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

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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 9.54e-98

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  Cd Length: 248  Bit Score: 293.10  E-value: 9.54e-98
                        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_4 pfam14555
UBA-like domain;
28-63 2.22e-07

UBA-like domain;


:

Pssm-ID: 258693  Cd Length: 43  Bit Score: 47.07  E-value: 2.22e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 23510348    28 LCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:pfam14555   3 LISQFQAITGADEEVARQYLEANNWDLEAAVNAYFD 38
 
Name Accession Description Interval E-value
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
114-358 9.54e-98

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  Cd Length: 248  Bit Score: 293.10  E-value: 9.54e-98
                        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
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
117-351 2.03e-15

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: 251907  Cd Length: 228  Bit Score: 73.33  E-value: 2.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   117 ITWNIDGLdlNNLSERARGVCSYLALYSPDVIFLQEV---------IPPYYSYLKKRSSNYE--IITGHEEGYFTAIMlk 185
Cdd:pfam03372   1 LTWNVNGL--RAGLKKLEALADLLRAHDPDVLALQETddypasdalLTGLAGELGFNGSDALgrYGGGDAGGGGVALL-- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   186 kSRVKLKSQEIIPFP--STKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESatVIFAGDT 263
Cdd:pfam03372  77 -SRYPLSSSIQLILSelGCPGIRVLRLLSGGKGIVKVSLVNVHLPPGNGLREADLRALLQLLSDLLADLRP--VVLAGDF 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   264 NLRDREVT---RCGGLPNNIVDVWEFLGKPKHcQYTWDTQMNSNLGitaackLRFDRIFFRAAAEEghIIPRSLDLLgle 340
Cdd:pfam03372 154 NAAHAEAGnsgRGEGLPDLFRLLLEDPLLPGI-AGTGDTYTNKNGP------SRLDYILVSSGLAA--LVVVATLVL--- 221
                         250
                  ....*....|.
gi 23510348   341 kldcGRFPSDH 351
Cdd:pfam03372 222 ----PPRGSDH 228
UBA_4 pfam14555
UBA-like domain;
28-63 2.22e-07

UBA-like domain;


Pssm-ID: 258693  Cd Length: 43  Bit Score: 47.07  E-value: 2.22e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 23510348    28 LCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:pfam14555   3 LISQFQAITGADEEVARQYLEANNWDLEAAVNAYFD 38
ElsH COG3568
Metal-dependent hydrolase [General function prediction only]
113-360 2.04e-05

Metal-dependent hydrolase [General function prediction only]


Pssm-ID: 226098  Cd Length: 259  Bit Score: 44.31  E-value: 2.04e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 113 MFSLITWNI-------DG-LDLNNLSERARGVcsylalySPDVIFLQEV-------------IPPYYSYLKKRS-----S 166
Cdd:COG3568   9 RFKVLTYNIhkgfgafDRrFDLPRIAEVIREV-------GADIVALQEVdgafgrhrdglldLPHLLGRLGLAPywwsgA 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 167 NYEIITGHeeGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRN-LLCVHVNVSGNELCLMTSHLESTrghAAERMNQLKMVL 245
Cdd:COG3568  82 AFGAVYGE--GQHGNAILSRLPIRDVENLALPDPTGLEPRGaLLAEIELPGGKPLRVINAHLGLS---EESRLRQAAALL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 246 KKMQEAPESATVIfAGDTNLRDREVTrcgglpnnivdvWEFLGKPKHCQ-------------YTWDTqMNSNLGitaacK 312
Cdd:COG3568 157 ALAGLPALNPTVL-MGDFNNEPGSAE------------YRLAARSPLNAqaaltgafapavgRTIRT-FPSNTP-----L 217
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 23510348 313 LRFDRIFFR--AAAEEGHIIPRSLdllglekldcGRFPSDHWGLLCNLDI 360
Cdd:COG3568 218 LRLDRIFVSkeLAIRSVHVLTDRL----------ARVASDHLPLLAELRL 257
 
Name Accession Description Interval E-value
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
114-358 9.54e-98

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  Cd Length: 248  Bit Score: 293.10  E-value: 9.54e-98
                        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 1.84e-56

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  Cd Length: 241  Bit Score: 186.53  E-value: 1.84e-56
                        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
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
117-351 2.03e-15

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: 251907  Cd Length: 228  Bit Score: 73.33  E-value: 2.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   117 ITWNIDGLdlNNLSERARGVCSYLALYSPDVIFLQEV---------IPPYYSYLKKRSSNYE--IITGHEEGYFTAIMlk 185
Cdd:pfam03372   1 LTWNVNGL--RAGLKKLEALADLLRAHDPDVLALQETddypasdalLTGLAGELGFNGSDALgrYGGGDAGGGGVALL-- 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   186 kSRVKLKSQEIIPFP--STKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESatVIFAGDT 263
Cdd:pfam03372  77 -SRYPLSSSIQLILSelGCPGIRVLRLLSGGKGIVKVSLVNVHLPPGNGLREADLRALLQLLSDLLADLRP--VVLAGDF 153
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348   264 NLRDREVT---RCGGLPNNIVDVWEFLGKPKHcQYTWDTQMNSNLGitaackLRFDRIFFRAAAEEghIIPRSLDLLgle 340
Cdd:pfam03372 154 NAAHAEAGnsgRGEGLPDLFRLLLEDPLLPGI-AGTGDTYTNKNGP------SRLDYILVSSGLAA--LVVVATLVL--- 221
                         250
                  ....*....|.
gi 23510348   341 kldcGRFPSDH 351
Cdd:pfam03372 222 ----PPRGSDH 228
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
115-358 7.25e-14

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  Cd Length: 252  Bit Score: 69.17  E-value: 7.25e-14
                        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
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
114-321 1.65e-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  Cd Length: 266  Bit Score: 50.47  E-value: 1.65e-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_4 pfam14555
UBA-like domain;
28-63 2.22e-07

UBA-like domain;


Pssm-ID: 258693  Cd Length: 43  Bit Score: 47.07  E-value: 2.22e-07
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 23510348    28 LCVEFASVASCDAAVAQCFLAENDWEMERALNSYFE 63
Cdd:pfam14555   3 LISQFQAITGADEEVARQYLEANNWDLEAAVNAYFD 38
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
116-358 7.90e-06

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  Cd Length: 236  Bit Score: 45.42  E-value: 7.90e-06
                        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
Deadenylase_nocturnin cd09096
C-terminal deadenylase domain of nocturnin and related domains; This subfamily contains the ...
128-358 1.43e-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  Cd Length: 280  Bit Score: 44.72  E-value: 1.43e-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
ElsH COG3568
Metal-dependent hydrolase [General function prediction only]
113-360 2.04e-05

Metal-dependent hydrolase [General function prediction only]


Pssm-ID: 226098  Cd Length: 259  Bit Score: 44.31  E-value: 2.04e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 113 MFSLITWNI-------DG-LDLNNLSERARGVcsylalySPDVIFLQEV-------------IPPYYSYLKKRS-----S 166
Cdd:COG3568   9 RFKVLTYNIhkgfgafDRrFDLPRIAEVIREV-------GADIVALQEVdgafgrhrdglldLPHLLGRLGLAPywwsgA 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 167 NYEIITGHeeGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRN-LLCVHVNVSGNELCLMTSHLESTrghAAERMNQLKMVL 245
Cdd:COG3568  82 AFGAVYGE--GQHGNAILSRLPIRDVENLALPDPTGLEPRGaLLAEIELPGGKPLRVINAHLGLS---EESRLRQAAALL 156
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 23510348 246 KKMQEAPESATVIfAGDTNLRDREVTrcgglpnnivdvWEFLGKPKHCQ-------------YTWDTqMNSNLGitaacK 312
Cdd:COG3568 157 ALAGLPALNPTVL-MGDFNNEPGSAE------------YRLAARSPLNAqaaltgafapavgRTIRT-FPSNTP-----L 217
                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|
gi 23510348 313 LRFDRIFFR--AAAEEGHIIPRSLdllglekldcGRFPSDHWGLLCNLDI 360
Cdd:COG3568 218 LRLDRIFVSkeLAIRSVHVLTDRL----------ARVASDHLPLLAELRL 257
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
116-251 1.90e-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  Cd Length: 246  Bit Score: 41.13  E-value: 1.90e-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
XthA COG0708
Exonuclease III [DNA replication, recombination, and repair]
114-152 1.43e-03

Exonuclease III [DNA replication, recombination, and repair]


Pssm-ID: 223780  Cd Length: 261  Bit Score: 38.35  E-value: 1.43e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 23510348 114 FSLITWNIDGLdlnnlseRAR--GVCSYLALYSPDVIFLQE 152
Cdd:COG0708   1 MKIASWNVNGL-------RARlkKLLDWLEEEQPDVLCLQE 34
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
114-153 2.06e-03

Human Ape1-like subfamily of the ExoIII family purinic/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  Cd Length: 253  Bit Score: 37.92  E-value: 2.06e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 23510348 114 FSLITWNIDGLdlnnlseRAR---GVCSYLALYSPDVIFLQEV 153
Cdd:cd09087   1 LKIISWNVNGL-------RALlkkGLLDYVKKEDPDILCLQET 36
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.11
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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