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Conserved domains on  [gi|1668804593|ref|NP_001357676|]
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protein angel homolog 1 isoform 2 [Homo sapiens]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 248-449 2.39e-43

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


The actual alignment was detected with superfamily member cd09097:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 329  Bit Score: 159.39  E-value: 2.39e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 248 MSYNILAqDLMQqSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTGC 327
Cdd:cd09097     2 MCYNVLC-DKYA-TRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSRA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 328 KT---------DGCAVCYKPTRFRLLCASPVEY---------FRPGLELLNR----DNVGLVL---LLQPLVPEGLGQvs 382
Cdd:cd09097    80 KTmseaerkhvDGCAIFFKTSKFKLVEKHLIEFnqlamanadAEGSEDMLNRvmtkDNIALIVvleARETSYEGNKGQ-- 157

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1668804593 383 vaPLCVANTHILYNPRRGDVKLAQMAILLAEVDKVA------RLSDGSHCPIILCGDLNSVPDSPLYNFIRDG 449
Cdd:cd09097   158 --LLIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAekfsryPYEDSADIPLVVCGDFNSLPDSGVYELLSNG 228
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 248-449 2.39e-43

C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1 (called Pop2 in yeast), is a DEDD-type protein and does not belong in this superfamily. Saccharomyces cerevisiae CCR4 (or Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. Ccr4p degrades both poly(A) and single-stranded DNA. There are two vertebrate homologs of Ccr4p, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b (also called CNOT6-like or CNOT6L), which independently associate with other components to form distinct CCR4-NOT multisubunit complexes. The nuclease domain of CNOT6 and CNOT6L exhibits Mg2+-dependent deadenylase activity, with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation. CCR4b regulates p27/Kip1 mRNA levels, thereby influencing cell cycle progression. They both contribute to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197331 [Multi-domain]  Cd Length: 329  Bit Score: 159.39  E-value: 2.39e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 248 MSYNILAqDLMQqSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTGC 327
Cdd:cd09097     2 MCYNVLC-DKYA-TRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSRA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 328 KT---------DGCAVCYKPTRFRLLCASPVEY---------FRPGLELLNR----DNVGLVL---LLQPLVPEGLGQvs 382
Cdd:cd09097    80 KTmseaerkhvDGCAIFFKTSKFKLVEKHLIEFnqlamanadAEGSEDMLNRvmtkDNIALIVvleARETSYEGNKGQ-- 157

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1668804593 383 vaPLCVANTHILYNPRRGDVKLAQMAILLAEVDKVA------RLSDGSHCPIILCGDLNSVPDSPLYNFIRDG 449
Cdd:cd09097   158 --LLIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAekfsryPYEDSADIPLVVCGDFNSLPDSGVYELLSNG 228
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 245-449 1.95e-37

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 148.34  E-value: 1.95e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 245 FTLMSYNILAqDLMQqSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRR 324
Cdd:PLN03144  255 FTVLSYNILS-DLYA-TSDMYSYCPPWALSWTYRRQNLLREIVGYRADILCLQEVQSDHFEEFFAPELDKHGYQALYKKK 332

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 325 TG-------CKTDGCAVCYKPTRFRLLCASPVEYFRPGLEL-------------LNR---DNVG------LVLLLQPLVP 375
Cdd:PLN03144  333 TTevytgntYVIDGCATFFRRDRFSLVKKYEVEFNKAAQSLtealipsaqkkaaLNRllkDNVAlivvleAKFGNQGADN 412

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1668804593 376 EGLGQVsvapLCVANTHILYNPRRGDVKLAQMAILLAEVDKVARLSDgshCPIILCGDLNSVPDSPLYNFIRDG 449
Cdd:PLN03144  413 GGKRQL----LCVANTHIHANQELKDVKLWQVHTLLKGLEKIAASAD---IPMLVCGDFNSVPGSAPHCLLATG 479
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
241-455 8.82e-27

mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 112.94  E-value: 8.82e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 241 PQFQFTLMSYNILAQDLMqqSSELYLHCHPdILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCF 320
Cdd:COG5239    27 KDTDFTIMTYNVLAQTYA--TRKMYPYSGW-ALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLGKLGYDGI 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 321 YKRRTG----------CKTDGCAVCYK----PTRFRLLCASPV---------EYFRPGLELLNR----DNVGLVLLLQPL 373
Cdd:COG5239   104 FIPKERkvkwmidydtTKVDGCAIFLKrfidSSKLGLILAVTHlfwhpygyyERFRQTYILLNRigekDNIAWVCLFVGL 183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 374 VPEGLGQvsvaPLCVANTHILYNPRRGDVKLAQMAILLAEVDKVA---RLSDGSHC--------PIILCGDLNSVPDSPL 442
Cdd:COG5239   184 FNKEPGD----TPYVANTHLPWDPKYRDVKLIQCSLLYRELKKVLkeeLNDDKEEGdiksypevDILITGDFNSLRASLV 259

                         250
                  ....*....|...
gi 1668804593 443 YNFIRDGELQYHG 455
Cdd:COG5239   260 YKFLVTSQIQLHE 272
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 248-436 2.88e-12

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 65.71  E-value: 2.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 248 MSYNILaqdlmqqsselylHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTGC 327
Cdd:pfam03372   1 LTWNVN-------------GGNADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 328 KTDGCAVCYKPTRFRLLCASPVEYFRPGLELLNRDNVGLvlllqplvpeglgqvsvaplcVANTHILYNPRRGDVKLAQM 407
Cdd:pfam03372  68 GGGGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAGV---------------------LVVPLVLTLAPHASPRLARD 126

                         170       180
                  ....*....|....*....|....*....
gi 1668804593 408 AILLAEVDKVARLSDGSHCPIILCGDLNS 436
Cdd:pfam03372 127 EQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 248-449 2.39e-43

C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1 (called Pop2 in yeast), is a DEDD-type protein and does not belong in this superfamily. Saccharomyces cerevisiae CCR4 (or Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. Ccr4p degrades both poly(A) and single-stranded DNA. There are two vertebrate homologs of Ccr4p, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b (also called CNOT6-like or CNOT6L), which independently associate with other components to form distinct CCR4-NOT multisubunit complexes. The nuclease domain of CNOT6 and CNOT6L exhibits Mg2+-dependent deadenylase activity, with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation. CCR4b regulates p27/Kip1 mRNA levels, thereby influencing cell cycle progression. They both contribute to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197331 [Multi-domain]  Cd Length: 329  Bit Score: 159.39  E-value: 2.39e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 248 MSYNILAqDLMQqSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTGC 327
Cdd:cd09097     2 MCYNVLC-DKYA-TRQQYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKSRA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 328 KT---------DGCAVCYKPTRFRLLCASPVEY---------FRPGLELLNR----DNVGLVL---LLQPLVPEGLGQvs 382
Cdd:cd09097    80 KTmseaerkhvDGCAIFFKTSKFKLVEKHLIEFnqlamanadAEGSEDMLNRvmtkDNIALIVvleARETSYEGNKGQ-- 157

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1668804593 383 vaPLCVANTHILYNPRRGDVKLAQMAILLAEVDKVA------RLSDGSHCPIILCGDLNSVPDSPLYNFIRDG 449
Cdd:cd09097   158 --LLIVANTHIHWDPEFSDVKLVQTMMLLEELEKIAekfsryPYEDSADIPLVVCGDFNSLPDSGVYELLSNG 228
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 245-449 1.95e-37

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 148.34  E-value: 1.95e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 245 FTLMSYNILAqDLMQqSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRR 324
Cdd:PLN03144  255 FTVLSYNILS-DLYA-TSDMYSYCPPWALSWTYRRQNLLREIVGYRADILCLQEVQSDHFEEFFAPELDKHGYQALYKKK 332

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 325 TG-------CKTDGCAVCYKPTRFRLLCASPVEYFRPGLEL-------------LNR---DNVG------LVLLLQPLVP 375
Cdd:PLN03144  333 TTevytgntYVIDGCATFFRRDRFSLVKKYEVEFNKAAQSLtealipsaqkkaaLNRllkDNVAlivvleAKFGNQGADN 412

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1668804593 376 EGLGQVsvapLCVANTHILYNPRRGDVKLAQMAILLAEVDKVARLSDgshCPIILCGDLNSVPDSPLYNFIRDG 449
Cdd:PLN03144  413 GGKRQL----LCVANTHIHANQELKDVKLWQVHTLLKGLEKIAASAD---IPMLVCGDFNSVPGSAPHCLLATG 479
Deadenylase_CCR4b cd10312
C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit ...
 247-472 8.91e-28

C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit 6-like; This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4b, also known as CCR4-NOT transcription complex subunit 6-like (CNOT6L). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b. CCR4b associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4b exhibits Mg2+-dependent deadenylase activity with strict specificity for poly (A) RNA as substrate. CCR4b is mainly localized in the cytoplasm. It regulates cell growth and influences cell cycle progression by regulating p27/Kip1 mRNA levels. It contributes to the prevention of cell death by regulating insulin-like growth factor-binding protein 5.


Pssm-ID: 197339  Cd Length: 348  Bit Score: 115.12  E-value: 8.91e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 247 LMSYNILAQDLmqQSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTG 326
Cdd:cd10312     1 VMCYNVLCDKY--ATRQLYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 327 CK---------TDGCAVCYKPTRFRLLCASPVEYFRPGLE-------LLNR----DNVG-LVLLLQPLVPEGLGQVSVAP 385
Cdd:cd10312    79 AKimseqerkhVDGCAIFFKTEKFSLVQKHTVEFNQVAMAnsegseaMLNRvmtkDNIGvAVVLEVHKELFGAGMKPIHA 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 386 -----LCVANTHILYNPRRGDVKLAQMAILLAEVDKVAR---------LSDGSHCPIILCGDLNSVPDSPLYNFIRDG-- 449
Cdd:cd10312   159 adkqlLIVANAHMHWDPEYSDVKLIQTMMFVSELKNILEkassrpgspTADPNSIPLVLCADLNSLPDSGVVEYLSNGgv 238

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1668804593 450 --------ELQYHgmpawkslALLPRLECNG 472
Cdd:cd10312   239 adnhkdfkELRYN--------ECLMNFSCNG 261
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
241-455 8.82e-27

mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 112.94  E-value: 8.82e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 241 PQFQFTLMSYNILAQDLMqqSSELYLHCHPdILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCF 320
Cdd:COG5239    27 KDTDFTIMTYNVLAQTYA--TRKMYPYSGW-ALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLGKLGYDGI 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 321 YKRRTG----------CKTDGCAVCYK----PTRFRLLCASPV---------EYFRPGLELLNR----DNVGLVLLLQPL 373
Cdd:COG5239   104 FIPKERkvkwmidydtTKVDGCAIFLKrfidSSKLGLILAVTHlfwhpygyyERFRQTYILLNRigekDNIAWVCLFVGL 183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 374 VPEGLGQvsvaPLCVANTHILYNPRRGDVKLAQMAILLAEVDKVA---RLSDGSHC--------PIILCGDLNSVPDSPL 442
Cdd:COG5239   184 FNKEPGD----TPYVANTHLPWDPKYRDVKLIQCSLLYRELKKVLkeeLNDDKEEGdiksypevDILITGDFNSLRASLV 259

                         250
                  ....*....|...
gi 1668804593 443 YNFIRDGELQYHG 455
Cdd:COG5239   260 YKFLVTSQIQLHE 272
Deadenylase_CCR4a cd10313
C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; ...
 247-472 2.39e-24

C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4a, also known as CCR4-NOT transcription complex subunit 6 (CNOT6). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a and CCR4b (also called CNOT6-like or CNOT6L). CCR4a associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4a exhibits Mg2+-dependent deadenylase activity with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation of various P-body components. It also plays a role in cellular responses to DNA damage, by regulating Chk2 activity.


Pssm-ID: 197340  Cd Length: 350  Bit Score: 105.13  E-value: 2.39e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 247 LMSYNILAQDLmqQSSELYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTG 326
Cdd:cd10313     1 VMCYNVLCDKY--ATRQLYGYCPSWALNWDYRKKAIMQEILSCNADIISLQEVETEQYYSFFLVELKERGYNGFFSPKSR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 327 CKT---------DGCAVCYKPTRFRLLCASPVEYFRPGL-------ELLNR----DNVGlVLLLQPLVPEGLGQVSVAP- 385
Cdd:cd10313    79 ARTmseqerkhvDGCAIFFKTEKFTLVQKHTVEFNQLAMansegseAMLNRvmtkDNIG-VAVLLELRKELIEMSSGKPh 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 386 -------LCVANTHILYNPRRGDVKLAQMAILLAEV----DKVAR------LSDGSHCPIILCGDLNSVPDSPLYNFIRD 448
Cdd:cd10313   158 lgmekqlILVANAHMHWDPEYSDVKLVQTMMFLSEVkniiDKASRslkssvLGETGTIPLVLCADLNSLPDSGVVEYLST 237

                         250       260
                  ....*....|....*....|....*.
gi 1668804593 449 G--ELQYHGMPAWKSLALLPRLECNG 472
Cdd:cd10313   238 GgvETNHKDFKELRYNESLTNFSCNG 263
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 247-444 3.62e-23

C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the C-terminal catalytic domain of the deadenylase, nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes. In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197330 [Multi-domain]  Cd Length: 280  Bit Score: 100.19  E-value: 3.62e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 247 LMSYNILAQDLMQQSSElYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVqeDHYWEQLEPSLRMMGFTC--FYKRR 324
Cdd:cd09096     2 VMQWNILAQALGEGKDG-FVRCPCEALKWEERKYLILEEILTYDPDILCLQEV--DHYKDTLQPLLSRLGYQGtfFPKPD 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 325 TGC-------KTDGCAVCYKPTRFrllcaspveyfrpglELLNRDNVGLVLLLQPLVPEGLGQV-----SVAPLCVANTH 392
Cdd:cd09096    79 SPClyiennnGPDGCALFFRKDRF---------------ELVNTEKIRLSAMTLKTNQVAIACTlrckeTGREICLAVTH 143

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1668804593 393 IlyNPRRG--DVKLAQMAILLaevDKVARLSDGSHCPIILCGDLNSVPDSPLYN 444
Cdd:cd09096   144 L--KARTGweRLRSEQGKDLL---QNLQSFIEGAKIPLIICGDFNAEPTEPVYK 192
Deadenylase cd09082
C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains ...
 247-443 1.20e-12

C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains the C-terminal catalytic domains of the deadenylases, CCR4 and nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of the Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. Saccharomyces cerevisiae CCR4p is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. The deadenylase activities of Ccr4p and nocturnin differ: nocturnin degrades poly(A), Ccr4p degrades both poly(A) and single-stranded DNA, and in contrast to Ccr4p, nocturnin appears to function in a highly processive manner. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197316 [Multi-domain]  Cd Length: 348  Bit Score: 70.07  E-value: 1.20e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 247 LMSYNILAQDLMQQSSelYLHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFY--KRR 324
Cdd:cd09082     1 VMCYNVLCDKYATRQL--YGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFspKSR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 325 TGC-------KTDGCAVCYKPTRFRLLCASPVEyfrpgLELLNRDNVGLVLLLQPLVPEGLGQVSVAP------------ 385
Cdd:cd09082    79 AKImseqerkHVDGCAIFFKTEKFTLVQKHTVE-----FNQVAMANSDGSEAMLNRVMTKDNIGVAVVlevhkelfgagm 153

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1668804593 386 ----------LCVANTHILYNPRRGDVKLAQMAILLAEVDKVAR---------LSDGSHCPIILCGDLNSVPDSPLY 443
Cdd:cd09082   154 kpihaadkqlLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEkassrpgspTADPNSIPLVLCADLNSLPDSGVV 230
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 248-436 2.88e-12

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 65.71  E-value: 2.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 248 MSYNILaqdlmqqsselylHCHPDILNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYKRRTGC 327
Cdd:pfam03372   1 LTWNVN-------------GGNADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGGG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 328 KTDGCAVCYKPTRFRLLCASPVEYFRPGLELLNRDNVGLvlllqplvpeglgqvsvaplcVANTHILYNPRRGDVKLAQM 407
Cdd:pfam03372  68 GGGGVAILSRYPLSSVILVDLGEFGDPALRGAIAPFAGV---------------------LVVPLVLTLAPHASPRLARD 126

                         170       180
                  ....*....|....*....|....*....
gi 1668804593 408 AILLAEVDKVARLSDGSHCPIILCGDLNS 436
Cdd:pfam03372 127 EQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 273-440 1.58e-07

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 52.87  E-value: 1.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 273 LNWNYRFVNLMQEFQHWDPDILCLQEVQEDHYWEQLEPSLRMMGFTCFYK-RRTGCKTDGCAVCYKPtrfRLLCASPVEY 351
Cdd:cd08372     9 LNAATRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGYHQYQSgPSRKEGYEGVAILSKT---PKFKIVEKHQ 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 352 FRPGLE-LLNRDNVGLVlllqplvpeglGQVSVAPLCVANTHILYNPRRGDVKLAQ-MAILlaevDKVARLSDGSHCPII 429
Cdd:cd08372    86 YKFGEGdSGERRAVVVK-----------FDVHDKELCVVNAHLQAGGTRADVRDAQlKEVL----EFLKRLRQPNSAPVV 150

                         170
                  ....*....|.
gi 1668804593 430 LCGDLNSVPDS 440
Cdd:cd08372   151 ICGDFNVRPSE 161
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 246-463 5.29e-07

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 51.45  E-value: 5.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 246 TLMSYNI---LAQDlmqqsselylhcHPDilNWNYRFVNLMQEFQHWDPDILCLQEVQedhyWEQLEPSLRMM-GFTCFY 321
Cdd:cd09083     1 RVMTFNIrydNPSD------------GEN--SWENRKDLVAELIKFYDPDIIGTQEAL----PHQLADLEELLpEYDWIG 62

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 322 KRRTGCKTDG--CAVCYKPTRFRLLCA-----SPVEYFRPG-------------LELLNRDnvglvlllqplvpeglgqv 381
Cdd:cd09083    63 VGRDDGKEKGefSAIFYRKDRFELLDSgtfwlSETPDVVGSkgwdaalprictwARFKDKK------------------- 123

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1668804593 382 SVAPLCVANTHilYNPRRGDVKLAQMAILLaevDKVARLSDGShcPIILCGDLNSVPDSPLYNFIRDGELQyhgmPAWKS 461
Cdd:cd09083   124 TGKEFYVFNTH--LDHVGEEAREESAKLIL---ERIKEIAGDL--PVILTGDFNAEPDSEPYKTLTSGGLK----DARDT 192


                  ..
gi 1668804593 462 LA 463
Cdd:cd09083   193 AA 194
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 412-452 5.86e-04

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 42.67  E-value: 5.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1668804593 412 AEVDKVARLSDGSHCPIILCGDLNSVPDSPLY-NFIRDGELQ 452
Cdd:COG3021   212 AELAALAKAVAALDGPVIVAGDFNATPWSPTLrRLLRASGLR 253
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 380-436 2.01e-03

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 39.51  E-value: 2.01e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1668804593 380 QVSVAPLCVANTHILYNPRRgdVKLAQMAILLAEVDKVARlsdgsHCPIILCGDLNS 436
Cdd:COG3568    79 DVPGKPLRVVNTHLDLRSAA--ARRRQARALAELLAELPA-----GAPVILAGDFND 128
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 412-449 3.48e-03

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins.


Pssm-ID: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 39.97  E-value: 3.48e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1668804593 412 AEVDKVARLSDGSHCPIILCGDLNSVPDSPLYNFIRDG 449
Cdd:cd09084   153 AQADLLAADIAASPYPVIVCGDFNDTPASYVYRTLKKG 190
 
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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