCDGRSRRDYRPMDLETGLvsnASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVDC 85
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFGL---EYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVEL 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  86 SANATPEFEGRGGSDLAQELILSLQNAYESPLAFNYRTLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKL 165
Cdd:cd11368  78 SPMASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRR 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 166 PRVTATmldaGITDLIISDNPYDCTRIGIETVPLLVTVC--KIGDYVLVDPSAEEEVCSTVSMVVSVsmrNGQAFLSGTH 243
Cdd:cd11368 158 PDVTVD----GEEVTVHSPEEREPVPLSIHHIPICVTFAffDDGEIVVVDPTLLEEAVADGSLTVAL---NKHREICALS 230

                       250       260
                ....*....|....*....|....*....
gi 28573444 244 LTGGGAMHRDTMRNCLELGLAIGEHLDRL 272
Cdd:cd11368 231 KSGGAPLSPSQILRCVKIAAAKAKELTEL 259
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-166 1.51e-27

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: 103.44  E-value: 1.51e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444    31 DYRPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPNPLTPEFGKLEFFVDCSANATPEFEGRGG-SDLAQELILSL 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRpSEREIEISRLI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 28573444   110 QNAYESplafnyrtLCLIPGQQCWKLYIDILILECGGNLHDAVSLAAKAALFNTKLP 166
Cdd:pfam01138  81 DRALRP--------SIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 33-264 9.58e-10

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: 57.19  E-value: 9.58e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  33 RPMDLETGLVSNASGSARLRLANTDILVGVKTEIDVPnPLTPEFGKLEFFVDCS-AN-ATPEFEGRGGSDLAQELILSLQ 110
Cdd:cd11371   2 RPIFLKTGVVSQAKGSAYVELGNTKVICSVYGPRPIP-GRTEFSDRGRLNCEVKfAPfATPGRRRHGQDSEERELSSLLH 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 111 NAYESplafnyrTLCL--IPgqqcwKLYID--ILILECGGNLHDAVSLAAKAALfntklprvtatmLDAGI--TDLIISd 184
Cdd:cd11371  81 QALEP-------AVRLekYP-----KSQIDvfVTVLESDGSVLAAAITAASLAL------------ADAGIemYDLVTA- 135

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 185 npydctrigietvpllVTVCKIGDYVLVDPSAEEEVCSTVSMVvsvsmrngQAFLSG----THLTGGGAMHRDTMRNCLE 260
Cdd:cd11371 136 ----------------CSAALIGDELLLDPTREEEEASSGGVM--------LAYMPSlnqvTQLWQSGEMDVDQLEEALD 191


                ....
gi 28573444 261 LGLA 264
Cdd:cd11371 192 LCID 195
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 196-265 1.04e-08

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: 51.04  E-value: 1.04e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444   196 TVPLLVTVCKIGDYVLVDPSAEEEVCSTVSMVVSVsmrNGQAFLSGTHLTGGGAMHRDTMRNCLELGLAI 265
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAV---AGTGEIVALMKEGGAGLTEDELLEALELAKEA 67
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 33-262 6.13e-07

RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA.


Pssm-ID: 206771 [Multi-domain]  Cd Length: 214  Bit Score: 49.25  E-value: 6.13e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  33 RPMDLETGLVSNASGSARLRLANTDILVGV--KTEIDVPNPLTPEFGKLEFFVDCSANATPEFEGRGGSDLAQELILSLQ 110
Cdd:cd11366   3 RPIKIEVGVLKNADGSAYVEWGNNKIIAAVygPREVHPRHLQLPDRAVIRVRYNMAPFSVDERKRPGPDRREIEISKVIK 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 111 NAYESPLAFNyrtlcLIPgqqcwKLYIDIL--ILECGGNLHDAVSLAAKAALfntklprvtatmLDAGI--TDLIISdnp 186
Cdd:cd11366  83 EALEPAIILE-----EFP-----RTAIDVFveVLQADAGTRVAGLNAASLAL------------ADAGIpmRDLVAA--- 137

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 28573444 187 ydctrigietvpllVTVCKIGDYVLVDPSAEEEVCSTVSMVVSVSMRNGQAFLsgthLTGGGAMHRDTMRNCLELG 262
Cdd:cd11366 138 --------------CAAGKVDGKIVLDLNKEEDNYGEADMPIAMMPNLGEITL----LQLDGDLTPDEFKQAIELA 195
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 19-62 2.21e-06

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 47.71  E-value: 2.21e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 28573444   19 EDDFRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGV 62
Cdd:PRK03983  11 EDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV 54
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 22-200 2.40e-04

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: 41.37  E-value: 2.40e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444  22 FRCDGRSRRDYRPMDLETGLVSNASGSARLRLANTDILVGVK--TEIDVPNPLTPEFGKLEFFVDCSANATPEFEGRGGS 99
Cdd:cd11370   2 LRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYgpHEPRNRSQALHDRAVVNCEYSMATFSTGERKRRGKG 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573444 100 D-LAQELILSLQNAYESPLAFNyrtlcLIPGQQcwklyIDIL--ILEC-GGNLHDAVSlAAKAALfntklprvtatmLDA 175
Cdd:cd11370  82 DrRSTELSLAIRQTFEAVILTH-----LYPRSQ-----IDIYvqVLQAdGGLLAACIN-AATLAL------------IDA 138

                       170       180
                ....*....|....*....|....*..
gi 28573444 176 GI--TDLIISdnpydCTRIGIETVPLL 200
Cdd:cd11370 139 GIpmKDYVCA-----CSAGYLDSTPLL 160
 
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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