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Conserved domains on  [gi|1016080627|ref|NP_001309106|]
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2',5'-phosphodiesterase 12 isoform 3 precursor [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03144 super family cl28585
Carbon catabolite repressor protein 4 homolog; Provisional
 225-461 4.81e-34

Carbon catabolite repressor protein 4 homolog; Provisional


The actual alignment was detected with superfamily member PLN03144:

Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 134.86  E-value: 4.81e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 225 WTETDvEERVYTPSNADIGLRLKLHCTPGD---GQRFGHSRELESVCVVEAgPGTC---------TFDHRHLYTKKVTED 292
Cdd:PLN03144  174 WIEVG-RSKTYTPTADDVGHVLKFECVVVDaetGLPVGHPQSILTSRVIPA-PSPTprrliqvngLDGMGHLDLDGRTSS 251

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 293 ALIRTV-SYNILADTYAQTEFsrtvlYPYCAPYALELDYR-QNLIqKELTGYNADVICLQEVDRAVFSDSLVPALEAFGL 370
Cdd:PLN03144  252 AGTFTVlSYNILSDLYATSDM-----YSYCPPWALSWTYRrQNLL-REIVGYRADILCLQEVQSDHFEEFFAPELDKHGY 325

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 371 EGVFRIKQHE----------GLATFYRKSKFSLLSQHDISFYEALESdplhkeLLEKLVlyPSAQEKV----LQRSSVLQ 436
Cdd:PLN03144  326 QALYKKKTTEvytgntyvidGCATFFRRDRFSLVKKYEVEFNKAAQS------LTEALI--PSAQKKAalnrLLKDNVAL 397

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1016080627 437 VSVL------QSTKDSSKR--ICVANTHLYWHP 461
Cdd:PLN03144  398 IVVLeakfgnQGADNGGKRqlLCVANTHIHANQ 430
 
Name Accession Description Interval E-value
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 225-461 4.81e-34

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 134.86  E-value: 4.81e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 225 WTETDvEERVYTPSNADIGLRLKLHCTPGD---GQRFGHSRELESVCVVEAgPGTC---------TFDHRHLYTKKVTED 292
Cdd:PLN03144  174 WIEVG-RSKTYTPTADDVGHVLKFECVVVDaetGLPVGHPQSILTSRVIPA-PSPTprrliqvngLDGMGHLDLDGRTSS 251

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 293 ALIRTV-SYNILADTYAQTEFsrtvlYPYCAPYALELDYR-QNLIqKELTGYNADVICLQEVDRAVFSDSLVPALEAFGL 370
Cdd:PLN03144  252 AGTFTVlSYNILSDLYATSDM-----YSYCPPWALSWTYRrQNLL-REIVGYRADILCLQEVQSDHFEEFFAPELDKHGY 325

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 371 EGVFRIKQHE----------GLATFYRKSKFSLLSQHDISFYEALESdplhkeLLEKLVlyPSAQEKV----LQRSSVLQ 436
Cdd:PLN03144  326 QALYKKKTTEvytgntyvidGCATFFRRDRFSLVKKYEVEFNKAAQS------LTEALI--PSAQKKAalnrLLKDNVAL 397

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1016080627 437 VSVL------QSTKDSSKR--ICVANTHLYWHP 461
Cdd:PLN03144  398 IVVLeakfgnQGADNGGKRqlLCVANTHIHANQ 430
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 299-462 1.04e-32

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: 126.65  E-value: 1.04e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 299 SYNILADTYAQTEfsrtvLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQ 378
Cdd:cd09097     3 CYNVLCDKYATRQ-----QYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 379 H------------EGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLvlypsaqEKVLQRSSVLQVSVLQSTKDS 446
Cdd:cd09097    78 RaktmseaerkhvDGCAIFFKTSKFKLVEKHLIEFNQLAMANADAEGSEDML-------NRVMTKDNIALIVVLEARETS 150

                         170       180
                  ....*....|....*....|.
gi 1016080627 447 SK-----RICVANTHLYWHPK 462
Cdd:cd09097   151 YEgnkgqLLIVANTHIHWDPE 171
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
287-471 4.72e-21

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


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 94.45  E-value: 4.72e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 287 KKVTEDALIRTVSYNILADTYAqtefsRTVLYPYCAPyALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALE 366
Cdd:COG5239    23 HYAEKDTDFTIMTYNVLAQTYA-----TRKMYPYSGW-ALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLG 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 367 AFGLEGVF-------------RIKQHEGLATFYRK----SKFSLLSQHDISFYEALESDplhkellEKLVLYPSAQEKVL 429
Cdd:COG5239    97 KLGYDGIFipkerkvkwmidyDTTKVDGCAIFLKRfidsSKLGLILAVTHLFWHPYGYY-------ERFRQTYILLNRIG 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1016080627 430 QRSSVLQVSVLQS--TKDSSKRICVANTHLYWHPKGRFYLVSQV 471
Cdd:COG5239   170 EKDNIAWVCLFVGlfNKEPGDTPYVANTHLPWDPKYRDVKLIQC 213
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 323-401 1.29e-04

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: 42.98  E-value: 1.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 323 PYALELDYRQNLIQKELTGYNADVICLQEVD---RAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDI 399
Cdd:pfam03372  10 ADAAGDDRKLDALAALIRAYDPDVVALQETDdddASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPLSSVILVDLG 89


                  ..
gi 1016080627 400 SF 401
Cdd:pfam03372  90 EF 91
 
Name Accession Description Interval E-value
PLN03144 PLN03144
Carbon catabolite repressor protein 4 homolog; Provisional
 225-461 4.81e-34

Carbon catabolite repressor protein 4 homolog; Provisional


Pssm-ID: 178689 [Multi-domain]  Cd Length: 606  Bit Score: 134.86  E-value: 4.81e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 225 WTETDvEERVYTPSNADIGLRLKLHCTPGD---GQRFGHSRELESVCVVEAgPGTC---------TFDHRHLYTKKVTED 292
Cdd:PLN03144  174 WIEVG-RSKTYTPTADDVGHVLKFECVVVDaetGLPVGHPQSILTSRVIPA-PSPTprrliqvngLDGMGHLDLDGRTSS 251

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 293 ALIRTV-SYNILADTYAQTEFsrtvlYPYCAPYALELDYR-QNLIqKELTGYNADVICLQEVDRAVFSDSLVPALEAFGL 370
Cdd:PLN03144  252 AGTFTVlSYNILSDLYATSDM-----YSYCPPWALSWTYRrQNLL-REIVGYRADILCLQEVQSDHFEEFFAPELDKHGY 325

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 371 EGVFRIKQHE----------GLATFYRKSKFSLLSQHDISFYEALESdplhkeLLEKLVlyPSAQEKV----LQRSSVLQ 436
Cdd:PLN03144  326 QALYKKKTTEvytgntyvidGCATFFRRDRFSLVKKYEVEFNKAAQS------LTEALI--PSAQKKAalnrLLKDNVAL 397

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1016080627 437 VSVL------QSTKDSSKR--ICVANTHLYWHP 461
Cdd:PLN03144  398 IVVLeakfgnQGADNGGKRqlLCVANTHIHANQ 430
Deadenylase_CCR4 cd09097
C-terminal deadenylase domain of CCR4 and related domains; This subfamily contains the ...
 299-462 1.04e-32

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: 126.65  E-value: 1.04e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 299 SYNILADTYAQTEfsrtvLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQ 378
Cdd:cd09097     3 CYNVLCDKYATRQ-----QYGYCPSWALNWDYRKQNILKEILSYNADILCLQEVETDQYEDFFLPELKQHGYDGVFKPKS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 379 H------------EGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLvlypsaqEKVLQRSSVLQVSVLQSTKDS 446
Cdd:cd09097    78 RaktmseaerkhvDGCAIFFKTSKFKLVEKHLIEFNQLAMANADAEGSEDML-------NRVMTKDNIALIVVLEARETS 150

                         170       180
                  ....*....|....*....|.
gi 1016080627 447 SK-----RICVANTHLYWHPK 462
Cdd:cd09097   151 YEgnkgqLLIVANTHIHWDPE 171
CCR4 COG5239
mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification];
287-471 4.72e-21

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


Pssm-ID: 227564 [Multi-domain]  Cd Length: 378  Bit Score: 94.45  E-value: 4.72e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 287 KKVTEDALIRTVSYNILADTYAqtefsRTVLYPYCAPyALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALE 366
Cdd:COG5239    23 HYAEKDTDFTIMTYNVLAQTYA-----TRKMYPYSGW-ALKWSYRSRLLLQELLYYNADILCLQEVDAEDFEDFWKDQLG 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 367 AFGLEGVF-------------RIKQHEGLATFYRK----SKFSLLSQHDISFYEALESDplhkellEKLVLYPSAQEKVL 429
Cdd:COG5239    97 KLGYDGIFipkerkvkwmidyDTTKVDGCAIFLKRfidsSKLGLILAVTHLFWHPYGYY-------ERFRQTYILLNRIG 169

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1016080627 430 QRSSVLQVSVLQS--TKDSSKRICVANTHLYWHPKGRFYLVSQV 471
Cdd:COG5239   170 EKDNIAWVCLFVGlfNKEPGDTPYVANTHLPWDPKYRDVKLIQC 213
Deadenylase_CCR4b cd10312
C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit ...
 300-462 6.64e-18

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: 84.69  E-value: 6.64e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 300 YNILADTYAQTEfsrtvLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVF----- 374
Cdd:cd10312     4 YNVLCDKYATRQ-----LYGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFspksr 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 375 ------RIKQH-EGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLeklvlypsaQEKVLQRSSVLQVSVLQSTKD-- 445
Cdd:cd10312    79 akimseQERKHvDGCAIFFKTEKFSLVQKHTVEFNQVAMANSEGSEAM---------LNRVMTKDNIGVAVVLEVHKElf 149

                         170       180
                  ....*....|....*....|....*..
gi 1016080627 446 ----------SSKRICVANTHLYWHPK 462
Cdd:cd10312   150 gagmkpihaaDKQLLIVANAHMHWDPE 176
Deadenylase_CCR4a cd10313
C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6; ...
 300-462 6.58e-17

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: 82.02  E-value: 6.58e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 300 YNILADTYAQTEfsrtvLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQH 379
Cdd:cd10313     4 YNVLCDKYATRQ-----LYGYCPSWALNWDYRKKAIMQEILSCNADIISLQEVETEQYYSFFLVELKERGYNGFFSPKSR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 380 ------------EGLATFYRKSKFSLLSQHDISFYE-ALESDPLHKELLEKLVLYPSAQEKVL--QRSSVLQVSVLQSTK 444
Cdd:cd10313    79 artmseqerkhvDGCAIFFKTEKFTLVQKHTVEFNQlAMANSEGSEAMLNRVMTKDNIGVAVLleLRKELIEMSSGKPHL 158

                         170
                  ....*....|....*....
gi 1016080627 445 DSSKR-ICVANTHLYWHPK 462
Cdd:cd10313   159 GMEKQlILVANAHMHWDPE 177
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 296-457 6.52e-15

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: 74.77  E-value: 6.52e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 296 RTVSYNILADTYAQT--EFSRtvlypyCAPYALELDYRQNLIQKELTGYNADVICLQEVDRavFSDSLVPALEAFGLEGV 373
Cdd:cd09096     1 RVMQWNILAQALGEGkdGFVR------CPCEALKWEERKYLILEEILTYDPDILCLQEVDH--YKDTLQPLLSRLGYQGT 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 374 F---------RIKQH---EGLATFYRKSKFSLLSQhdisfyealesdplhkellEKLVLypsaQEKVLQRSSVLQVSVLQ 441
Cdd:cd09096    73 FfpkpdspclYIENNngpDGCALFFRKDRFELVNT-------------------EKIRL----SAMTLKTNQVAIACTLR 129

                         170
                  ....*....|....*.
gi 1016080627 442 sTKDSSKRICVANTHL 457
Cdd:cd09096   130 -CKETGREICLAVTHL 144
Deadenylase cd09082
C-terminal deadenylase domain of CCR4, nocturnin, and related domains; This family contains ...
 298-457 3.44e-09

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: 58.52  E-value: 3.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 298 VSYNILADTYAQTEFsrtvlYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIK 377
Cdd:cd09082     2 MCYNVLCDKYATRQL-----YGYCPSWALNWEYRKKGIMEEIVNCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPK 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 378 --------QH----EGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQ---EKVLQRSSVLQVSVLQS 442
Cdd:cd09082    77 srakimseQErkhvDGCAIFFKTEKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIgvaVVLEVHKELFGAGMKPI 156

                         170
                  ....*....|....*
gi 1016080627 443 TKDSSKRICVANTHL 457
Cdd:cd09082   157 HAADKQLLIVANAHM 171
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 323-401 1.29e-04

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: 42.98  E-value: 1.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1016080627 323 PYALELDYRQNLIQKELTGYNADVICLQEVD---RAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDI 399
Cdd:pfam03372  10 ADAAGDDRKLDALAALIRAYDPDVVALQETDdddASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPLSSVILVDLG 89


                  ..
gi 1016080627 400 SF 401
Cdd:pfam03372  90 EF 91
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 329-398 1.92e-04

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: 42.97  E-value: 1.92e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1016080627 329 DYRQNLIQKELTGYNADVICLQEVDRAVFSDsLVPALEAFGLEGVFRIKQH---EGLATFYRKSKFSLLSQHD 398
Cdd:cd09083    20 ENRKDLVAELIKFYDPDIIGTQEALPHQLAD-LEELLPEYDWIGVGRDDGKekgEFSAIFYRKDRFELLDSGT 91
 
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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