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Conserved domains on  [gi|1160351512|ref|NP_001336370|]
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endonuclease 8-like 2 isoform b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FpgNei_N super family cl03119
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 62-124 4.31e-38

N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins.


The actual alignment was detected with superfamily member cd08968:

Pssm-ID: 470740  Cd Length: 126  Bit Score: 130.26  E-value: 4.31e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1160351512  62 PAGDAGRWLRVSFGLFGSVWVNDFSRAKKANKRGDWRDPSPRLVLHFGGGGFLAFYNCQLSWS 124
Cdd:cd08968    64 PDRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVLHFESGGFLVFYNCRMSWC 126
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
65-259 5.66e-22

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0266:

Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 92.11  E-value: 5.66e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512  65 DAGRWLRVSFGLFGSVWVNDfsrAKKANKRGDwrdpspRLVLHFGGGGFLAFYN------CQLSWSSSPVVTPTC----- 133
Cdd:COG0266    64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADprrfgaLELLTPDELEVHPLLarlgp 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 134 DILSEKFHRGQALEAL-GQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ 212
Cdd:COG0266   135 EPLDPDFDPEYLAARLrRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1160351512 213 ----------------GKFQgrpQHTQVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 259
Cdd:COG0266   215 aggttlrdyvnadgepGYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
 
Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 62-124 4.31e-38

N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes.


Pssm-ID: 176802  Cd Length: 126  Bit Score: 130.26  E-value: 4.31e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1160351512  62 PAGDAGRWLRVSFGLFGSVWVNDFSRAKKANKRGDWRDPSPRLVLHFGGGGFLAFYNCQLSWS 124
Cdd:cd08968    64 PDRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVLHFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
65-259 5.66e-22

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 92.11  E-value: 5.66e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512  65 DAGRWLRVSFGLFGSVWVNDfsrAKKANKRGDwrdpspRLVLHFGGGGFLAFYN------CQLSWSSSPVVTPTC----- 133
Cdd:COG0266    64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADprrfgaLELLTPDELEVHPLLarlgp 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 134 DILSEKFHRGQALEAL-GQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ 212
Cdd:COG0266   135 EPLDPDFDPEYLAARLrRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1160351512 213 ----------------GKFQgrpQHTQVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 259
Cdd:COG0266   215 aggttlrdyvnadgepGYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
158-260 1.46e-17

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 80.13  E-value: 1.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 158 TLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE---------------FSTAwlQGK---FQgrp 219
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAvlaeaieqggttlrdYVNA--DGKpgyFQ--- 235

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1160351512 220 QHTQVY--QKEQCPA-GHQVMKEAFGpedglQRLTWWCPQCQPQ 260
Cdd:PRK01103  236 QSLQVYgrEGEPCRRcGTPIEKIKQG-----GRSTFFCPRCQKR 274
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 159-258 2.03e-15

DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 73.87  E-value: 2.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 159 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE------------FST----AWLQGKFQGRpqhT 222
Cdd:TIGR00577 162 LLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEvlrkaiemggttIRDfsqsDGHNGYFQQE---L 238

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1160351512 223 QVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQ 258
Cdd:TIGR00577 239 QVYGRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 159-205 6.14e-12

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 60.38  E-value: 6.14e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1160351512 159 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE 205
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
 
Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 62-124 4.31e-38

N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes.


Pssm-ID: 176802  Cd Length: 126  Bit Score: 130.26  E-value: 4.31e-38
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1160351512  62 PAGDAGRWLRVSFGLFGSVWVNDFSRAKKANKRGDWRDPSPRLVLHFGGGGFLAFYNCQLSWS 124
Cdd:cd08968    64 PDRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVLHFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
65-259 5.66e-22

Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 92.11  E-value: 5.66e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512  65 DAGRWLRVSFGLFGSVWVNDfsrAKKANKRGDwrdpspRLVLHFGGGGFLAFYN------CQLSWSSSPVVTPTC----- 133
Cdd:COG0266    64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADprrfgaLELLTPDELEVHPLLarlgp 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 134 DILSEKFHRGQALEAL-GQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ 212
Cdd:COG0266   135 EPLDPDFDPEYLAARLrRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIE 214

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1160351512 213 ----------------GKFQgrpQHTQVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 259
Cdd:COG0266   215 aggttlrdyvnadgepGYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
158-260 1.46e-17

bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 80.13  E-value: 1.46e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 158 TLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE---------------FSTAwlQGK---FQgrp 219
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAvlaeaieqggttlrdYVNA--DGKpgyFQ--- 235

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1160351512 220 QHTQVY--QKEQCPA-GHQVMKEAFGpedglQRLTWWCPQCQPQ 260
Cdd:PRK01103  236 QSLQVYgrEGEPCRRcGTPIEKIKQG-----GRSTFFCPRCQKR 274
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 159-258 2.03e-15

DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 73.87  E-value: 2.03e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 159 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE------------FST----AWLQGKFQGRpqhT 222
Cdd:TIGR00577 162 LLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEvlrkaiemggttIRDfsqsDGHNGYFQQE---L 238

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1160351512 223 QVYQK--EQCPA-GHQVMKEAFGpedglQRLTWWCPQCQ 258
Cdd:TIGR00577 239 QVYGRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 159-205 6.14e-12

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 60.38  E-value: 6.14e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1160351512 159 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE 205
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 136-259 1.04e-09

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 57.50  E-value: 1.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 136 LSEKFHRGQALEALGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASR--------REVLVDHVVEFS 207
Cdd:PRK14811  127 LSDDFTEPEFVRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEarrlyraiREVMAEAVEAGG 206

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1160351512 208 TAWLQGKFQ---GRPQHTQ----VYQKE--QCPA-GHQVMKEAFGpedglQRLTWWCPQCQP 259
Cdd:PRK14811  207 STLSDGSYRqpdGEPGGFQfqhaVYGREgqPCPRcGTPIEKIVVG-----GRGTHFCPQCQP 263
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 159-259 1.47e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 51.47  E-value: 1.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 159 LLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVE------------FS----TAWLQGKFQGRpqhT 222
Cdd:PRK13945  171 LLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEvlktsigaggttFSdfrdLEGVNGNYGGQ---A 247

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1160351512 223 QVYQKEQCP---AGHQVMKEAFGpedglQRLTWWCPQCQP 259
Cdd:PRK13945  248 WVYRRTGKPcrkCGTPIERIKLA-----GRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 62-258 1.81e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 51.06  E-value: 1.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512  62 PAGDAGRWLrVSFGLFGSVWVndfsrakkankrGDWRDPSPR---LVLHFGGGGFLAFYNCQL-------SWSSSPVVTP 131
Cdd:PRK14810   68 PGEPRGQWI-IHLGMTGKLLL------------GGPDTPSPKhthAVLTLSSGKELRFVDSRQfgcieysEAFPKRFARP 134

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 132 TCDILSEKFHRGQALeALGQAQPVCYTLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWL 211
Cdd:PRK14810  135 GPEPLEISFEDFAAL-FRGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAI 213

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1160351512 212 Q----------------GKFQGRpqhTQVYQK--EQCPAGHQVMKEAFGPedglQRLTWWCPQCQ 258
Cdd:PRK14810  214 ElggssvsdyvdaegrsGFFQLS---HRVYQRtgEPCLNCKTPIRRVVVA----GRSSHYCPHCQ 271
PRK10445 PRK10445
endonuclease VIII; Provisional
 135-259 6.96e-06

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 46.18  E-value: 6.96e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1160351512 135 ILSEKFHRGQaLEALgqaqpvcytLLDQRYFSGLGNIIKNEALYRAGIHPLSLGSVLSASRREVLVDHVVEFSTAWLQ-- 212
Cdd:PRK10445  144 LLSPRFRNRQ-FSGL---------LLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYAtr 213

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1160351512 213 -----GKFQGRPQHTQVYQK-----EQCpaGHQVMKEAFGpedglQRLTWWCPQCQP 259
Cdd:PRK10445  214 gqvdeNKHHGALFRFKVFHRdgeacERC--GGIIEKTTLS-----SRPFYWCPGCQK 263
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 65-118 1.11e-05

N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins.


Pssm-ID: 176798  Cd Length: 117  Bit Score: 43.51  E-value: 1.11e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1160351512  65 DAGRWLRVSFGLFGSVWVNDfsrakkankRGDWRDPSPRLVLHFGGGGFLAFYN 118
Cdd:cd08773    64 SGGPWLVIHLGMTGRLRVCP---------EGEPPPKHDRLVLRLANGSQLRFTD 108
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 70-121 7.11e-03

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines, and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_2 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain. Most also contain a zinc-finger motif.


Pssm-ID: 176808  Cd Length: 98  Bit Score: 35.38  E-value: 7.11e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1160351512  70 LRVSFGLFGSVWVNDfsraKKankrgdwrDPSPRLVLHFGGGGfLAFYNCQL 121
Cdd:cd08974    60 VRIHLLLFGSYRINE----RK--------DAPPRLSLGFDNGE-LNFYTCSV 98
 
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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