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Conserved domains on  [gi|2462588209|ref|XP_054201729|]
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exosome complex component RRP42 isoform X2 [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 ...
 5-195 3.56e-110

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: 316.46  E-value: 3.56e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   5 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 84
Cdd:cd11367    82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  85 PRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 164
Cdd:cd11367   162 PKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGG 241

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2462588209 165 SLDPESIFEMMETGKRVGKVLHASLQSVVHK 195
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 ...
 5-195 3.56e-110

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: 316.46  E-value: 3.56e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   5 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 84
Cdd:cd11367    82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  85 PRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 164
Cdd:cd11367   162 PKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGG 241

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2462588209 165 SLDPESIFEMMETGKRVGKVLHASLQSVVHK 195
Cdd:cd11367   242 SLEPESIIEMIETAKEVGKKLNAALDKALKE 272
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 38-186 4.22e-36

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: 127.23  E-value: 4.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  38 VDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVleDEEGSKDIELSDDPydcirLSVENVP 117
Cdd:COG2123   119 IDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEV--GEDGVVVDKGEDTP-----LPVNTLP 191

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462588209 118 CIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLH 186
Cdd:COG2123   192 VSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEEIDKAIDIALEKGKELR 260
PRK04282 PRK04282
exosome complex protein Rrp42;
8-193 1.38e-35

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 126.14  E-value: 1.38e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   8 ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRV 87
Cdd:PRK04282   91 ASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAV 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  88 RvlEDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLD 167
Cdd:PRK04282  171 E--EGEDGVVDKLGEDFP-----LPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFT 243

                         170       180
                  ....*....|....*....|....*.
gi 2462588209 168 PESIFEMMETGKRVGKVLHASLQSVV 193
Cdd:PRK04282  244 EEEVDKAIDIALEKAKELREKLKEAL 269
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 115-180 1.23e-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: 65.68  E-value: 1.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462588209 115 NVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKR 180
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKE 66
 
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 ...
 5-195 3.56e-110

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: 316.46  E-value: 3.56e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   5 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 84
Cdd:cd11367    82 SPNASPEFEGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRI 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  85 PRVRVLEDEEGSKDIELSDDPYDCIRLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKG 164
Cdd:cd11367   162 PKVEVSEDDEGTKEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGG 241

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2462588209 165 SLDPESIFEMMETGKRVGKVLHASLQSVVHK 195
Cdd:cd11367   242 SLEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 3-185 2.01e-43

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: 144.78  E-value: 2.01e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   3 SSSASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDlktlcISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNT 82
Cdd:cd11358    54 EISPGAVGERRQGPPGDEEMEISRLLERTIEASVILD-----KSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDA 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  83 RIPRVRVLEdeegskdielsddpYDCIRLSVENVPCIVTLCKI-GYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKV 161
Cdd:cd11358   129 GIPRVFVDE--------------RSPPLLLMKDLIVAVSVGGIsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKV 194

                         170       180
                  ....*....|....*....|....
gi 2462588209 162 GKGSLDPESIFEMMETGKRVGKVL 185
Cdd:cd11358   195 GGGSLDTEEIKECLELAKKRSLHL 218
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 38-186 4.22e-36

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: 127.23  E-value: 4.22e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  38 VDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVleDEEGSKDIELSDDPydcirLSVENVP 117
Cdd:COG2123   119 IDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEV--GEDGVVVDKGEDTP-----LPVNTLP 191

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462588209 118 CIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKRVGKVLH 186
Cdd:COG2123   192 VSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEEIDKAIDIALEKGKELR 260
PRK04282 PRK04282
exosome complex protein Rrp42;
8-193 1.38e-35

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 126.14  E-value: 1.38e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   8 ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRV 87
Cdd:PRK04282   91 ASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVPAV 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  88 RvlEDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLD 167
Cdd:PRK04282  171 E--EGEDGVVDKLGEDFP-----LPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGSFT 243

                         170       180
                  ....*....|....*....|....*.
gi 2462588209 168 PESIFEMMETGKRVGKVLHASLQSVV 193
Cdd:PRK04282  244 EEEVDKAIDIALEKAKELREKLKEAL 269
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 8-186 8.89e-35

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: 123.48  E-value: 8.89e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   8 ATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRV 87
Cdd:cd11365    83 ASPTFEPGPPDENAIELARVVDRGIRESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPEY 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  88 RVleDEEGSKDIELSDDPydcirLSVENVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLD 167
Cdd:cd11365   163 EV--DENEVIEVLGEELP-----LPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGGSFT 235

                         170
                  ....*....|....*....
gi 2462588209 168 PESIFEMMETGKRVGKVLH 186
Cdd:cd11365   236 EDEIDKAIDIALEKAAELR 254
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 5-187 6.30e-26

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: 100.68  E-value: 6.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   5 SASATPEFEGRGGDDLGTEIANTLYRIFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRI 84
Cdd:cd11368    78 SPMASPAFEPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRR 157

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  85 PRVRVledeEGSKDIELSDDPYDCIRLSVENVPCIVT--LCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVG 162
Cdd:cd11368   158 PDVTV----DGEEVTVHSPEEREPVPLSIHHIPICVTfaFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSG 233

                         170       180
                  ....*....|....*....|....*
gi 2462588209 163 KGSLDPESIFEMMETGKRVGKVLHA 187
Cdd:cd11368   234 GAPLSPSQILRCVKIAAAKAKELTE 258
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 31-180 9.47e-24

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: 94.93  E-value: 9.47e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209  31 IFNNKSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVleDEEGSKDIELSDDPydcIR 110
Cdd:cd11369   107 ILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRLPAVTI--DEETELVVVNPEER---RP 181

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462588209 111 LSVENVPCIVTLCKIGYRHV-VDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKR 180
Cdd:cd11369   182 LNLKNLPVSTTFAVFDDKHLlADPTAEEELLASGLVTVVVDENGELCSVHKPGGSPLSQAQLQECIELAKK 252
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 115-180 1.23e-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: 65.68  E-value: 1.23e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462588209 115 NVPCIVTLCKIGYRHVVDATLQEEACSLASLLVSVTSKGVVTCMRKVGKGSLDPESIFEMMETGKR 180
Cdd:pfam03725   1 DPVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAKE 66
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 5-85 9.47e-12

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: 59.91  E-value: 9.47e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462588209   5 SASATPEFEGRGG-DDLGTEIANTLYRIFnnKSSVDLktlcisPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTR 83
Cdd:pfam01138  56 APFASGERPGEGRpSEREIEISRLIDRAL--RPSIPL------EGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAG 127


                  ..
gi 2462588209  84 IP 85
Cdd:pfam01138 128 IP 129
 
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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