NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1227483609|pdb|5VZJ|E]
View 

Chain E, Exosome complex component RRP42

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 ...
6-268 1.23e-81

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: 246.35  E-value: 1.23e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        6 SLSVAEKSYLYDSLAStpSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDgSECIVSIKSKVVDH---HVENELLQV 82
Cdd:cd11367   1 KLSEAEKSYIIHGVEQ--NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGN-TDVLVGVKAEVGSPdpeTPNKGRLEF 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       83 DVDIAGQ-------RDDALVVETITSLLNKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPVSLISFAIYSALN 154
Cdd:cd11367  78 FVDCSPNaspefegRGGEELATELSSALERALKSGSAIDLSKLCIVPgKQCWVLYVDVLVLESGGNLLDAISIAVKAALF 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E      155 STYLPKLISAFDDLE--VEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWS-NGKITSPIR 231
Cdd:cd11367 158 NTRIPKVEVSEDDEGtkEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNaKGRICGVQK 237
                       250       260       270
                ....*....|....*....|....*....|....*..
5VZJ_E      232 SVALNDSNvkSFKPHLLKQGLAMVEKYAPDVVRSLEN 268
Cdd:cd11367 238 SGGGSLEP--ESIIEMIETAKEVGKKLNAALDKALKE 272
 
Name Accession Description Interval E-value
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
6-268 1.23e-81

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: 246.35  E-value: 1.23e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        6 SLSVAEKSYLYDSLAStpSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDgSECIVSIKSKVVDH---HVENELLQV 82
Cdd:cd11367   1 KLSEAEKSYIIHGVEQ--NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGN-TDVLVGVKAEVGSPdpeTPNKGRLEF 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       83 DVDIAGQ-------RDDALVVETITSLLNKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPVSLISFAIYSALN 154
Cdd:cd11367  78 FVDCSPNaspefegRGGEELATELSSALERALKSGSAIDLSKLCIVPgKQCWVLYVDVLVLESGGNLLDAISIAVKAALF 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E      155 STYLPKLISAFDDLE--VEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWS-NGKITSPIR 231
Cdd:cd11367 158 NTRIPKVEVSEDDEGtkEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNaKGRICGVQK 237
                       250       260       270
                ....*....|....*....|....*....|....*..
5VZJ_E      232 SVALNDSNvkSFKPHLLKQGLAMVEKYAPDVVRSLEN 268
Cdd:cd11367 238 SGGGSLEP--ESIIEMIETAKEVGKKLNAALDKALKE 272
PRK04282 PRK04282
exosome complex protein Rrp42;
12-267 2.05e-07

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 51.03  E-value: 2.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        12 KSYLYDSLAStpSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDgSECIVSIKSKVV----DhhVENE-LLQVDVD- 85
Cdd:PRK04282  13 KDYILSLLKK--GKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGN-TQVLAGVKLEIGepfpD--TPNEgVLIVNAEl 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        86 --IAGQ-------RDDAL----VVEtitsllnKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPVSLISFAIYS 151
Cdd:PRK04282  88 lpLASPtfepgppDENAIelarVVD-------RGIRESKAIDLEKLVIEPgKKVWVVFIDVYVLDHDGNLLDASMLAAVA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       152 ALNSTYLPKLIsafddlEVEELPTFHDYDMVKLDIN-PPLVFILAVVGNNMLLDPAANESEVANNGLIISWS-NGKItsp 229
Cdd:PRK04282 161 ALLNTKVPAVE------EGEDGVVDKLGEDFPLPVNdKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDeDGNI--- 231
                        250       260       270
                 ....*....|....*....|....*....|....*...
5VZJ_E       230 irsVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLE 267
Cdd:PRK04282 232 ---VAIQKSGIGSFTEEEVDKAIDIALEKAKELREKLK 266
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
26-70 7.34e-03

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 36.93  E-value: 7.34e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
5VZJ_E       26 RPDGRLPHQFRPIEIFTDFLPSSNGS-------SRIIasdgseCIVSIKSKV 70
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSvliefgdTKVL------CTASVEEGV 47
 
Name Accession Description Interval E-value
RNase_PH_RRP42 cd11367
RRP42 subunit of eukaryotic exosome; The RRP42 subunit of eukaryotic exosome is a member of ...
6-268 1.23e-81

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: 246.35  E-value: 1.23e-81
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        6 SLSVAEKSYLYDSLAStpSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDgSECIVSIKSKVVDH---HVENELLQV 82
Cdd:cd11367   1 KLSEAEKSYIIHGVEQ--NIRNDGRSRLDYRPIELETGVLSNTNGSARVRLGN-TDVLVGVKAEVGSPdpeTPNKGRLEF 77
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       83 DVDIAGQ-------RDDALVVETITSLLNKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPVSLISFAIYSALN 154
Cdd:cd11367  78 FVDCSPNaspefegRGGEELATELSSALERALKSGSAIDLSKLCIVPgKQCWVLYVDVLVLESGGNLLDAISIAVKAALF 157
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E      155 STYLPKLISAFDDLE--VEELPTFHDYDMVKLDINPPLVFILAVVGNNMLLDPAANESEVANNGLIISWS-NGKITSPIR 231
Cdd:cd11367 158 NTRIPKVEVSEDDEGtkEIELSDDPYDVKRLDVSNVPLIVTLSKIGNRHIVDATAEEEACSSARLLVAVNaKGRICGVQK 237
                       250       260       270
                ....*....|....*....|....*....|....*..
5VZJ_E      232 SVALNDSNvkSFKPHLLKQGLAMVEKYAPDVVRSLEN 268
Cdd:cd11367 238 SGGGSLEP--ESIIEMIETAKEVGKKLNAALDKALKE 272
RNase_PH_archRRP42 cd11365
RRP42 subunit of archaeal exosome; The RRP42 subunit of the archaeal exosome is a member of ...
26-262 7.41e-08

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: 52.22  E-value: 7.41e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       26 RPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDgSECIVSIKskvvdhhVENE----------LLQVDVDIA-------- 87
Cdd:cd11365  17 RIDGRGLDEYRDIEIETGVIPKAEGSALVKLGN-TQVLAGVK-------LEVGepfpdtpnegVLIVNAELLplasptfe 88
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       88 -GQRDD-----ALVVEtitsllnKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPVSLISFAIYSALNSTYLPK 160
Cdd:cd11365  89 pGPPDEnaielARVVD-------RGIRESKAIDLEKLVIEPgKKVWVVFIDIYVLDYDGNLFDASALAAVAALLNTKVPE 161
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E      161 liSAFDDLEVEELPTFhdydMVKLDIN-PPLVFILAVVGNNMLLDPAANESEVANNGLIISWS-NGKItspirsVALNDS 238
Cdd:cd11365 162 --YEVDENEVIEVLGE----ELPLPVNtLPVSVTVAKIGGYIVVDPTLEEELVMDARITITIDeDGNI------VALQKG 229
                       250       260
                ....*....|....*....|....
5VZJ_E      239 NVKSFKPHLLKQGLAMVEKYAPDV 262
Cdd:cd11365 230 GGGSFTEDEIDKAIDIALEKAAEL 253
PRK04282 PRK04282
exosome complex protein Rrp42;
12-267 2.05e-07

exosome complex protein Rrp42;


Pssm-ID: 235268 [Multi-domain]  Cd Length: 271  Bit Score: 51.03  E-value: 2.05e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        12 KSYLYDSLAStpSIRPDGRLPHQFRPIEIFTDFLPSSNGSSRIIASDgSECIVSIKSKVV----DhhVENE-LLQVDVD- 85
Cdd:PRK04282  13 KDYILSLLKK--GKRIDGRKLDEYRPIEIETGVIKKAEGSALVKLGN-TQVLAGVKLEIGepfpD--TPNEgVLIVNAEl 87
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        86 --IAGQ-------RDDAL----VVEtitsllnKVLKSGSGVDSSKLQLTK-KYSFKIFVDVLVISSHSHPVSLISFAIYS 151
Cdd:PRK04282  88 lpLASPtfepgppDENAIelarVVD-------RGIRESKAIDLEKLVIEPgKKVWVVFIDVYVLDHDGNLLDASMLAAVA 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       152 ALNSTYLPKLIsafddlEVEELPTFHDYDMVKLDIN-PPLVFILAVVGNNMLLDPAANESEVANNGLIISWS-NGKItsp 229
Cdd:PRK04282 161 ALLNTKVPAVE------EGEDGVVDKLGEDFPLPVNdKPVTVTFAKIGNYLIVDPTLEEESVMDARITITTDeDGNI--- 231
                        250       260       270
                 ....*....|....*....|....*....|....*...
5VZJ_E       230 irsVALNDSNVKSFKPHLLKQGLAMVEKYAPDVVRSLE 267
Cdd:PRK04282 232 ---VAIQKSGIGSFTEEEVDKAIDIALEKAKELREKLK 266
RNase_PH_RRP45 cd11368
RRP45 subunit of eukaryotic exosome; The RRP45 subunit of eukaryotic exosome is a member of ...
7-220 3.88e-05

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: 44.06  E-value: 3.88e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E        7 LSVAEKSYLYDSLASTpsIRPDGRLPHQFRPIEIftDFlPSSNGSSrIIASDGSECIVSIKSKVVDHHVE--NE-LLQVD 83
Cdd:cd11368   1 LSNNEREFILKALKEG--LRLDGRGLDEFRPIKI--TF-GLEYGCV-EVSLGKTRVLAQVSCEIVEPKPDrpNEgILFIN 74
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5VZJ_E       84 VDI--------AGQRDDALVVEtITSLLNKVLKSGSGVDSSKL-QLTKKYSFKIFVDVLVIsshSHPVSLI---SFAIYS 151
Cdd:cd11368  75 VELspmaspafEPGRPSEEEVE-LSRLLERALRDSRAVDTESLcIIAGEKVWSIRVDVHVL---NHDGNLIdaaSLAAIA 150
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
5VZJ_E      152 ALNSTYLPklisafdDLEVEE----LPTFHDYDMVKLDI-NPPLVFILAVV--GNNMLLDPAANESEVANNGLIIS 220
Cdd:cd11368 151 ALMHFRRP-------DVTVDGeevtVHSPEEREPVPLSIhHIPICVTFAFFddGEIVVVDPTLLEEAVADGSLTVA 219
Rph COG0689
Ribonuclease PH [Translation, ribosomal structure and biogenesis];
26-70 7.34e-03

Ribonuclease PH [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440453 [Multi-domain]  Cd Length: 238  Bit Score: 36.93  E-value: 7.34e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
5VZJ_E       26 RPDGRLPHQFRPIEIFTDFLPSSNGS-------SRIIasdgseCIVSIKSKV 70
Cdd:COG0689   2 RPDGRAPDQLRPVKITRGFTKHAEGSvliefgdTKVL------CTASVEEGV 47
 
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