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Conserved domains on  [gi|15242180|ref|NP_197617|]
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Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

Protein Classification

CAF1 family ribonuclease( domain architecture ID 581404)

CAF1 family ribonuclease such as Xenopus laevis CCR4-NOT transcription complex subunit 7 and Arabidopsis thaliana probable CCR4-associated factor 1 homolog

CATH:  3.30.420.10
EC:  3.1.13.-
SCOP:  4001124

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CAF1 super family cl23804
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
14-277 2.90e-76

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.


The actual alignment was detected with superfamily member COG5228:

Pssm-ID: 474062  Cd Length: 299  Bit Score: 234.04  E-value: 2.90e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180  14 IRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKAdLDVLRRGNpNYLYNLLKSNVDALSLIQVGLTLSDADGNLP 93
Cdd:COG5228  20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARP-IGTFKSSV-DYHYQTLRANVDFLKIIQLGLSLSDENGNKP 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180  94 dlggqkNRRYIWEFNFrDFDVERDPHAPDSIELLRRHGIDFERNRREGVESERFAELMMSSGLICNESVSWVTFHSAYDF 173
Cdd:COG5228  98 ------NGPSTWQFNF-EFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDF 170
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180 174 GYLVKILTRRQLPVALREFLGLLRAFFGDrVYDVKHIMRfCEQRLYGGLDRVARSLEVNRaVGKCHQAGSDSLLTWQAFQ 253
Cdd:COG5228 171 GYLIKILTNDPLPNNKEDFYWWLHQYFPN-FYDIKLVYK-SVLNNSKGLQEIKNDLQLQR-SGQQHQAGSDALLTADEFF 247
                       250       260
                ....*....|....*....|....
gi 15242180 254 RMRDLYFVEDGAEKHAGVLYGLEV 277
Cdd:COG5228 248 LPRFSIFTTSIGQSLLMLLSGCQL 271
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
14-277 2.90e-76

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 234.04  E-value: 2.90e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180  14 IRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKAdLDVLRRGNpNYLYNLLKSNVDALSLIQVGLTLSDADGNLP 93
Cdd:COG5228  20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARP-IGTFKSSV-DYHYQTLRANVDFLKIIQLGLSLSDENGNKP 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180  94 dlggqkNRRYIWEFNFrDFDVERDPHAPDSIELLRRHGIDFERNRREGVESERFAELMMSSGLICNESVSWVTFHSAYDF 173
Cdd:COG5228  98 ------NGPSTWQFNF-EFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDF 170
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180 174 GYLVKILTRRQLPVALREFLGLLRAFFGDrVYDVKHIMRfCEQRLYGGLDRVARSLEVNRaVGKCHQAGSDSLLTWQAFQ 253
Cdd:COG5228 171 GYLIKILTNDPLPNNKEDFYWWLHQYFPN-FYDIKLVYK-SVLNNSKGLQEIKNDLQLQR-SGQQHQAGSDALLTADEFF 247
                       250       260
                ....*....|....*....|....
gi 15242180 254 RMRDLYFVEDGAEKHAGVLYGLEV 277
Cdd:COG5228 248 LPRFSIFTTSIGQSLLMLLSGCQL 271
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
17-142 6.12e-10

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: 58.96  E-value: 6.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180    17 VWAYNLESEFDLIRGIVEDYPFISMDTEFPGvIYKADLDVLRRGNPNYLYNLLKSNVDALSLIQVGLTLSDADgnlpdlg 96
Cdd:pfam04857   1 VTRSNFKELLPEILKAIKEADFVAIDLEFTG-LGSPWRKSSLFDTPEERYLKLRDAAERFSILQFGLCCFRED------- 72
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 15242180    97 gQKNRRYIWE-FNF-----------RDFDVErdphaPDSIELLRRHGIDFERNRREGV 142
Cdd:pfam04857  73 -EEKSKYTAKpYNFylfprteldpdRDFSCQ-----ASSLQFLAKHGFDFNKLFYEGI 124
 
Name Accession Description Interval E-value
POP2 COG5228
mRNA deadenylase subunit [RNA processing and modification];
14-277 2.90e-76

mRNA deadenylase subunit [RNA processing and modification];


Pssm-ID: 227553  Cd Length: 299  Bit Score: 234.04  E-value: 2.90e-76
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180  14 IRDVWAYNLESEFDLIRGIVEDYPFISMDTEFPGVIYKAdLDVLRRGNpNYLYNLLKSNVDALSLIQVGLTLSDADGNLP 93
Cdd:COG5228  20 IRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARP-IGTFKSSV-DYHYQTLRANVDFLKIIQLGLSLSDENGNKP 97
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180  94 dlggqkNRRYIWEFNFrDFDVERDPHAPDSIELLRRHGIDFERNRREGVESERFAELMMSSGLICNESVSWVTFHSAYDF 173
Cdd:COG5228  98 ------NGPSTWQFNF-EFDLKKDMYATESIELLRKSGIDFKKHENLGIDVFEFSELLMDSGLVMDESVTWITFHSAYDF 170
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180 174 GYLVKILTRRQLPVALREFLGLLRAFFGDrVYDVKHIMRfCEQRLYGGLDRVARSLEVNRaVGKCHQAGSDSLLTWQAFQ 253
Cdd:COG5228 171 GYLIKILTNDPLPNNKEDFYWWLHQYFPN-FYDIKLVYK-SVLNNSKGLQEIKNDLQLQR-SGQQHQAGSDALLTADEFF 247
                       250       260
                ....*....|....*....|....
gi 15242180 254 RMRDLYFVEDGAEKHAGVLYGLEV 277
Cdd:COG5228 248 LPRFSIFTTSIGQSLLMLLSGCQL 271
CAF1 pfam04857
CAF1 family ribonuclease; The major pathways of mRNA turnover in eukaryotes initiate with ...
17-142 6.12e-10

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: 58.96  E-value: 6.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242180    17 VWAYNLESEFDLIRGIVEDYPFISMDTEFPGvIYKADLDVLRRGNPNYLYNLLKSNVDALSLIQVGLTLSDADgnlpdlg 96
Cdd:pfam04857   1 VTRSNFKELLPEILKAIKEADFVAIDLEFTG-LGSPWRKSSLFDTPEERYLKLRDAAERFSILQFGLCCFRED------- 72
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 15242180    97 gQKNRRYIWE-FNF-----------RDFDVErdphaPDSIELLRRHGIDFERNRREGV 142
Cdd:pfam04857  73 -EEKSKYTAKpYNFylfprteldpdRDFSCQ-----ASSLQFLAKHGFDFNKLFYEGI 124
 
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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