NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|254675240|ref|NP_001157042|]
View 

exosome complex component RRP43 isoform 1 [Mus musculus]

Protein Classification

exosome complex component RRP43( domain architecture ID 10183523)

exosome complex component RRP43 similar to Saccharomyces cerevisiae exosome RRP43 subunit which is involved in pre-rRNA processing and found both in the nucleus and in the cytoplasm.

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_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 6-270 1.21e-160

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: 446.62  E-value: 1.21e-160
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240   6 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVflsvP 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLV----P 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  86 NVDLPPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:cd11369   77 NVDLPPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALK 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:cd11369  157 NLRLPAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGS 236

                        250       260
                 ....*....|....*....|....*
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLL 270
Cdd:cd11369  237 PLSQAQLQECIELAKKRAKELQKLI 261
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 6-270 1.21e-160

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: 446.62  E-value: 1.21e-160
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240   6 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVflsvP 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLV----P 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  86 NVDLPPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:cd11369   77 NVDLPPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALK 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:cd11369  157 NLRLPAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGS 236

                        250       260
                 ....*....|....*....|....*
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLL 270
Cdd:cd11369  237 PLSQAQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
12-276 5.13e-79

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 240.16  E-value: 5.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGyvVFlsVPNVDLPP 91
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEG--VL--IVNAELLP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  92 LCSSRFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:PRK04282  90 LASPTFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALL 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:PRK04282 164 NTKVPAVEEGEDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG 240

                        250       260       270
                 ....*....|....*....|....*....|.
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLLDEVIQS 276
Cdd:PRK04282 241 SFTEEEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 12-271 1.72e-75

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: 230.84  E-value: 1.72e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGyvVFlsVPNVDLPP 91
Cdd:COG2123   12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEG--VL--IVNAELLP 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  92 LCSSRFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:COG2123   88 LASPTFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:COG2123  162 TTKVPKVEVGEDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSG 238

                        250       260
                 ....*....|....*....|....*.
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLLD 271
Cdd:COG2123  239 SFTEEEIDKAIDIALEKGKELRELLK 264
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-170 2.43e-29

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


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 108.06  E-value: 2.43e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240   31 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVFlsvpNVDLPPLCSSRF-RTGPPGEEAQVT 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTV----EYELAPFASGERpGEGRPSEREIEI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 254675240  110 SQFIADVVdnsqvikkEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 170
Cdd:pfam01138  77 SRLIDRAL--------RPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
 
Name Accession Description Interval E-value
RNase_PH_RRP43 cd11369
RRP43 subunit of eukaryotic exosome; The RRP43 subunit of eukaryotic exosome is a member of ...
 6-270 1.21e-160

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: 446.62  E-value: 1.21e-160
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240   6 KTVEPLEYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVflsvP 85
Cdd:cd11369    1 KKLHPLEYYRRFLAENVRPDGRELDEFRPTSVNVGSISTADGSALVKLGNTTVLCGIKAEVATPAADTPDEGYLV----P 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  86 NVDLPPLCSSRFRTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:cd11369   77 NVDLPPLCSSKFRPGPPSEEAQVLSSFLADILLNSNVLDLEQLCIVPGKLAWVLYCDVYCLDYDGNLLDAALLALVAALK 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETALAEVNLKKKSYLNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:cd11369  157 NLRLPAVTIDEETELVVVNPEERRPLNLKNLPVSTTFAVFDDKHLLADPTAEEELLASGLVTVVVDENGELCSVHKPGGS 236

                        250       260
                 ....*....|....*....|....*
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLL 270
Cdd:cd11369  237 PLSQAQLQECIELAKKRAKELQKLI 261
PRK04282 PRK04282
exosome complex protein Rrp42;
12-276 5.13e-79

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 240.16  E-value: 5.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGyvVFlsVPNVDLPP 91
Cdd:PRK04282  14 DYILSLLKKGKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGNTQVLAGVKLEIGEPFPDTPNEG--VL--IVNAELLP 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  92 LCSSRFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:PRK04282  90 LASPTFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDVYVLDHDGNLLDASMLAAVAALL 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:PRK04282 164 NTKVPAVEEGEDG--VVDKLGEDFPLPVNDKPVTVTFAKIGN-YLIVDPTLEEESVMDARITITTDEDGNIVAIQKSGIG 240

                        250       260       270
                 ....*....|....*....|....*....|.
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLLDEVIQS 276
Cdd:PRK04282 241 SFTEEEVDKAIDIALEKAKELREKLKEALGI 271
Rrp42 COG2123
Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, ...
 12-271 1.72e-75

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: 230.84  E-value: 1.72e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGyvVFlsVPNVDLPP 91
Cdd:COG2123   12 DYILSLLKKGKRIDGRGLDEYRPIEIETGVIEKAEGSALVKLGNTQVLAGVKVEPGEPFPDTPNEG--VL--IVNAELLP 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  92 LCSSRFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:COG2123   88 LASPTFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWMVFIDIYVLDYDGNLFDASSLAAVAALL 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDtLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:COG2123  162 TTKVPKVEVGEDG--VVVDKGEDTPLPVNTLPVSVTMAKIGD-YLVVDPTLEEESVMDARITITTDEDGNIVAMQKGGSG 238

                        250       260
                 ....*....|....*....|....*.
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKLLD 271
Cdd:COG2123  239 SFTEEEIDKAIDIALEKGKELRELLK 264
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
 12-269 5.49e-75

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: 229.41  E-value: 5.49e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  12 EYYRRFLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGyvVFLSvpNVDLPP 91
Cdd:cd11365    6 DYILSLLEKGKRIDGRGLDEYRDIEIETGVIPKAEGSALVKLGNTQVLAGVKLEVGEPFPDTPNEG--VLIV--NAELLP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  92 LCSSRFRTGPPGEEAqvtsqfI--ADVVD----NSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALK 165
Cdd:cd11365   82 LASPTFEPGPPDENA------IelARVVDrgirESKAIDLEKLVIEPGKKVWVVFIDIYVLDYDGNLFDASALAAVAALL 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 166 NVQLPEVTINEETalAEVNLKKKSYLNVRTNPVATSFAVFDDTlLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGS 245
Cdd:cd11365  156 NTKVPEYEVDENE--VIEVLGEELPLPVNTLPVSVTVAKIGGY-IVVDPTLEEELVMDARITITIDEDGNIVALQKGGGG 232

                        250       260
                 ....*....|....*....|....
gi 254675240 246 GLTGAKLQDCMSRAVTRHKEVSKL 269
Cdd:cd11365  233 SFTEDEIDKAIDIALEKAAELREK 256
RNase_PH cd11358
RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...
 32-266 1.31e-74

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: 227.21  E-value: 1.31e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  32 FRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVD-APDRGYVVflsvPNVDLPPLCSSRFRTGPPGEEAQVTS 110
Cdd:cd11358    1 FRPVEIETGVLNQADGSALVKLGNTKVICAVTGPIVEPDKLeRPDKGTLY----VNVEISPGAVGERRQGPPGDEEMEIS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 111 QFIADVVDNSQVIKKedlciSPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETalaevnlkkKSY 190
Cdd:cd11358   77 RLLERTIEASVILDK-----STRKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPRVFVDERS---------PPL 142

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 254675240 191 LNVRTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCMSRAVTRHKEV 266
Cdd:cd11358  143 LLMKDLIVAVSVGGISDGVLLLDPTGEEEELADSTLTVAVDKSGKLCLLSKVGGGSLDTEEIKECLELAKKRSLHL 218
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
 18-269 5.90e-57

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: 183.50  E-value: 5.90e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  18 LKENCRPDGRELGEFRATTVNIGsisTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVFlsvpNVDLPPLCSSRF 97
Cdd:cd11368   13 LKEGLRLDGRGLDEFRPIKITFG---LEYGCVEVSLGKTRVLAQVSCEIVEPKPDRPNEGILFI----NVELSPMASPAF 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  98 RTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEE 177
Cdd:cd11368   86 EPGRPSEEEVELSRLLERALRDSRAVDTESLCIIAGEKVWSIRVDVHVLNHDGNLIDAASLAAIAALMHFRRPDVTVDGE 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 178 talaEVNLKKKSY-----LNVRTNPVATSFAVFDD-TLLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAK 251
Cdd:cd11368  166 ----EVTVHSPEErepvpLSIHHIPICVTFAFFDDgEIVVVDPTLLEEAVADGSLTVALNKHREICALSKSGGAPLSPSQ 241

                        250
                 ....*....|....*...
gi 254675240 252 LQDCMSRAVTRHKEVSKL 269
Cdd:cd11368  242 ILRCVKIAAAKAKELTEL 259
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
 18-274 6.40e-53

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: 173.55  E-value: 6.40e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  18 LKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVFlsvpNVDLPPLCSSRF 97
Cdd:cd11367   14 VEQNIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGNTDVLVGVKAEVGSPDPETPNKGRLEF----FVDCSPNASPEF 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  98 RTGPPGEEAQVTSQFIADVVDNSQVIKKEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEE 177
Cdd:cd11367   90 EGRGGEELATELSSALERALKSGSAIDLSKLCIVPGKQCWVLYVDVLVLESGGNLLDAISIAVKAALFNTRIPKVEVSED 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 178 TA-LAEVNLKKK----SYLNVRTNPVATSFAVFDDTlLIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKL 252
Cdd:cd11367  170 DEgTKEIELSDDpydvKRLDVSNVPLIVTLSKIGNR-HIVDATAEEEACSSARLLVAVNAKGRICGVQKSGGGSLEPESI 248

                        250       260
                 ....*....|....*....|..
gi 254675240 253 QDCMSRAVTRHKEVSKLLDEVI 274
Cdd:cd11367  249 IEMIETAKEVGKKLNAALDKAL 270
RNase_PH pfam01138
3' exoribonuclease family, domain 1; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 31-170 2.43e-29

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


Pssm-ID: 426074 [Multi-domain]  Cd Length: 129  Bit Score: 108.06  E-value: 2.43e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240   31 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVFlsvpNVDLPPLCSSRF-RTGPPGEEAQVT 109
Cdd:pfam01138   1 ELRPIEIETGVLSQADGSALVELGDTKVLATVTGPIEPKEDRDFAPGRLTV----EYELAPFASGERpGEGRPSEREIEI 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 254675240  110 SQFIADVVdnsqvikkEDLCISPGKLAWVLYCDLICLDYDGNILDACTFALLAALKNVQLP 170
Cdd:pfam01138  77 SRLIDRAL--------RPSIPLEGYPRWTIRIDVTVLSSDGSLLDAAINAASLALADAGIP 129
RNase_PH_C pfam03725
3' exoribonuclease family, domain 2; This family includes 3'-5' exoribonucleases. Ribonuclease ...
 197-259 2.56e-16

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: 71.45  E-value: 2.56e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 254675240  197 PVATSFAVFDDTLlIVDPTGEEEHLSTGTLTVVTDEDGKLCCLHKPGGSGLTGAKLQDCMSRA 259
Cdd:pfam03725   3 VAAVTVGKIDGQL-VVDPTLEEESLSDSDLTVAVAGTGEIVALMKEGGAGLTEDELLEALELA 64
RNase_PH_RRP46 cd11372
RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...
 33-261 7.67e-07

RRP46 subunit of eukaryotic exosome; The RRP46 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: 206777 [Multi-domain]  Cd Length: 199  Bit Score: 48.71  E-value: 7.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  33 RATTVNIGSISTADGSALVKLGNTTVICGVKAefaapPVDA------PDRGYVvflsvpNVDLPPlcssrfRTGPPGEEA 106
Cdd:cd11372    2 RPLSCELGLLSRADGSARFSQGDTSVLAAVYG-----PIEVklrkelPDRATL------EVIVRP------KSGLPGVKE 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 107 QVTSQFIADVVDNsqVIKKED---LCISpgklawvlycdLIC--LDYDGNILDACTFALLAALKNvqlpevtineetalA 181
Cdd:cd11372   65 KLLELLLRSTLEP--IILLHLhprTLIS-----------VVLqvLQDDGSLLACAINAACLALLD--------------A 117

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 182 EVNLKkksylnvrTNPVATSFAVFDDTLLIVDPTGEEEHLSTGTLTVVTD--EDGKLCCLHKPGgsGLTGAKLQDCMSRA 259
Cdd:cd11372  118 GVPMK--------GLFAAVTCAITEDGEIILDPTAEEEKEAKAVATFAFDsgEEKNLVLSESEG--SFTEEELFACLELA 187


                 ..
gi 254675240 260 VT 261
Cdd:cd11372  188 QA 189
PRK03983 PRK03983
exosome complex exonuclease Rrp41; Provisional
 17-62 1.90e-06

exosome complex exonuclease Rrp41; Provisional


Pssm-ID: 235187 [Multi-domain]  Cd Length: 244  Bit Score: 47.71  E-value: 1.90e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 254675240  17 FLKENCRPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGV 62
Cdd:PRK03983   9 ILEDGLRLDGRKPDELRPIKIEVGVLKNADGSAYLEWGNNKIIAAV 54
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
23-60 3.60e-06

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 46.95  E-value: 3.60e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 254675240  23 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVIC 60
Cdd:COG0689    2 RPDGRAPDQLRPVKITRGFTKHAEGSVLIEFGDTKVLC 39
RNase_PH_RRP41 cd11370
RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...
 23-63 4.96e-06

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: 46.38  E-value: 4.96e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 254675240  23 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVK 63
Cdd:cd11370    3 RLDGRRPNELRRIRCRIGVFSSADGSAYLEQGNTKVLAAVY 43
rph PRK00173
ribonuclease PH; Reviewed
 23-70 6.53e-06

ribonuclease PH; Reviewed


Pssm-ID: 178914  Cd Length: 238  Bit Score: 46.26  E-value: 6.53e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 254675240  23 RPDGRELGEFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPP 70
Cdd:PRK00173   2 RPDGRAADQLRPVTITRNFTKHAEGSVLVEFGDTKVLCTASVEEGVPR 49
RNase_PH_MTR3 cd11371
MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...
 32-228 1.95e-04

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: 41.40  E-value: 1.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240  32 FRATTVNIGSISTADGSALVKLGNTTVICGV--------KAEFAappvdapDRGYVvflsvpNVDL---PPLCSSRFRTG 100
Cdd:cd11371    1 IRPIFLKTGVVSQAKGSAYVELGNTKVICSVygprpipgRTEFS-------DRGRL------NCEVkfaPFATPGRRRHG 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 254675240 101 PPGEEAQVTS---QFIADVVD-----NSQVikkeDLCISpgklawvlycdliCLDYDGNILDACTFALLAALKNVQLPEV 172
Cdd:cd11371   68 QDSEERELSSllhQALEPAVRlekypKSQI----DVFVT-------------VLESDGSVLAAAITAASLALADAGIEMY 130

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 254675240 173 TIneetalaevnlkkksylnvrtnpVATSFAVFDDTLLIVDPTGEEEHLSTGTLTV 228
Cdd:cd11371  131 DL-----------------------VTACSAALIGDELLLDPTREEEEASSGGVML 163
RNase_PH_archRRP41 cd11366
RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...
 31-62 2.96e-03

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: 38.08  E-value: 2.96e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 254675240  31 EFRATTVNIGSISTADGSALVKLGNTTVICGV 62
Cdd:cd11366    1 ELRPIKIEVGVLKNADGSAYVEWGNNKIIAAV 32
RNase_PH_bact cd11362
Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that ...
 31-70 3.64e-03

Ribonuclease PH; Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA.


Pssm-ID: 206767 [Multi-domain]  Cd Length: 227  Bit Score: 37.98  E-value: 3.64e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 254675240  31 EFRATTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPP 70
Cdd:cd11362    1 QLRPISITRGFNKHAEGSVLIEFGDTKVLCTASVEEKVPP 40
 
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