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Conserved domains on  [gi|1907119920|ref|XP_036016049|]
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poly(A)-specific ribonuclease PARN isoform X3 [Mus musculus]

Protein Classification

CAF1 family ribonuclease( domain architecture ID 11154053)

CAF1 family ribonuclease such as human poly(A)-specific ribonuclease PNLDC1, a 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, and target of EGR1 protein 1 (TOE1) that inhibits cell growth rate and cell cycle

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 5-190 2.23e-56

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


:

Pssm-ID: 461457  Cd Length: 375  Bit Score: 190.32  E-value: 2.23e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920   5 CHRFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLV 84
Cdd:pfam04857 185 DNPVSRLLLQQLLKHQLVRVLLVELLSRGKQKVVQVVKKSSEDEELLEKEEKKDEEEERLESAVGFRLVFDALSKSRKPI 264

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920  85 VGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQ-PFKDIINNTSLAELEKRLKETPFDPPKVESA 163
Cdd:pfam04857 265 VGHNGLLDLLFLYQQFYGPLPETLEEFKALIHELFPGIYDTKYLATTDaEFKVRLPSSSLEELFEKLCKENFSSPSVETP 344

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1907119920 164 EGFPSYDT----ASEQLHEAGYDAYITGLCF 190
Cdd:pfam04857 345 PFESDYHDesskYGGKAHEAGYDAYMTGYVF 375
RNA_bind pfam08675
RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ...
 238-312 1.32e-37

RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).


:

Pssm-ID: 400835  Cd Length: 75  Bit Score: 131.32  E-value: 1.32e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907119920 238 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYAEY 312
Cdd:pfam08675   1 KDPNPSREHVFHVTFPKEWKTSDILQLFSPFGGVYVSWLNDTSAFVSLHRRDQASAVLKTIKYHASYTIQTYAQY 75
 
Name Accession Description Interval E-value
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 5-190 2.23e-56

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 190.32  E-value: 2.23e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920   5 CHRFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLV 84
Cdd:pfam04857 185 DNPVSRLLLQQLLKHQLVRVLLVELLSRGKQKVVQVVKKSSEDEELLEKEEKKDEEEERLESAVGFRLVFDALSKSRKPI 264

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920  85 VGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQ-PFKDIINNTSLAELEKRLKETPFDPPKVESA 163
Cdd:pfam04857 265 VGHNGLLDLLFLYQQFYGPLPETLEEFKALIHELFPGIYDTKYLATTDaEFKVRLPSSSLEELFEKLCKENFSSPSVETP 344

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1907119920 164 EGFPSYDT----ASEQLHEAGYDAYITGLCF 190
Cdd:pfam04857 345 PFESDYHDesskYGGKAHEAGYDAYMTGYVF 375
RNA_bind pfam08675
RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ...
 238-312 1.32e-37

RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).


Pssm-ID: 400835  Cd Length: 75  Bit Score: 131.32  E-value: 1.32e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907119920 238 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYAEY 312
Cdd:pfam08675   1 KDPNPSREHVFHVTFPKEWKTSDILQLFSPFGGVYVSWLNDTSAFVSLHRRDQASAVLKTIKYHASYTIQTYAQY 75
RRM_PARN cd12428
RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; ...
 244-309 2.92e-36

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.


Pssm-ID: 409862 [Multi-domain]  Cd Length: 66  Bit Score: 127.42  E-value: 2.92e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907119920 244 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTY 309
Cdd:cd12428     1 RDHVFHLTFPKEWKTSDLYQLFSPFGGIQVSWIDDTSAFVALSDPEQVNIALKTITYHPSYRIRSY 66
R3H_PARN cd02637
R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease ...
 5-45 7.71e-16

R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100066 [Multi-domain]  Cd Length: 65  Bit Score: 71.59  E-value: 7.71e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907119920   5 CHRFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVD 45
Cdd:cd02637    24 CNGFQRKLIYQTLEQKYPKGIHVETLETEKKERLIVIEKGD 64
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 62-195 6.61e-03

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 37.08  E-value: 6.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920  62 EELNDAVGFSRVIHAIAN--SGKLVVGHNMLLDV---MHTIHQFYCPLPAdlnefkemaicvfPRLLDTKLMAsTQPFKD 136
Cdd:COG0847    59 EDVADAPPFAEVLPELLEflGGAVLVAHNAAFDLgflNAELRRAGLPLPP-------------FPVLDTLRLA-RRLLPG 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907119920 137 IINNtSLAELEKRLketpfdppkvesaeGFPSYDTaseqlHEAGYDAYITGLCFISMAN 195
Cdd:COG0847   125 LPSY-SLDALCERL--------------GIPFDER-----HRALADAEATAELFLALLR 163
 
Name Accession Description Interval E-value
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
 5-190 2.23e-56

CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution.


Pssm-ID: 461457  Cd Length: 375  Bit Score: 190.32  E-value: 2.23e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920   5 CHRFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVDEEERKRREQEKYTKEQEELNDAVGFSRVIHAIANSGKLV 84
Cdd:pfam04857 185 DNPVSRLLLQQLLKHQLVRVLLVELLSRGKQKVVQVVKKSSEDEELLEKEEKKDEEEERLESAVGFRLVFDALSKSRKPI 264

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920  85 VGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTKLMASTQ-PFKDIINNTSLAELEKRLKETPFDPPKVESA 163
Cdd:pfam04857 265 VGHNGLLDLLFLYQQFYGPLPETLEEFKALIHELFPGIYDTKYLATTDaEFKVRLPSSSLEELFEKLCKENFSSPSVETP 344

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1907119920 164 EGFPSYDT----ASEQLHEAGYDAYITGLCF 190
Cdd:pfam04857 345 PFESDYHDesskYGGKAHEAGYDAYMTGYVF 375
RNA_bind pfam08675
RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ...
 238-312 1.32e-37

RNA binding domain; This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN).


Pssm-ID: 400835  Cd Length: 75  Bit Score: 131.32  E-value: 1.32e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1907119920 238 PDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTYAEY 312
Cdd:pfam08675   1 KDPNPSREHVFHVTFPKEWKTSDILQLFSPFGGVYVSWLNDTSAFVSLHRRDQASAVLKTIKYHASYTIQTYAQY 75
RRM_PARN cd12428
RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; ...
 244-309 2.92e-36

RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins; The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding.


Pssm-ID: 409862 [Multi-domain]  Cd Length: 66  Bit Score: 127.42  E-value: 2.92e-36
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1907119920 244 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVQIAVNTSKYAESYRIQTY 309
Cdd:cd12428     1 RDHVFHLTFPKEWKTSDLYQLFSPFGGIQVSWIDDTSAFVALSDPEQVNIALKTITYHPSYRIRSY 66
R3H_PARN cd02637
R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease ...
 5-45 7.71e-16

R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.


Pssm-ID: 100066 [Multi-domain]  Cd Length: 65  Bit Score: 71.59  E-value: 7.71e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1907119920   5 CHRFQRKLIYQTLSWKYPKGIHVETLETDKKERHIVISKVD 45
Cdd:cd02637    24 CNGFQRKLIYQTLEQKYPKGIHVETLETEKKERLIVIEKGD 64
RRM3_CELF1-6 cd12362
RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, ...
 247-297 2.66e-04

RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins; This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts.


Pssm-ID: 409797 [Multi-domain]  Cd Length: 73  Bit Score: 39.14  E-value: 2.66e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920 247 VLHVtfPKEWKTSDLYQLFSAFGNIqIS---WIDDTS------AFVSLSQPEQVQIAVNT 297
Cdd:cd12362     3 VYHL--PNEFTDQDLYQLFAPFGNV-VSakvFVDKNTgrskgfGFVSYDNPLSAQAAIKA 59
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 248-289 1.63e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 36.99  E-value: 1.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1907119920 248 LHVT-FPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPE 289
Cdd:cd12340     2 LFVRpFPPDTSESAIREIFSPYGPVKEVKMlsDSNFAFVEFEELE 46
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 248-296 4.54e-03

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 35.72  E-value: 4.54e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907119920 248 LHVT-FPKEWKTSDLYQLFSAFGNIQ-ISWIDDTS------AFVSLSQPEQVQIAVN 296
Cdd:cd00590     1 LFVGnLPPDTTEEDLRELFSKFGEVVsVRIVRDRDgkskgfAFVEFESPEDAEKALE 57
DnaQ COG0847
DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination ...
 62-195 6.61e-03

DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair];


Pssm-ID: 440608 [Multi-domain]  Cd Length: 163  Bit Score: 37.08  E-value: 6.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907119920  62 EELNDAVGFSRVIHAIAN--SGKLVVGHNMLLDV---MHTIHQFYCPLPAdlnefkemaicvfPRLLDTKLMAsTQPFKD 136
Cdd:COG0847    59 EDVADAPPFAEVLPELLEflGGAVLVAHNAAFDLgflNAELRRAGLPLPP-------------FPVLDTLRLA-RRLLPG 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907119920 137 IINNtSLAELEKRLketpfdppkvesaeGFPSYDTaseqlHEAGYDAYITGLCFISMAN 195
Cdd:COG0847   125 LPSY-SLDALCERL--------------GIPFDER-----HRALADAEATAELFLALLR 163
 
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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