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Conserved domains on  [gi|755548515|ref|XP_011243410|]
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endonuclease 8-like 2 isoform X2 [Mus musculus]

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) ...
 4-151 1.17e-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: 132.58  E-value: 1.17e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515   4 MTPRRIRRTLLTY--VHGKKLFLRFDPDEEMEPlnsspqpiqgmwqkeavdrelalgpsaqepsagpsgsgepvpsrsae 81
Cdd:cd08968   32 INPNDLQGLRLQDsqVHGKNLFLHFDLDEEMGP----------------------------------------------- 64

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  82 tynlgkipSADAQRWLEVRFGLFGSIWVNDFSRAKKANKKGDWRDPVPRLVLHFSGGGFLVFYNCQMSWS 151
Cdd:cd08968   65 --------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVLHFESGGFLVFYNCRMSWC 126
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
92-286 3.54e-16

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: 76.70  E-value: 3.54e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  92 DAQRWLEVRFGLFGSIWVNDfsrAKKANKKGDwrdpvpRLVLHFSGGGFLVFYNCQ----MSWSPPPVIE---------P 158
Cdd:COG0266   64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADPRrfgaLELLTPDELEvhpllarlgP 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 159 tcDILSEKFHRGQALEALSQAQ-PVCYTLLDQRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHVVEFSKDW 237
Cdd:COG0266  135 --EPLDPDFDPEYLAARLRRRRrPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREA 212

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755548515 238 -------LRD---------KFQgkeRHTQIYQK--EQCPS-GHQVMKETFGppdglQRLTWWCPQCQP 286
Cdd:COG0266  213 ieaggttLRDyvnadgepgYFQ---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 ...
 4-151 1.17e-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: 132.58  E-value: 1.17e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515   4 MTPRRIRRTLLTY--VHGKKLFLRFDPDEEMEPlnsspqpiqgmwqkeavdrelalgpsaqepsagpsgsgepvpsrsae 81
Cdd:cd08968   32 INPNDLQGLRLQDsqVHGKNLFLHFDLDEEMGP----------------------------------------------- 64

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  82 tynlgkipSADAQRWLEVRFGLFGSIWVNDFSRAKKANKKGDWRDPVPRLVLHFSGGGFLVFYNCQMSWS 151
Cdd:cd08968   65 --------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVLHFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
92-286 3.54e-16

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 76.70  E-value: 3.54e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  92 DAQRWLEVRFGLFGSIWVNDfsrAKKANKKGDwrdpvpRLVLHFSGGGFLVFYNCQ----MSWSPPPVIE---------P 158
Cdd:COG0266   64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADPRrfgaLELLTPDELEvhpllarlgP 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 159 tcDILSEKFHRGQALEALSQAQ-PVCYTLLDQRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHVVEFSKDW 237
Cdd:COG0266  135 --EPLDPDFDPEYLAARLRRRRrPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREA 212

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755548515 238 -------LRD---------KFQgkeRHTQIYQK--EQCPS-GHQVMKETFGppdglQRLTWWCPQCQP 286
Cdd:COG0266  213 ieaggttLRDyvnadgepgYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 121-285 6.45e-13

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: 67.32  E-value: 6.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  121 KGDWRDPVPRLVLHFSGGGFLVFYNCQ----MSWSPPPVIEPTC-------DILSEKF-HRGQALEALSQAQPVCYTLLD 188
Cdd:TIGR00577  85 VPDAPDKHDHVDFLFDDGTELRYHDPRrfgtWLLLDRGQVENIPllaklgpEPLSEDFtAEYLFEKLAKSKRKIKTALLD 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  189 QRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHV-------VEFSKDWLRD---------KFQGKerhTQIY 252
Cdd:TIGR00577 165 QRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIkevlrkaIEMGGTTIRDfsqsdghngYFQQE---LQVY 241

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 755548515  253 QK--EQCPS-GHQVMKETFGppdglQRLTWWCPQCQ 285
Cdd:TIGR00577 242 GRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
130-287 5.38e-12

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 64.72  E-value: 5.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 130 RLVLHFSGGGFLVfYNCQ-----MSWSP-------PPV----IEPtcdiLSEKFHrGQALEALSQ--AQPVCYTLLDQRY 191
Cdd:PRK01103  94 HVDFVLDDGTVLR-YNDPrrfgaMLLTPkgdleahPLLahlgPEP----LSDAFD-GEYLAAKLRkkKTAIKPALLDQTV 167

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 192 FSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHVVEF----------SkdwLRD---------KFQgkeRHTQIY 252
Cdd:PRK01103 168 VVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVlaeaieqggtT---LRDyvnadgkpgYFQ---QSLQVY 241

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 755548515 253 --QKEQCPS-GHQVMKETFGppdglQRLTWWCPQCQPQ 287
Cdd:PRK01103 242 grEGEPCRRcGTPIEKIKQG-----GRSTFFCPRCQKR 274
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 152-211 1.48e-09

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: 53.84  E-value: 1.48e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755548515  152 PPPVIEP-TCDILSEKFHRgqalealsQAQPVCYTLLDQRYFSGLGNIIKNEALYRARIHP 211
Cdd:pfam06831   3 PEPLSEDfTVDYFAERLAK--------KKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHP 55
 
Name Accession Description Interval E-value
MeNeil2_N cd08968
N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2); This family contains the ...
 4-151 1.17e-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: 132.58  E-value: 1.17e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515   4 MTPRRIRRTLLTY--VHGKKLFLRFDPDEEMEPlnsspqpiqgmwqkeavdrelalgpsaqepsagpsgsgepvpsrsae 81
Cdd:cd08968   32 INPNDLQGLRLQDsqVHGKNLFLHFDLDEEMGP----------------------------------------------- 64

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  82 tynlgkipSADAQRWLEVRFGLFGSIWVNDFSRAKKANKKGDWRDPVPRLVLHFSGGGFLVFYNCQMSWS 151
Cdd:cd08968   65 --------DRDAGRWLRFHFGLFGSVRANEFSRAKKANKRGDWKDPNPRLVLHFESGGFLVFYNCRMSWC 126
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
92-286 3.54e-16

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 76.70  E-value: 3.54e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  92 DAQRWLEVRFGLFGSIWVNDfsrAKKANKKGDwrdpvpRLVLHFSGGGFLVFYNCQ----MSWSPPPVIE---------P 158
Cdd:COG0266   64 DGGLTLLIHLGMSGRLRVVP---PGEPPEKHD------HVRLVLDDGTELRFADPRrfgaLELLTPDELEvhpllarlgP 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 159 tcDILSEKFHRGQALEALSQAQ-PVCYTLLDQRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHVVEFSKDW 237
Cdd:COG0266  135 --EPLDPDFDPEYLAARLRRRRrPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREA 212

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 755548515 238 -------LRD---------KFQgkeRHTQIYQK--EQCPS-GHQVMKETFGppdglQRLTWWCPQCQP 286
Cdd:COG0266  213 ieaggttLRDyvnadgepgYFQ---QRLYVYGRegEPCPRcGTPIERIVLG-----GRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 121-285 6.45e-13

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: 67.32  E-value: 6.45e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  121 KGDWRDPVPRLVLHFSGGGFLVFYNCQ----MSWSPPPVIEPTC-------DILSEKF-HRGQALEALSQAQPVCYTLLD 188
Cdd:TIGR00577  85 VPDAPDKHDHVDFLFDDGTELRYHDPRrfgtWLLLDRGQVENIPllaklgpEPLSEDFtAEYLFEKLAKSKRKIKTALLD 164

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515  189 QRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHV-------VEFSKDWLRD---------KFQGKerhTQIY 252
Cdd:TIGR00577 165 QRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIkevlrkaIEMGGTTIRDfsqsdghngYFQQE---LQVY 241

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 755548515  253 QK--EQCPS-GHQVMKETFGppdglQRLTWWCPQCQ 285
Cdd:TIGR00577 242 GRkgEPCRRcGTTIEKEKVG-----GRGTHFCPQCQ 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
130-287 5.38e-12

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 64.72  E-value: 5.38e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 130 RLVLHFSGGGFLVfYNCQ-----MSWSP-------PPV----IEPtcdiLSEKFHrGQALEALSQ--AQPVCYTLLDQRY 191
Cdd:PRK01103  94 HVDFVLDDGTVLR-YNDPrrfgaMLLTPkgdleahPLLahlgPEP----LSDAFD-GEYLAAKLRkkKTAIKPALLDQTV 167

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 192 FSGLGNIIKNEALYRARIHPLSLGSCLSSSSREALVDHVVEF----------SkdwLRD---------KFQgkeRHTQIY 252
Cdd:PRK01103 168 VVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVlaeaieqggtT---LRDyvnadgkpgYFQ---QSLQVY 241

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 755548515 253 --QKEQCPS-GHQVMKETFGppdglQRLTWWCPQCQPQ 287
Cdd:PRK01103 242 grEGEPCRRcGTPIEKIKQG-----GRSTFFCPRCQKR 274
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 152-211 1.48e-09

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: 53.84  E-value: 1.48e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755548515  152 PPPVIEP-TCDILSEKFHRgqalealsQAQPVCYTLLDQRYFSGLGNIIKNEALYRARIHP 211
Cdd:pfam06831   3 PEPLSEDfTVDYFAERLAK--------KKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHP 55
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 163-286 8.01e-08

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 52.49  E-value: 8.01e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 163 LSEKFHRGQALEALSQAQPVCYTLLDQRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSS--------REALVDhVVEFS 234
Cdd:PRK14811 127 LSDDFTEPEFVRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEarrlyraiREVMAE-AVEAG 205

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755548515 235 KDWLRDK-----------FQGKERhtqIYQKE--QCPS-GHQVMKETFGppdglQRLTWWCPQCQP 286
Cdd:PRK14811 206 GSTLSDGsyrqpdgepggFQFQHA---VYGREgqPCPRcGTPIEKIVVG-----GRGTHFCPQCQP 263
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 92-145 3.99e-06

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: 45.05  E-value: 3.99e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 755548515  92 DAQRWLEVRFGLFGSIWVNDFsrakkankkGDWRDPVPRLVLHFSGGGFLVFYN 145
Cdd:cd08773   64 SGGPWLVIHLGMTGRLRVCPE---------GEPPPKHDRLVLRLANGSQLRFTD 108
PRK10445 PRK10445
endonuclease VIII; Provisional
 153-286 9.46e-05

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 43.09  E-value: 9.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 153 PPVIEPTCD-------ILSEKFHRGQaLEALsqaqpvcytLLDQRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSSREA 225
Cdd:PRK10445 128 PDVLDPNLTpeqvkerLLSPRFRNRQ-FSGL---------LLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDA 197

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 755548515 226 LVDHVVEFSKDWLRDK------------FQGKERHTQIYQKEQCpsGHQVMKETFGppdglQRLTWWCPQCQP 286
Cdd:PRK10445 198 LAHALLDIPRLSYATRgqvdenkhhgalFRFKVFHRDGEACERC--GGIIEKTTLS-----SRPFYWCPGCQK 263
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 122-211 1.39e-04

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 42.59  E-value: 1.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 122 GDWRDPVPR---LVLHFSGGGFLVFYNCQM-------SWSPPPVIEPTCDILSEKFHRGQALeALSQAQPVCYTLLDQRY 191
Cdd:PRK14810  88 GGPDTPSPKhthAVLTLSSGKELRFVDSRQfgcieysEAFPKRFARPGPEPLEISFEDFAAL-FRGRKTRIKSALLNQTL 166

                         90       100
                 ....*....|....*....|
gi 755548515 192 FSGLGNIIKNEALYRARIHP 211
Cdd:PRK14810 167 LRGVGNIYADEALFRAGIRP 186
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 186-286 4.87e-04

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 41.07  E-value: 4.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755548515 186 LLDQRYFSGLGNIIKNEALYRARIHPLSLGSCLSSSS----REALVDhVVEFS--------KDWlRD------KFQGKer 247
Cdd:PRK13945 171 LLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQlerlREAIIE-VLKTSigaggttfSDF-RDlegvngNYGGQ-- 246

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 755548515 248 hTQIYQKEQCP---SGHQVMKETFGppdglQRLTWWCPQCQP 286
Cdd:PRK13945 247 -AWVYRRTGKPcrkCGTPIERIKLA-----GRSTHWCPNCQK 282
 
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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