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Conserved domains on  [gi|23510348|ref|NP_057698|]
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tyrosyl-DNA phosphodiesterase 2 [Homo sapiens]

Protein Classification

tyrosyl-DNA phosphodiesterase 2( domain architecture ID 10198669)

tyrosyl-DNA phosphodiesterase 2 (TDP2) is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks

CATH:  1.10.8.10|3.60.10.10
EC:  3.1.4.-
Gene Symbol:  TDP2
Gene Ontology:  GO:0046872|GO:0070260|GO:0006302|GO:0003697
PubMed:  11478795|12062168
SCOP:  4000749

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 114-358 6.98e-99

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 293.10  E-value: 6.98e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 114 FSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYL---KKRSSNYEIITGHEE----GYFTAIMLKK 186
Cdd:cd09080   1 LKVLTWNVDFLDDVNLAERMRAILKLLEELDPDVIFLQEVTPPFLAYLlsqPWVRKNYYFSEGPPSpavdPYGVLILSKK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 187 SRVklksQEIIPFPSTKMMRNLLCVHVNVS-GNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNL 265
Cdd:cd09080  81 SLV----VRRVPFTSTRMGRNLLAAEINLGsGEPLRLATTHLESLKSHSSERTAQLEEIAKKLKKPPGAANVILGGDFNL 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 266 RDREVtRCGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNL-GITAACKLRFDRIFFRAAAEeghiIPRSLDLLGLEKLDC 344
Cdd:cd09080 157 RDKED-DTGGLPNGFVDAWEELGPPGEPGYTWDTQKNPMLrKGEAGPRKRFDRVLLRGSDL----KPKSIELIGTEPIPG 231

                       250
                ....*....|....*..
gi 23510348 345 ---GRFPSDHWGLLCNL 358
Cdd:cd09080 232 deeGLFPSDHFGLLAEL 248
UBA_TYDP2 cd14344
UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; TDP2, ...
 27-63 8.40e-18

UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; TDP2, also called ETS1-associated protein II (EAPII) or TRAF and TNF receptor-associated protein (Ttrap), is a 5'-Tyr-DNA phosphodiesterase, a member of the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. TDP2 is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation. It can associate with CD40, tumor necrosis factor receptor-75 (TNF-R75) and TNF receptor-associated factors (TRAFs) and may inhibit the activation of nuclear factor-kappa B (NF-kappaB).


:

Pssm-ID: 270529  Cd Length: 37  Bit Score: 75.97  E-value: 8.40e-18
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 23510348  27 LLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:cd14344   1 LLCLEFANVTSCDEAVAQRYLAENGWHMERALNAYFE 37
 
Name Accession Description Interval E-value
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 114-358 6.98e-99

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 293.10  E-value: 6.98e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 114 FSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYL---KKRSSNYEIITGHEE----GYFTAIMLKK 186
Cdd:cd09080   1 LKVLTWNVDFLDDVNLAERMRAILKLLEELDPDVIFLQEVTPPFLAYLlsqPWVRKNYYFSEGPPSpavdPYGVLILSKK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 187 SRVklksQEIIPFPSTKMMRNLLCVHVNVS-GNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNL 265
Cdd:cd09080  81 SLV----VRRVPFTSTRMGRNLLAAEINLGsGEPLRLATTHLESLKSHSSERTAQLEEIAKKLKKPPGAANVILGGDFNL 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 266 RDREVtRCGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNL-GITAACKLRFDRIFFRAAAEeghiIPRSLDLLGLEKLDC 344
Cdd:cd09080 157 RDKED-DTGGLPNGFVDAWEELGPPGEPGYTWDTQKNPMLrKGEAGPRKRFDRVLLRGSDL----KPKSIELIGTEPIPG 231

                       250
                ....*....|....*..
gi 23510348 345 ---GRFPSDHWGLLCNL 358
Cdd:cd09080 232 deeGLFPSDHFGLLAEL 248
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 107-268 6.86e-18

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 79.95  E-value: 6.86e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 107 QQENGSMFSLITWNI-DGLDLNNLSERARgVCSYLALYSPDVIFLQEVippyysylkkrssnyeiitgheegyftAIMlk 185
Cdd:COG3568   1 AAAAAATLRVMTYNIrYGLGTDGRADLER-IARVIRALDPDVVALQEN---------------------------AIL-- 50

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 186 kSRVKLKSQEIIPFP-STKMMRNLLCVHVNVSGNELCLMTSHLESTrgHAAERMNQLKMVLKKMQEAPESATVIFAGDTN 264
Cdd:COG3568  51 -SRYPIVSSGTFDLPdPGGEPRGALWADVDVPGKPLRVVNTHLDLR--SAAARRRQARALAELLAELPAGAPVILAGDFN 127


                ....
gi 23510348 265 LRDR 268
Cdd:COG3568 128 DIDY 131
UBA_TYDP2 cd14344
UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; TDP2, ...
 27-63 8.40e-18

UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; TDP2, also called ETS1-associated protein II (EAPII) or TRAF and TNF receptor-associated protein (Ttrap), is a 5'-Tyr-DNA phosphodiesterase, a member of the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. TDP2 is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation. It can associate with CD40, tumor necrosis factor receptor-75 (TNF-R75) and TNF receptor-associated factors (TRAFs) and may inhibit the activation of nuclear factor-kappa B (NF-kappaB).


Pssm-ID: 270529  Cd Length: 37  Bit Score: 75.97  E-value: 8.40e-18
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 23510348  27 LLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:cd14344   1 LLCLEFANVTSCDEAVAQRYLAENGWHMERALNAYFE 37
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 117-268 2.23e-09

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: 56.46  E-value: 2.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   117 ITWNIDGL--DLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYE------IITGHEEGYFTAIMLKKSR 188
Cdd:pfam03372   1 LTWNVNGGnaDAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGgflsygGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   189 VKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESatVIFAGDTNLrDR 268
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEP--VILAGDFNA-DY 157
UBA_4 pfam14555
UBA-like domain;
31-63 1.61e-07

UBA-like domain;


Pssm-ID: 464207  Cd Length: 43  Bit Score: 47.06  E-value: 1.61e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 23510348    31 EFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:pfam14555   6 QFQAITGADEEVARQYLEAHNWDLEAAVNAFFD 38
 
Name Accession Description Interval E-value
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 114-358 6.98e-99

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. 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: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 293.10  E-value: 6.98e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 114 FSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYL---KKRSSNYEIITGHEE----GYFTAIMLKK 186
Cdd:cd09080   1 LKVLTWNVDFLDDVNLAERMRAILKLLEELDPDVIFLQEVTPPFLAYLlsqPWVRKNYYFSEGPPSpavdPYGVLILSKK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 187 SRVklksQEIIPFPSTKMMRNLLCVHVNVS-GNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNL 265
Cdd:cd09080  81 SLV----VRRVPFTSTRMGRNLLAAEINLGsGEPLRLATTHLESLKSHSSERTAQLEEIAKKLKKPPGAANVILGGDFNL 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 266 RDREVtRCGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNL-GITAACKLRFDRIFFRAAAEeghiIPRSLDLLGLEKLDC 344
Cdd:cd09080 157 RDKED-DTGGLPNGFVDAWEELGPPGEPGYTWDTQKNPMLrKGEAGPRKRFDRVLLRGSDL----KPKSIELIGTEPIPG 231

                       250
                ....*....|....*..
gi 23510348 345 ---GRFPSDHWGLLCNL 358
Cdd:cd09080 232 deeGLFPSDHFGLLAEL 248
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 116-358 2.98e-57

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: 186.53  E-value: 2.98e-57
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 116 LITWNIDGLDLNN-LSERARGVCSYlalySPDVIFLQEVIPPYYS------YLKKRSSNYEIITGHEEGYFTAIMLKKSR 188
Cdd:cd08372   1 VASYNVNGLNAATrASGIARWVREL----DPDIVCLQEVKDSQYSavalnqLLPEGYHQYQSGPSRKEGYEGVAILSKTP 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 189 VklksQEIIPFPSTKM------MRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEA--PESATVIFA 260
Cdd:cd08372  77 K----FKIVEKHQYKFgegdsgERRAVVVKFDVHDKELCVVNAHLQAGGTRADVRDAQLKEVLEFLKRLrqPNSAPVVIC 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 261 GDTNLRDREVTR-------CGGLPNNIVDVWEFLgkpkHCQYTWDTQMnsnlgitAACKLRFDRIFFRAAAEeghIIPRS 333
Cdd:cd08372 153 GDFNVRPSEVDSenpssmlRLFVALNLVDSFETL----PHAYTFDTYM-------HNVKSRLDYIFVSKSLL---PSVKS 218

                       250       260
                ....*....|....*....|....*
gi 23510348 334 LDLLGLEKLdcGRFPSDHWGLLCNL 358
Cdd:cd08372 219 SKILSDAAR--ARIPSDHYPIEVTL 241
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 107-268 6.86e-18

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 79.95  E-value: 6.86e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 107 QQENGSMFSLITWNI-DGLDLNNLSERARgVCSYLALYSPDVIFLQEVippyysylkkrssnyeiitgheegyftAIMlk 185
Cdd:COG3568   1 AAAAAATLRVMTYNIrYGLGTDGRADLER-IARVIRALDPDVVALQEN---------------------------AIL-- 50

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 186 kSRVKLKSQEIIPFP-STKMMRNLLCVHVNVSGNELCLMTSHLESTrgHAAERMNQLKMVLKKMQEAPESATVIFAGDTN 264
Cdd:COG3568  51 -SRYPIVSSGTFDLPdPGGEPRGALWADVDVPGKPLRVVNTHLDLR--SAAARRRQARALAELLAELPAGAPVILAGDFN 127


                ....
gi 23510348 265 LRDR 268
Cdd:COG3568 128 DIDY 131
UBA_TYDP2 cd14344
UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; TDP2, ...
 27-63 8.40e-18

UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; TDP2, also called ETS1-associated protein II (EAPII) or TRAF and TNF receptor-associated protein (Ttrap), is a 5'-Tyr-DNA phosphodiesterase, a member of the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. TDP2 is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation. It can associate with CD40, tumor necrosis factor receptor-75 (TNF-R75) and TNF receptor-associated factors (TRAFs) and may inhibit the activation of nuclear factor-kappa B (NF-kappaB).


Pssm-ID: 270529  Cd Length: 37  Bit Score: 75.97  E-value: 8.40e-18
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 23510348  27 LLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:cd14344   1 LLCLEFANVTSCDEAVAQRYLAENGWHMERALNAYFE 37
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 115-358 1.99e-13

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: 69.17  E-value: 1.99e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 115 SLITWNI----DGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEII-----TGHEEGYFTAIMLK 185
Cdd:cd09083   1 RVMTFNIrydnPSDGENSWENRKDLVAELIKFYDPDIIGTQEALPHQLADLEELLPEYDWIgvgrdDGKEKGEFSAIFYR 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 186 KSRVKLKSQ---------EIIPFPSTKMMRNLLCVHVNV----SGNELCLMTSHLEstrgHAAE--RMNQLKMVLKKMQE 250
Cdd:cd09083  81 KDRFELLDSgtfwlsetpDVVGSKGWDAALPRICTWARFkdkkTGKEFYVFNTHLD----HVGEeaREESAKLILERIKE 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 251 APESATVIFAGDTNLRDREVTRCGGLPNNIVDVWEFLgkPKHCQYTWDTqMNSNLGITaaCKLRFDRIFFRA--AAEEGH 328
Cdd:cd09083 157 IAGDLPVILTGDFNAEPDSEPYKTLTSGGLKDARDTA--ATTDGGPEGT-FHGFKGPP--GGSRIDYIFVSPgvKVLSYE 231

                       250       260       270
                ....*....|....*....|....*....|
gi 23510348 329 IIPRSLDllglekldcGRFPSDHWGLLCNL 358
Cdd:cd09083 232 ILTDRYD---------GRYPSDHFPVVADL 252
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 117-268 2.23e-09

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: 56.46  E-value: 2.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   117 ITWNIDGL--DLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYE------IITGHEEGYFTAIMLKKSR 188
Cdd:pfam03372   1 LTWNVNGGnaDAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGgflsygGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   189 VKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESatVIFAGDTNLrDR 268
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEP--VILAGDFNA-DY 157
UBA_4 pfam14555
UBA-like domain;
31-63 1.61e-07

UBA-like domain;


Pssm-ID: 464207  Cd Length: 43  Bit Score: 47.06  E-value: 1.61e-07
                          10        20        30
                  ....*....|....*....|....*....|...
gi 23510348    31 EFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:pfam14555   6 QFQAITGADEEVARQYLEAHNWDLEAAVNAFFD 38
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 114-321 4.28e-07

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. 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: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 50.47  E-value: 4.28e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 114 FSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEV-------------------IPPYYSYLkkRSSNYEIITGH 174
Cdd:cd10283   1 LRIASWNILNFGNSKGKEKNPAIAEIISAFDLDLIALQEVmdngggldalaklvnelnkPGGTWKYI--VSDKTGGSSGD 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 175 EEgyFTAIMLKKSRVKLKSQEIIP--FPSTKMMRNLLCVH--VNVSGNELCLMTSHL----ESTRGHAAERMNQLKMVLK 246
Cdd:cd10283  79 KE--RYAFLYKSSKVRKVGKAVLEkdSNTDGFARPPYAAKfkSGGTGFDFTLVNVHLksggSSKSGQGAKRVAEAQALAE 156

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 23510348 247 KMQEAPESAT---VIFAGDTNLRDREvtrcgglpnnivDVWEFLGKPKhcqYTWDTQMNSNLGITAACKLR-FDRIFFR 321
Cdd:cd10283 157 YLKELADEDPdddVILLGDFNIPADE------------DAFKALTKAG---FKSLLPDSTNLSTSFKGYANsYDNIFVS 220
UBA_ceTYDP2_like cd14672
UBA-like domain found in Caenorhabditis elegans tyrosyl-DNA phosphodiesterase 2 (TDP2) and ...
 28-63 5.69e-07

UBA-like domain found in Caenorhabditis elegans tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; The family includes C. elegans TDP2 and its homologs found in bilateria. TDP2 (also known as TTRAP or EAPII) belongs to the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. It required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation.


Pssm-ID: 270612  Cd Length: 37  Bit Score: 45.38  E-value: 5.69e-07
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 23510348  28 LCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:cd14672   2 LCEEFAEITGTDEALAQFYLQDRDWDLEKALDVYFG 37
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 102-360 1.16e-06

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 49.61  E-value: 1.16e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 102 PSEDTQQENGSMFSLITWNIDGldlNNLseRARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYE--IITGHEEGYF 179
Cdd:COG3021  83 PAPKSAPAGGPDLRVLTANVLF---GNA--DAEALAALVREEDPDVLVLQETTPAWEEALAALEADYPyrVLCPLDNAYG 157

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 180 TAIMlkkSRVKLKSQEIIPFPSTKmmRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESatVIF 259
Cdd:COG3021 158 MALL---SRLPLTEAEVVYLVGDD--IPSIRATVELPGGPVRLVAVHPAPPVGGSAERDAELAALAKAVAALDGP--VIV 230

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 260 AGDTN-------LRDreVTRCGGLPNniVDVWEFLGkpkhcqYTWDTQMnsnlgitAACKLRFDRIFFRaaaeeghiipR 332
Cdd:COG3021 231 AGDFNatpwsptLRR--LLRASGLRD--ARAGRGLG------PTWPANL-------PFLRLPIDHVLVS----------R 283

                       250       260
                ....*....|....*....|....*...
gi 23510348 333 SLDLLGLEKLDCGRfpSDHWGLLCNLDI 360
Cdd:COG3021 284 GLTVVDVRVLPVIG--SDHRPLLAELAL 309
UBA_p47 cd14348
UBA-like domain found in NSFL1 cofactor p47 and similar proteins; p47, also called UBX ...
 31-63 1.77e-06

UBA-like domain found in NSFL1 cofactor p47 and similar proteins; p47, also called UBX domain-containing protein 2C, is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. p47, together with p97, forms the p97-p47 complex that plays an important role in regulation of membrane fusion events. p47 contains an N-terminal ubiquitin-associated (UBA)-like domain, a central SEP (named after shp1, eyc and p47) domain, and a ubiquitin-like (UBX) domain. UBA-like domain is responsible for forming a highly stable complex with ubiquitin. SEP domain and UBX domain may involve in p47 trimerization or forms a stable complex with the p97 N-terminal domain.


Pssm-ID: 270533  Cd Length: 40  Bit Score: 44.07  E-value: 1.77e-06
                        10        20        30
                ....*....|....*....|....*....|...
gi 23510348  31 EFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:cd14348   6 QFVSVTGADEDRAKFFLESAGWDLEAALSSFFE 38
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 116-358 2.06e-05

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. 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: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 45.42  E-value: 2.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 116 LITWNIDGLdlnNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEII-----TGHEEGyfTAIMLKKS--R 188
Cdd:cd09076   1 IGTLNVRGL---RSPGKRAQLLEELKRKKLDILGLQETHWTGEGELKKKREGGTILysgsdSGKSRG--VAILLSKTaaN 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 189 VKLKSQEIIPfpstkmmRNLLCVHVNVSGNELCLMTSHLeSTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNL--- 265
Cdd:cd09076  76 KLLEYTKVVS-------GRIIMVRFKIKGKRLTIINVYA-PTARDEEEKEEFYDQLQDVLDKVPRHDTLIIGGDFNAvlg 147

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 266 RDREVTRCGGLPN--------------NIVDVWEFLGKPKHcQYTWdtqmNSNLGITAAcklRFDRIFFRaaaeeGHIIP 331
Cdd:cd09076 148 PKDDGRKGLDKRNengeralsalieehDLVDVWRENNPKTR-EYTW----RSPDHGSRS---RIDRILVS-----KRLRV 214

                       250       260       270
                ....*....|....*....|....*....|
gi 23510348 332 RsldllgleKLDCGRFP---SDHWGLLCNL 358
Cdd:cd09076 215 K--------VKKTKITPgagSDHRLVTLKL 236
UBA_TAP-C_like cd14273
UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; ...
 32-62 2.45e-05

UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. Its biological function remains unclear. TDP2 is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks. OTU7A and OTU7B are zinc finger proteins that function as deubiquitinating enzymes. p47 is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. DCNL1 plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. The biological function of DCNL2 remains unclear. Yeast DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity.


Pssm-ID: 270459  Cd Length: 31  Bit Score: 40.85  E-value: 2.45e-05
                        10        20        30
                ....*....|....*....|....*....|.
gi 23510348  32 FASVASCDAAVAQCFLAENDWEMERALNSYF 62
Cdd:cd14273   1 FMEITGADPETARQYLESNNWDLEAAINLYF 31
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
 128-358 3.89e-05

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: 44.72  E-value: 3.89e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 128 NLSERARGVCSYLALYSPDVIFLQEViPPYYSYLKK--RSSNYEiitgheeGYF-------------------TAIMLKK 186
Cdd:cd09096  28 KWEERKYLILEEILTYDPDILCLQEV-DHYKDTLQPllSRLGYQ-------GTFfpkpdspclyiennngpdgCALFFRK 99

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 187 SRVKLKSQEIIPFPSTKMMRN---LLCVHV-NVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESAT--VIFA 260
Cdd:cd09096 100 DRFELVNTEKIRLSAMTLKTNqvaIACTLRcKETGREICLAVTHLKARTGWERLRSEQGKDLLQNLQSFIEGAKipLIIC 179

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 261 GDTNLRDRE--VTRCGGLPNNIVDVWEFLG--KPKHCQY-TWDTQMnsnlgiTAACKLRFDRIFFRAAAEEghiIPRSLD 335
Cdd:cd09096 180 GDFNAEPTEpvYKTFSNSSLNLNSAYKLLSadGQSEPPYtTWKIRT------SGECRHTLDYIFYSKDALS---VEQLLD 250

                       250       260
                ....*....|....*....|....*...
gi 23510348 336 LLGLE-----KLDCGRFPSDHWGLLCNL 358
Cdd:cd09096 251 LPTEEqigpnRLPSFNYPSDHLSLVCDF 278
UBA_DCN1 cd14352
UBA-like domain found in yeast defective in cullin neddylation protein 1 (DCN1) and similar ...
 31-62 2.21e-04

UBA-like domain found in yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins; DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity. It contains an N-terminal ubiquitin-associated (UBA)-like domain and a unique C-terminal PONY domain that is essential for the neddylation function of DCN1.


Pssm-ID: 270537  Cd Length: 36  Bit Score: 38.03  E-value: 2.21e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 23510348  31 EFASVASCDAAVAQCFLAENDWEMERALNSYF 62
Cdd:cd14352   5 QFREITATSPEVARDYLQRSNWNLNYAVDDFY 36
UBA_Ubx1_like cd14351
UBA-like domain found in yeast UBX domain-containing protein 1 (Ubx1) and similar proteins; ...
 32-62 3.61e-04

UBA-like domain found in yeast UBX domain-containing protein 1 (Ubx1) and similar proteins; Ubx1, also called suppressor of high-copy PP1 protein (Shp1), is the substrate-recruiting cofactor of AAA-adenosine triphosphatase Cdc48 in Saccharomyces cerevisiae. In concert with ubiquitin-like Atg8, Cdc48 and Ubx1 are involved in the regulation of autophagosome biogenesis. Ubx1 also functions as a regulator of phosphoprotein phosphatase 1 (PP1) with differential effects on glycogen metabolism, meiotic differentiation, and mitotic cell cycle progression. All family members contain an N-terminal ubiquitin-associated (UBA)-like domain.


Pssm-ID: 270536  Cd Length: 37  Bit Score: 37.45  E-value: 3.61e-04
                        10        20        30
                ....*....|....*....|....*....|.
gi 23510348  32 FASVASCDAAVAQCFLAENDWEMERALNSYF 62
Cdd:cd14351   7 FMELTGASPEVAQQYLEEYGGDLNDAINAYF 37
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 116-251 5.12e-04

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: 41.13  E-value: 5.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 116 LITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEvippYYSYLKKRSS-----------NYEIITGHEEGYFTAIMl 184
Cdd:cd09084   1 VMSYNVRSFNRYKWKDDPDKILDFIKKQDPDILCLQE----YYGSEGDKDDdlrlllkgypyYYVVYKSDSGGTGLAIF- 75

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 23510348 185 kkSRVKLKSQEIIPFPSTKmmRNLLCVHVNVSGNELCLMTSHLESTR---------GHAAERMNQLKMVLKKMQEA 251
Cdd:cd09084  76 --SKYPILNSGSIDFPNTN--NNAIFADIRVGGDTIRVYNVHLESFRitpsdkelyKEEKKAKELSRNLLRKLAEA 147
UBA_DCNL cd14350
UBA-like domain found in DCN1-like protein DCNL1, DCNL2 and similar proteins; DCNL1 (defective ...
 24-65 6.52e-04

UBA-like domain found in DCN1-like protein DCNL1, DCNL2 and similar proteins; DCNL1 (defective in cullin neddylation protein 1-like protein 1), also called DCUN1 domain-containing protein 1, is encoded by squamous cell carcinoma-related oncogene SCCRO (DCUN1D1). It interacts with known cullin isoforms as well as ROC1, Ubc12 and CAND1, the components of the neddylation pathway. It plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. DCNL1 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that binds to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. DCNL2 (defective in cullin neddylation protein 1-like protein 2), also called DCUN1 domain-containing protein 2, is encoded by gene DCUN1D2. Although its biological function remains unclear, DCNL2 shows high sequence similarity with DCNL1 and may also contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. Like DCNL1, DCNL2 contains an N-terminal UBA-like domain and a C-terminal cullin binding domain.


Pssm-ID: 270535  Cd Length: 42  Bit Score: 36.85  E-value: 6.52e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 23510348  24 KRRLLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFEPP 65
Cdd:cd14350   1 SQKDKVRQFMSITQANEKTAIQCLKDADWNLELAVDAYFQNP 42
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 114-153 5.69e-03

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 37.92  E-value: 5.69e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 23510348 114 FSLITWNIDGLdlnnlseRAR---GVCSYLALYSPDVIFLQEV 153
Cdd:cd09087   1 LKIISWNVNGL-------RALlkkGLLDYVKKEDPDILCLQET 36
XthA COG0708
Exonuclease III [Replication, recombination and repair];
116-153 9.98e-03

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 37.36  E-value: 9.98e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 23510348 116 LITWNIDGLdlnnlseRAR--GVCSYLALYSPDVIFLQEV 153
Cdd:COG0708   3 IASWNVNGI-------RARlpKLLDWLAEEDPDVLCLQET 35
 
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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