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Conserved domains on  [gi|24762324|ref|NP_611807|]
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Rrp4, isoform A [Drosophila melanogaster]

Protein Classification

exosome complex component RRP4( domain architecture ID 20732369)

exosome complex component RRP4 is one of the RNA-binding proteins of the exosome complex.

Gene Ontology:  GO:0003723|GO:0006402

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 172-290 1.53e-51

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411953  Cd Length: 123  Bit Score: 165.52  E-value: 1.53e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324 172 GILVKVFPALVKRRKMHFHNLPCGASVILGNNGYIWISPT--KGQEEEGGEGGFAQNLNEHVPRADREVIARLRNSILAL 249
Cdd:cd22525   1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTveESGEEAGGSAAIYSNNNEPVSPETREAIARVRNCIKAL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 24762324 250 AKCKLMIYDTSIQYAYEESL--RYEAHELLQQNAIYDIGQQTQ 290
Cdd:cd22525  81 AALHIPITDTSILAVYEASLelGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 78-169 1.69e-38

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


:

Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 130.75  E-value: 1.69e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324  78 RYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSILLLSSVNLPggelrrRSAEDEQMMRRYLDEGDLISAEVQNIFEEGSL 157
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                        90
                ....*....|..
gi 24762324 158 SLYTRSLKYGKL 169
Cdd:cd05789  75 SLHTRSLKYGKL 86
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 29-66 1.46e-12

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


:

Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 60.84  E-value: 1.46e-12
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 24762324    29 VYTPGEVLMPEAGFMRGHGTFVEDENIKSSVAGVIQKV 66
Cdd:pfam14382   1 IVLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 172-290 1.53e-51

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 165.52  E-value: 1.53e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324 172 GILVKVFPALVKRRKMHFHNLPCGASVILGNNGYIWISPT--KGQEEEGGEGGFAQNLNEHVPRADREVIARLRNSILAL 249
Cdd:cd22525   1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTveESGEEAGGSAAIYSNNNEPVSPETREAIARVRNCIKAL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 24762324 250 AKCKLMIYDTSIQYAYEESL--RYEAHELLQQNAIYDIGQQTQ 290
Cdd:cd22525  81 AALHIPITDTSILAVYEASLelGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 78-169 1.69e-38

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 130.75  E-value: 1.69e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324  78 RYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSILLLSSVNLPggelrrRSAEDEQMMRRYLDEGDLISAEVQNIFEEGSL 157
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                        90
                ....*....|..
gi 24762324 158 SLYTRSLKYGKL 169
Cdd:cd05789  75 SLHTRSLKYGKL 86
PRK04163 PRK04163
exosome complex protein Rrp4;
31-209 3.14e-30

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 113.83  E-value: 3.14e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324   31 TPGEVLmPEAGFMRGHGTFVEDENIKSSVAGVIQKVNKLISVRPLKSRYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSI 110
Cdd:PRK04163  12 VPGDLL-AEGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAY 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324  111 LLLSSVnlpggeLRRRSAEDEQMMRRYLDEGDLISAEVQNIFE--EGSLSLYTRSLkyGKLSQGILVKVFPALVKR---R 185
Cdd:PRK04163  91 LPVSEV------LGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRtrDVVLTLKGKGL--GKIEGGTIVEIKPVKVPRvigK 162

                        170       180
                 ....*....|....*....|....*..
gi 24762324  186 KMHFHNL---PCGASVILGNNGYIWIS 209
Cdd:PRK04163 163 KGSMINMlkeETGCDIIVGQNGRIWIK 189
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 29-66 1.46e-12

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 60.84  E-value: 1.46e-12
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 24762324    29 VYTPGEVLMPEAGFMRGHGTFVEDENIKSSVAGVIQKV 66
Cdd:pfam14382   1 IVLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 172-211 4.96e-10

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 53.98  E-value: 4.96e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 24762324   172 GILVKVFPALVKRRKMHF--HNLPC--GASVILGNNGYIWISPT 211
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSHflHELGKkgPFEIAVGLNGRIWIKSE 44
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 23-98 6.59e-09

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 54.60  E-value: 6.59e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24762324   23 TEEQPRVYTPGEVLMPEAGFMRGHGTFVEDENIKSSVAG--VIQKVNKLISVRPLKSR-YVGEIGDVVVARVSEVQQKR 98
Cdd:PRK09521   1 MVKQGDLVLPGDYLAVIEEYLPGEGTYEDNGEVYASVVGkvFIDDINRKISVIPFKKTpPLLKKGDIVYGRVVDVKEQR 79
 
Name Accession Description Interval E-value
KH-I_Rrp4_eukar cd22525
type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from ...
 172-290 1.53e-51

type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote; The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411953  Cd Length: 123  Bit Score: 165.52  E-value: 1.53e-51
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324 172 GILVKVFPALVKRRKMHFHNLPCGASVILGNNGYIWISPT--KGQEEEGGEGGFAQNLNEHVPRADREVIARLRNSILAL 249
Cdd:cd22525   1 GILVKVPPSLIKRQKSHFHNLPCGVDVILGLNGYIWISPTveESGEEAGGSAAIYSNNNEPVSPETREAIARVRNCIKAL 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 24762324 250 AKCKLMIYDTSIQYAYEESL--RYEAHELLQQNAIYDIGQQTQ 290
Cdd:cd22525  81 AALHIPITDTSILAVYEASLelGIEVKDLLKPEVMEEIVEEAR 123
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 78-169 1.69e-38

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 130.75  E-value: 1.69e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324  78 RYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSILLLSSVNLPggelrrRSAEDEQMMRRYLDEGDLISAEVQNIFEEGSL 157
Cdd:cd05789   1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP------RTDEDELNMRSYLDEGDLIVAEVQSVDSDGSV 74

                        90
                ....*....|..
gi 24762324 158 SLYTRSLKYGKL 169
Cdd:cd05789  75 SLHTRSLKYGKL 86
PRK04163 PRK04163
exosome complex protein Rrp4;
31-209 3.14e-30

exosome complex protein Rrp4;


Pssm-ID: 235233 [Multi-domain]  Cd Length: 235  Bit Score: 113.83  E-value: 3.14e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324   31 TPGEVLmPEAGFMRGHGTFVEDENIKSSVAGVIQKVNKLISVRPLKSRYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSI 110
Cdd:PRK04163  12 VPGDLL-AEGEFKAGRGTYKENGKIYSTVVGLVDIKDDKVRVIPLEGKYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAY 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324  111 LLLSSVnlpggeLRRRSAEDEQMMRRYLDEGDLISAEVQNIFE--EGSLSLYTRSLkyGKLSQGILVKVFPALVKR---R 185
Cdd:PRK04163  91 LPVSEV------LGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRtrDVVLTLKGKGL--GKIEGGTIVEIKPVKVPRvigK 162

                        170       180
                 ....*....|....*....|....*..
gi 24762324  186 KMHFHNL---PCGASVILGNNGYIWIS 209
Cdd:PRK04163 163 KGSMINMlkeETGCDIIVGQNGRIWIK 189
S1_Rrp4_like cd04454
S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in ...
 78-169 7.23e-25

S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 239901 [Multi-domain]  Cd Length: 82  Bit Score: 95.31  E-value: 7.23e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324  78 RYVGEIGDVVVARVSEVQQKRWRVDTNSRLDSILLLSSVNLPggelrrrsaeDEQMMRRYLDEGDLISAEVQNIFEEGSL 157
Cdd:cd04454   1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK----------DKKEIRKSLQPGDLILAKVISLGDDMNV 70

                        90
                ....*....|..
gi 24762324 158 SLYTRSLKYGKL 169
Cdd:cd04454  71 LLTTADNELGVI 82
KH-I_Rrp4_Rrp40 cd22445
type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and ...
 172-266 1.08e-14

type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and similar proteins; The family includes two ribosomal RNA-processing proteins, Rrp4 and Rrp40. They are non-catalytic components of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Eukaryotic Rrp4 and Rrp40 contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411873 [Multi-domain]  Cd Length: 78  Bit Score: 68.05  E-value: 1.08e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24762324 172 GILVKVFPALVKRRK------MHFHNLPCGASVILGNNGYIWISPTKgqeeeggeggfaqnlnehvpradREVIARLRNS 245
Cdd:cd22445   1 GLLVKVTPGLVRRLLapdceiIQEVGKLYPLEIVFGMNGRIWVKAKT-----------------------RQQTSILANI 57

                        90       100
                ....*....|....*....|.
gi 24762324 246 ILALAKCKLMIYDTSIQYAYE 266
Cdd:cd22445  58 IEACEHMHTSDQRKQIFSRLA 78
ECR1_N pfam14382
Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the ...
 29-66 1.46e-12

Exosome complex exonuclease RRP4 N-terminal region; ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology.


Pssm-ID: 464162 [Multi-domain]  Cd Length: 38  Bit Score: 60.84  E-value: 1.46e-12
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 24762324    29 VYTPGEVLMPEAGFMRGHGTFVEDENIKSSVAGVIQKV 66
Cdd:pfam14382   1 IVLPGERLGSDEEYMPGHGTYVRDGNIYASVAGTVEIV 38
KH_6 pfam15985
KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause ...
 172-211 4.96e-10

KH domain; KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia.


Pssm-ID: 464959 [Multi-domain]  Cd Length: 47  Bit Score: 53.98  E-value: 4.96e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 24762324   172 GILVKVFPALVKRRKMHF--HNLPC--GASVILGNNGYIWISPT 211
Cdd:pfam15985   1 GMLVKVSLSLVRRLLKSHflHELGKkgPFEIAVGLNGRIWIKSE 44
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 23-98 6.59e-09

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 54.60  E-value: 6.59e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24762324   23 TEEQPRVYTPGEVLMPEAGFMRGHGTFVEDENIKSSVAG--VIQKVNKLISVRPLKSR-YVGEIGDVVVARVSEVQQKR 98
Cdd:PRK09521   1 MVKQGDLVLPGDYLAVIEEYLPGEGTYEDNGEVYASVVGkvFIDDINRKISVIPFKKTpPLLKKGDIVYGRVVDVKEQR 79
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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