NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|18398046|ref|NP_566318|]
View 

3'-5'-exoribonuclease family protein [Arabidopsis thaliana]

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.

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
3-278 1.25e-132

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: 376.55  E-value: 1.25e-132
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   3 LSLGEQHFIKGGIAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDC 82
Cdd:cd11367   2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  83 SPTAEPTFGGRGGEELSSELALALQRCLLGGKSgagagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAAL 162
Cdd:cd11367  82 SPNASPEFEGRGGEELATELSSALERALKSGSA-----IDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAAL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 163 TNTAIPKVNVSAEvaDDEQPEIDISDEEY--LQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICG 240
Cdd:cd11367 157 FNTRIPKVEVSED--DEGTKEIELSDDPYdvKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICG 234
                       250       260       270
                ....*....|....*....|....*....|....*...
gi 18398046 241 LTKRSGSGLDPSVILDMISVAKHVTETLMSKLDSEISA 278
Cdd:cd11367 235 VQKSGGGSLEPESIIEMIETAKEVGKKLNAALDKALKE 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 ...
3-278 1.25e-132

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: 376.55  E-value: 1.25e-132
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   3 LSLGEQHFIKGGIAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDC 82
Cdd:cd11367   2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  83 SPTAEPTFGGRGGEELSSELALALQRCLLGGKSgagagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAAL 162
Cdd:cd11367  82 SPNASPEFEGRGGEELATELSSALERALKSGSA-----IDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAAL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 163 TNTAIPKVNVSAEvaDDEQPEIDISDEEY--LQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICG 240
Cdd:cd11367 157 FNTRIPKVEVSED--DEGTKEIELSDDPYdvKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICG 234
                       250       260       270
                ....*....|....*....|....*....|....*...
gi 18398046 241 LTKRSGSGLDPSVILDMISVAKHVTETLMSKLDSEISA 278
Cdd:cd11367 235 VQKSGGGSLEPESIIEMIETAKEVGKKLNAALDKALKE 272
PRK04282 PRK04282
exosome complex protein Rrp42;
9-276 9.12e-60

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 191.24  E-value: 9.12e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046    9 HFIKGGIAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAEP 88
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   89 TFGGRGGEELSSELALALQRCLLggKSGAgagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIP 168
Cdd:PRK04282  94 TFEPGPPDENAIELARVVDRGIR--ESKA---IDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVP 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  169 KVNVsaevaddEQPEIDISDEEYLQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGSG 248
Cdd:PRK04282 169 AVEE-------GEDGVVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGS 241
                        250       260
                 ....*....|....*....|....*...
gi 18398046  249 LDPSVILDMISVAKHVTETLMSKLDSEI 276
Cdd:PRK04282 242 FTEEEVDKAIDIALEKAKELREKLKEAL 269
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
15-273 1.44e-57

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: 185.39  E-value: 1.44e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  15 IAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAEPTF-GGR 93
Cdd:COG2123  18 LKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASPTFePGP 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  94 GGEElSSELALALQRCLLggKSGAgagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIPKVNVs 173
Cdd:COG2123  98 PDEN-AIELARVVDRGIR--ESKA---IDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEV- 170
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 174 aevaDDEQPEIDisDEEYLQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGSGLDPSV 253
Cdd:COG2123 171 ----GEDGVVVD--KGEDTPLPVNTLPVSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEE 244
                       250       260
                ....*....|....*....|
gi 18398046 254 ILDMISVAKHVTETLMSKLD 273
Cdd:COG2123 245 IDKAIDIALEKGKELRELLK 264
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
29-168 9.62e-30

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 109.22  E-value: 9.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046    29 YRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAEPTFGGRGG-EELSSELALALQ 107
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRpSEREIEISRLID 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18398046   108 RCLLggksgagaginlsSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIP 168
Cdd:pfam01138  82 RALR-------------PSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 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 ...
3-278 1.25e-132

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: 376.55  E-value: 1.25e-132
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   3 LSLGEQHFIKGGIAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDC 82
Cdd:cd11367   2 LSEAEKSYIIHGVEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEFFVDC 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  83 SPTAEPTFGGRGGEELSSELALALQRCLLGGKSgagagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAAL 162
Cdd:cd11367  82 SPNASPEFEGRGGEELATELSSALERALKSGSA-----IDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAAL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 163 TNTAIPKVNVSAEvaDDEQPEIDISDEEY--LQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICG 240
Cdd:cd11367 157 FNTRIPKVEVSED--DEGTKEIELSDDPYdvKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNAKGRICG 234
                       250       260       270
                ....*....|....*....|....*....|....*...
gi 18398046 241 LTKRSGSGLDPSVILDMISVAKHVTETLMSKLDSEISA 278
Cdd:cd11367 235 VQKSGGGSLEPESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
8-271 6.50e-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: 6.50e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   8 QHFIKGGIAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAE 87
Cdd:cd11365   5 RDYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEGVLIVNAELLPLAS 84
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  88 PTFGGRGGEELSSELALALQRCLLGGKSgagagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAI 167
Cdd:cd11365  85 PTFEPGPPDENAIELARVVDRGIRESKA-----IDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKV 159
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 168 PKVNVSAEVADDEqpeidisDEEYLQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGS 247
Cdd:cd11365 160 PEYEVDENEVIEV-------LGEELPLPVNTLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDEDGNIVALQKGGGG 232
                       250       260
                ....*....|....*....|....
gi 18398046 248 GLDPSVILDMISVAKHVTETLMSK 271
Cdd:cd11365 233 SFTEDEIDKAIDIALEKAAELREK 256
PRK04282 PRK04282
exosome complex protein Rrp42;
9-276 9.12e-60

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 191.24  E-value: 9.12e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046    9 HFIKGGIAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAEP 88
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEGVLIVNAELLPLASP 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   89 TFGGRGGEELSSELALALQRCLLggKSGAgagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIP 168
Cdd:PRK04282  94 TFEPGPPDENAIELARVVDRGIR--ESKA---IDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALLNTKVP 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  169 KVNVsaevaddEQPEIDISDEEYLQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGSG 248
Cdd:PRK04282 169 AVEE-------GEDGVVDKLGEDFPLPVNDKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIGS 241
                        250       260
                 ....*....|....*....|....*...
gi 18398046  249 LDPSVILDMISVAKHVTETLMSKLDSEI 276
Cdd:PRK04282 242 FTEEEVDKAIDIALEKAKELREKLKEAL 269
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
15-273 1.44e-57

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: 185.39  E-value: 1.44e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  15 IAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAEPTF-GGR 93
Cdd:COG2123  18 LKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEGVLIVNAELLPLASPTFePGP 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  94 GGEElSSELALALQRCLLggKSGAgagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIPKVNVs 173
Cdd:COG2123  98 PDEN-AIELARVVDRGIR--ESKA---IDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALLTTKVPKVEV- 170
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 174 aevaDDEQPEIDisDEEYLQFDTSSVPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGSGLDPSV 253
Cdd:COG2123 171 ----GEDGVVVD--KGEDTPLPVNTLPVSVTMAKIGDYLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSGSFTEEE 244
                       250       260
                ....*....|....*....|
gi 18398046 254 ILDMISVAKHVTETLMSKLD 273
Cdd:COG2123 245 IDKAIDIALEKGKELRELLK 264
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
15-270 5.06e-51

RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.


Pssm-ID: 206774 [Multi-domain]  Cd Length: 261  Bit Score: 168.50  E-value: 5.06e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  15 IAQDLRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFID----CSPTAEPtf 90
Cdd:cd11369  13 LAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLVPNVDlpplCSSKFRP-- 90
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  91 gGRGGEE---LSSELALALQRCLLggksgagagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAI 167
Cdd:cd11369  91 -GPPSEEaqvLSSFLADILLNSNV---------LDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALKNLRL 160
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 168 PKVNVSAEvadDEQPEIDIsdEEYLQFDTSSVPVIVTLTKV-GTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSG 246
Cdd:cd11369 161 PAVTIDEE---TELVVVNP--EERRPLNLKNLPVSTTFAVFdDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGG 235
                       250       260
                ....*....|....*....|....
gi 18398046 247 SGLDPSVILDMISVAKHVTETLMS 270
Cdd:cd11369 236 SPLSQAQLQECIELAKKRAKELQK 259
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
3-262 3.65e-41

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: 142.67  E-value: 3.65e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046   3 LSLGEQHFIKGGIAQDLRTDGRKRLTYRPIYVETGvipQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDC 82
Cdd:cd11368   1 LSNNEREFILKALKEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFINVEL 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  83 SPTAEPTFGGRGGEELSSELALALQRCLLGGKSgagagINLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAAL 162
Cdd:cd11368  78 SPMASPAFEPGRPSEEEVELSRLLERALRDSRA-----VDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAAL 152
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 163 TNTAIPKVNVsaevaDDEQPEIDISDE-EYLQFDTSSVPVIVT--LTKVGTHYIVDATAEEESQMSSAVSISVNRTGHIC 239
Cdd:cd11368 153 MHFRRPDVTV-----DGEEVTVHSPEErEPVPLSIHHIPICVTfaFFDDGEIVVVDPTLLEEAVADGSLTVALNKHREIC 227
                       250       260
                ....*....|....*....|...
gi 18398046 240 GLTKRSGSGLDPSVILDMISVAK 262
Cdd:cd11368 228 ALSKSGGAPLSPSQILRCVKIAA 250
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
29-262 5.40e-38

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: 133.22  E-value: 5.40e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  29 YRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQ-PDKGKVAVFIDCSPTAEPTFGGRGGEELSSELALALQ 107
Cdd:cd11358   1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLErPDKGTLYVNVEISPGAVGERRQGPPGDEEMEISRLLE 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 108 RCLLggksgagagiNLSSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIPKVNVSaevaDDEQPEIDIS 187
Cdd:cd11358  81 RTIE----------ASVILDKSTRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVD----ERSPPLLLMK 146
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18398046 188 DeeylqfdtssVPVIVTLTKV-GTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGSGLDPSVILDMISVAK 262
Cdd:cd11358 147 D----------LIVAVSVGGIsDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAK 212
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
29-168 9.62e-30

3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria.


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 109.22  E-value: 9.62e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046    29 YRPIYVETGVIPQANGSARVRIGGTDVIASVKAEIGRPSSLQPDKGKVAVFIDCSPTAEPTFGGRGG-EELSSELALALQ 107
Cdd:pfam01138   2 LRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTVEYELAPFASGERPGEGRpSEREIEISRLID 81
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18398046   108 RCLLggksgagaginlsSLLIKEGKVCWDLYIDGLVISSDGNLLDALGAAIKAALTNTAIP 168
Cdd:pfam01138  82 RALR-------------PSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
30-231 9.61e-11

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: 59.89  E-value: 9.61e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  30 RPIYVETGVIPQANGSARVRIGGTDVIASV----KAEIGRPSSlqpDKGKVAVFIDCSPTAEPTFGGRGGEELSSELALA 105
Cdd:cd11371   2 RPIFLKTGVVSQAKGSAYVELGNTKVICSVygprPIPGRTEFS---DRGRLNCEVKFAPFATPGRRRHGQDSEERELSSL 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046 106 LQRCLLGgksgagaginlSSLLIKEGKVCWDLYIdgLVISSDGNLLDALGAAIKAALTNTAIPKVN-VSAevaddeqpei 184
Cdd:cd11371  79 LHQALEP-----------AVRLEKYPKSQIDVFV--TVLESDGSVLAAAITAASLALADAGIEMYDlVTA---------- 135
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 18398046 185 disdeeylqfdtssvpviVTLTKVGTHYIVDATAEEESQMSSAVSIS 231
Cdd:cd11371 136 ------------------CSAALIGDELLLDPTREEEEASSGGVMLA 164
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
199-262 1.22e-10

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: 56.05  E-value: 1.22e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18398046   199 VPVIVTLTKVGTHYIVDATAEEESQMSSAVSISVNRTGHICGLTKRSGSGLDPSVILDMISVAK 262
Cdd:pfam03725   2 PVAAVTVGKIDGQLVVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELAK 65
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
19-168 1.54e-08

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: 54.09  E-value: 1.54e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  19 LRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASVK--AEIGRPSSLQPDKGKVAVFIDCSptaepTFGG---- 92
Cdd:cd11370   2 LRLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVYgpHEPRNRSQALHDRAVVNCEYSMA-----TFSTgerk 76
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18398046  93 --RGGEELSSELALALQRCLlggksgagaginlssllikEGKVCWDLY------IDGLVISSDGNLLDALGAAIKAALTN 164
Cdd:cd11370  77 rrGKGDRRSTELSLAIRQTF-------------------EAVILTHLYprsqidIYVQVLQADGGLLAACINAATLALID 137

                ....
gi 18398046 165 TAIP 168
Cdd:cd11370 138 AGIP 141
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
19-59 8.54e-07

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 48.86  E-value: 8.54e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 18398046   19 LRTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVIASV 59
Cdd:PRK03983  14 LRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV 54
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
30-59 1.46e-05

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: 45.02  E-value: 1.46e-05
                        10        20        30
                ....*....|....*....|....*....|
gi 18398046  30 RPIYVETGVIPQANGSARVRIGGTDVIASV 59
Cdd:cd11366   3 RPIKIEVGVLKNADGSAYVEWGNNKIIAAV 32
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
20-59 6.91e-04

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 40.01  E-value: 6.91e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 18398046  20 RTDGRKRLTYRPIYVETGVIPQANGSARVRIGGTDVI--ASV 59
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLctASV 43
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
11-46 6.68e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 37.72  E-value: 6.68e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 18398046   11 IKGGIaqdlRTDGRKRLTYRPIYVETGVIPQANGSA 46
Cdd:PRK11824 310 LEEGI----RIDGRKLDEIRPISIEVGVLPRTHGSA 341
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH
HHS Vulnerability Disclosure