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Conserved domains on  [gi|1519314895|ref|NP_060718|]
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endonuclease 8-like 3 [Homo sapiens]

Protein Classification

DNA glycosylase( domain architecture ID 12963224)

Fpg/Nei family DNA glycosylase similar to Escherichia coli DNA-formamidopyrimidine glycosylase (Fpg), a DNA repair enzyme that excises oxidized purines from damaged DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-151 1.98e-78

N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the N-terminal domain of the Metazoan Neil3. 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. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-terminal valine. The latter is a functional DNA glycosylase in vitro and in vivo. MmuNEIL3 prefers lesions in single-stranded DNA and in bubble structures. In duplex DNA, it recognizes the oxidized purines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), but not 8-oxo-7,8-dihydroguanine (8-oxoG). Since the expression of the MmuNeil3 glycosylase domain (MmuNeil3delta324) reduces both the high spontaneous mutation frequency and the FapyG level in a Escherichia coli mutant lacking Fpg, Nei and MutY glycosylase activites, NEIL3 may play a role in repairing FapyG in vivo. In addition to this MeNeil3_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc finger motif, plus a characteristic C-terminal extension that contains additional zinc fingers. Neil3 is one of three homologs found in eukaryotes.


:

Pssm-ID: 176803  Cd Length: 140  Bit Score: 244.25  E-value: 1.98e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895   1 MVEGPGCTLNGEKIRARVLPGQAVTGVRGSALRSLQGRALRLAASTVvvspqaaalnnDSSQNVLSLFNGYVYSGVETLG 80
Cdd:cd08969     1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGAGSK-----------DERSHVLDSLTGQVYTGVETLG 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1519314895  81 KELFMYFGPKALRIHFGMKGFIMINPLEYKYKNGASPVLEVQLTKDLICFFDSSVELRNSMESQQRIRMMK 151
Cdd:cd08969    70 KELFMYFGDKALRIHFGMNGSMRINPLESKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 552-596 2.13e-18

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


:

Pssm-ID: 462017  Cd Length: 45  Bit Score: 78.60  E-value: 2.13e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1519314895 552 PFCNHGKRSTMKTVLKIGPNNGKNFFVCPLGKEKQCNFFQWAENG 596
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 505-550 9.51e-16

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


:

Pssm-ID: 462017  Cd Length: 45  Bit Score: 71.28  E-value: 9.51e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1519314895 505 PRCsKHNRLCILRVVGKDGENKGRQFYACPLPREAQCGFFEWADLS 550
Cdd:pfam06839   1 PLC-PCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
PRK01103 super family cl35138
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
180-281 1.44e-14

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


The actual alignment was detected with superfamily member PRK01103:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 74.35  E-value: 1.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 180 VLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcRKAgLAL----------------- 242
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA--VL----AEA-IEQggttlrdyvnadgkpgy 233

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1519314895 243 -SKHYKVYKR-----PNCGQCHCRITVcrfgdNNRMTYFCPHCQK 281
Cdd:PRK01103  234 fQQSLQVYGRegepcRRCGTPIEKIKQ-----GGRSTFFCPRCQK 273
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
317-345 1.02e-04

Zn-finger in Ran binding protein and others;


:

Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 39.64  E-value: 1.02e-04
                          10        20
                  ....*....|....*....|....*....
gi 1519314895 317 SEEHWTCVVCTLINKPSSKACDACLTSRP 345
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQAPKP 29
 
Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-151 1.98e-78

N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the N-terminal domain of the Metazoan Neil3. 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. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-terminal valine. The latter is a functional DNA glycosylase in vitro and in vivo. MmuNEIL3 prefers lesions in single-stranded DNA and in bubble structures. In duplex DNA, it recognizes the oxidized purines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), but not 8-oxo-7,8-dihydroguanine (8-oxoG). Since the expression of the MmuNeil3 glycosylase domain (MmuNeil3delta324) reduces both the high spontaneous mutation frequency and the FapyG level in a Escherichia coli mutant lacking Fpg, Nei and MutY glycosylase activites, NEIL3 may play a role in repairing FapyG in vivo. In addition to this MeNeil3_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc finger motif, plus a characteristic C-terminal extension that contains additional zinc fingers. Neil3 is one of three homologs found in eukaryotes.


Pssm-ID: 176803  Cd Length: 140  Bit Score: 244.25  E-value: 1.98e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895   1 MVEGPGCTLNGEKIRARVLPGQAVTGVRGSALRSLQGRALRLAASTVvvspqaaalnnDSSQNVLSLFNGYVYSGVETLG 80
Cdd:cd08969     1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGAGSK-----------DERSHVLDSLTGQVYTGVETLG 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1519314895  81 KELFMYFGPKALRIHFGMKGFIMINPLEYKYKNGASPVLEVQLTKDLICFFDSSVELRNSMESQQRIRMMK 151
Cdd:cd08969    70 KELFMYFGDKALRIHFGMNGSMRINPLESKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
16-281 2.74e-20

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 90.96  E-value: 2.74e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895  16 ARVLPGQAVTGVRgsalrslqgralrlaastvVVSPQaaaLNNDSSQNVLSLFNGYVYSGVETLGKELFMYFGP-KALRI 94
Cdd:COG0266    14 APALVGRTITRVE-------------------VRSPR---LRFPVPEDFAARLTGRRITAVERRGKYLLLELDGgLTLLI 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895  95 HFGMKGFIMINPleykykNGASPVLEVQLtkdlICFFDSSVELR-------NSME-----SQQRIRMMKEL--DVCSPEF 160
Cdd:COG0266    72 HLGMSGRLRVVP------PGEPPEKHDHV----RLVLDDGTELRfadprrfGALElltpdELEVHPLLARLgpEPLDPDF 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 161 SFLRAESEVKKqKGRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcrKAGL 240
Cdd:COG0266   142 DPEYLAARLRR-RRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIRE--VL-----REAI 213

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1519314895 241 AL------------------SKHYKVYKR-----PNCGQCHCRITVcrfgdNNRMTYFCPHCQK 281
Cdd:COG0266   214 EAggttlrdyvnadgepgyfQQRLYVYGRegepcPRCGTPIERIVL-----GGRSTYYCPRCQR 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 552-596 2.13e-18

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 78.60  E-value: 2.13e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1519314895 552 PFCNHGKRSTMKTVLKIGPNNGKNFFVCPLGKEKQCNFFQWAENG 596
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 505-550 9.51e-16

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 71.28  E-value: 9.51e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1519314895 505 PRCsKHNRLCILRVVGKDGENKGRQFYACPLPREAQCGFFEWADLS 550
Cdd:pfam06839   1 PLC-PCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
180-281 1.44e-14

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 74.35  E-value: 1.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 180 VLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcRKAgLAL----------------- 242
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA--VL----AEA-IEQggttlrdyvnadgkpgy 233

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1519314895 243 -SKHYKVYKR-----PNCGQCHCRITVcrfgdNNRMTYFCPHCQK 281
Cdd:PRK01103  234 fQQSLQVYGRegepcRRCGTPIEKIKQ-----GGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 157-280 5.83e-14

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: 72.33  E-value: 5.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 157 SPEFSFlRAESEVKKQKGRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcR 236
Cdd:TIGR00577 139 SEDFTA-EYLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKE--VL----R 211

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1519314895 237 KA-------------GLALSKHYK----VYKRPN--CGQCHCRITVCRFGdnNRMTYFCPHCQ 280
Cdd:TIGR00577 212 KAiemggttirdfsqSDGHNGYFQqelqVYGRKGepCRRCGTTIEKEKVG--GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 157-227 2.71e-10

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: 57.30  E-value: 2.71e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1519314895 157 SPEFSFLRAESEVKKQKgRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRD 227
Cdd:pfam06831   7 SEDFTVDYFAERLAKKK-RPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
317-345 1.02e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 39.64  E-value: 1.02e-04
                          10        20
                  ....*....|....*....|....*....
gi 1519314895 317 SEEHWTCVVCTLINKPSSKACDACLTSRP 345
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQAPKP 29
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 319-343 1.03e-03

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 36.53  E-value: 1.03e-03
                           10        20
                   ....*....|....*....|....*
gi 1519314895  319 EHWTCVVCTLINKPSSKACDACLTS 343
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25
 
Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-151 1.98e-78

N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the N-terminal domain of the Metazoan Neil3. 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. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-terminal valine. The latter is a functional DNA glycosylase in vitro and in vivo. MmuNEIL3 prefers lesions in single-stranded DNA and in bubble structures. In duplex DNA, it recognizes the oxidized purines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), but not 8-oxo-7,8-dihydroguanine (8-oxoG). Since the expression of the MmuNeil3 glycosylase domain (MmuNeil3delta324) reduces both the high spontaneous mutation frequency and the FapyG level in a Escherichia coli mutant lacking Fpg, Nei and MutY glycosylase activites, NEIL3 may play a role in repairing FapyG in vivo. In addition to this MeNeil3_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc finger motif, plus a characteristic C-terminal extension that contains additional zinc fingers. Neil3 is one of three homologs found in eukaryotes.


Pssm-ID: 176803  Cd Length: 140  Bit Score: 244.25  E-value: 1.98e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895   1 MVEGPGCTLNGEKIRARVLPGQAVTGVRGSALRSLQGRALRLAASTVvvspqaaalnnDSSQNVLSLFNGYVYSGVETLG 80
Cdd:cd08969     1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGAGSK-----------DERSHVLDSLTGQVYTGVETLG 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1519314895  81 KELFMYFGPKALRIHFGMKGFIMINPLEYKYKNGASPVLEVQLTKDLICFFDSSVELRNSMESQQRIRMMK 151
Cdd:cd08969    70 KELFMYFGDKALRIHFGMNGSMRINPLESKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-141 1.69e-21

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: 90.11  E-value: 1.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895   2 VEGPGCTLNGEKIRARvLPGQAVTGVRGSALRSLQGRALRLAAstvvvspqaaalnndssqnvlsLFNGYVYSGVETLGK 81
Cdd:cd08773     1 PELPEVELLRRKLRRA-LKGKRVTRVEVSDPRRLFTPAAELAA----------------------ALIGRRVRGAERRGK 57

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1519314895  82 ELFMYF-GPKALRIHFGMKGFIMINPLEykYKNGASPVLEVQLT-KDLICFFDSSVELRNSM 141
Cdd:cd08773    58 YLLLELsGGPWLVIHLGMTGRLRVCPEG--EPPPKHDRLVLRLAnGSQLRFTDPRKFGRVEL 117
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
16-281 2.74e-20

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 90.96  E-value: 2.74e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895  16 ARVLPGQAVTGVRgsalrslqgralrlaastvVVSPQaaaLNNDSSQNVLSLFNGYVYSGVETLGKELFMYFGP-KALRI 94
Cdd:COG0266    14 APALVGRTITRVE-------------------VRSPR---LRFPVPEDFAARLTGRRITAVERRGKYLLLELDGgLTLLI 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895  95 HFGMKGFIMINPleykykNGASPVLEVQLtkdlICFFDSSVELR-------NSME-----SQQRIRMMKEL--DVCSPEF 160
Cdd:COG0266    72 HLGMSGRLRVVP------PGEPPEKHDHV----RLVLDDGTELRfadprrfGALElltpdELEVHPLLARLgpEPLDPDF 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 161 SFLRAESEVKKqKGRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcrKAGL 240
Cdd:COG0266   142 DPEYLAARLRR-RRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIRE--VL-----REAI 213

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1519314895 241 AL------------------SKHYKVYKR-----PNCGQCHCRITVcrfgdNNRMTYFCPHCQK 281
Cdd:COG0266   214 EAggttlrdyvnadgepgyfQQRLYVYGRegepcPRCGTPIERIVL-----GGRSTYYCPRCQR 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 552-596 2.13e-18

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 78.60  E-value: 2.13e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1519314895 552 PFCNHGKRSTMKTVLKIGPNNGKNFFVCPLGKEKQCNFFQWAENG 596
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 505-550 9.51e-16

GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396.


Pssm-ID: 462017  Cd Length: 45  Bit Score: 71.28  E-value: 9.51e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1519314895 505 PRCsKHNRLCILRVVGKDGENKGRQFYACPLPREAQCGFFEWADLS 550
Cdd:pfam06839   1 PLC-PCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
180-281 1.44e-14

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 74.35  E-value: 1.44e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 180 VLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcRKAgLAL----------------- 242
Cdd:PRK01103  161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA--VL----AEA-IEQggttlrdyvnadgkpgy 233

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1519314895 243 -SKHYKVYKR-----PNCGQCHCRITVcrfgdNNRMTYFCPHCQK 281
Cdd:PRK01103  234 fQQSLQVYGRegepcRRCGTPIEKIKQ-----GGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 157-280 5.83e-14

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: 72.33  E-value: 5.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 157 SPEFSFlRAESEVKKQKGRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILfyrcR 236
Cdd:TIGR00577 139 SEDFTA-EYLFEKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKE--VL----R 211

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1519314895 237 KA-------------GLALSKHYK----VYKRPN--CGQCHCRITVCRFGdnNRMTYFCPHCQ 280
Cdd:TIGR00577 212 KAiemggttirdfsqSDGHNGYFQqelqVYGRKGepCRRCGTTIEKEKVG--GRGTHFCPQCQ 272
PRK10445 PRK10445
endonuclease VIII; Provisional
 175-281 4.77e-12

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 66.59  E-value: 4.77e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 175 RMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDFSILFYRCR------KAGLALSKHyKV 248
Cdd:PRK10445  152 RQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRgqvdenKHHGALFRF-KV 230

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1519314895 249 YKRPN--CGQCHCRITVCRFGdnNRMTYFCPHCQK 281
Cdd:PRK10445  231 FHRDGeaCERCGGIIEKTTLS--SRPFYWCPGCQK 263
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 157-227 2.71e-10

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: 57.30  E-value: 2.71e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1519314895 157 SPEFSFLRAESEVKKQKgRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRD 227
Cdd:pfam06831   7 SEDFTVDYFAERLAKKK-RPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 157-281 1.22e-09

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 59.56  E-value: 1.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 157 SPEFS--FLRaesEVKKQKGRMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILFYR 234
Cdd:PRK13945  148 SPEFSveYLK---KKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIE--VLKTS 222

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1519314895 235 CRKAGLALSK---------HYK----VYKR-----PNCGQCHCRITVCrfgdnNRMTYFCPHCQK 281
Cdd:PRK13945  223 IGAGGTTFSDfrdlegvngNYGgqawVYRRtgkpcRKCGTPIERIKLA-----GRSTHWCPNCQK 282
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 175-284 2.22e-09

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 58.65  E-value: 2.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 175 RMLGDVLMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILFYRCRKAGLALSK---------- 244
Cdd:PRK14811  144 RPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIRE--VMAEAVEAGGSTLSDgsyrqpdgep 221

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1519314895 245 -----HYKVYKRPN--CGQCHCRITVCRFGdnNRMTYFCPHCQKENP 284
Cdd:PRK14811  222 ggfqfQHAVYGREGqpCPRCGTPIEKIVVG--GRGTHFCPQCQPLRP 266
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 181-281 1.62e-06

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 49.91  E-value: 1.62e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1519314895 181 LMDQNVLPGVGNIIKNEALFDSGLHPAVKVCQLTDEQIHHLMKMIRDfsILFYRCRKAGLALSKH-------------YK 247
Cdd:PRK14810  161 LLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE--VLREAIELGGSSVSDYvdaegrsgffqlsHR 238

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1519314895 248 VYKRPNCGQCHCRITVCRFGDNNRMTYFCPHCQK 281
Cdd:PRK14810  239 VYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
317-345 1.02e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 39.64  E-value: 1.02e-04
                          10        20
                  ....*....|....*....|....*....
gi 1519314895 317 SEEHWTCVVCTLINKPSSKACDACLTSRP 345
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQAPKP 29
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 319-343 1.03e-03

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 36.53  E-value: 1.03e-03
                           10        20
                   ....*....|....*....|....*
gi 1519314895  319 EHWTCVVCTLINKPSSKACDACLTS 343
Cdd:smart00547   1 GDWECPACTFLNFASRSKCFACGAP 25
AcNei1_N cd08970
N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains ...
 48-100 8.21e-03

N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains the N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. 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. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei1 (MtuNei1). MtuNei1 recognizes oxidized pyrimidines such as thymine glycol (Tg) and 5,6-dihydrouracil on both double stranded and single stranded DNA, it has a strong preference for the 5R isomer of Tg. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176804 [Multi-domain]  Cd Length: 110  Bit Score: 36.46  E-value: 8.21e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1519314895  48 VVSPQ----AAAlnndssqnvlSLFNGYVYSGVETLGKELFMYFGP-KALRIHFGMKG 100
Cdd:cd08970    25 VSSPQgrfaDGA----------ALLDGRVLADAEAHGKHLFLGFEGdRILHVHLGLYG 72
 
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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