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Conserved domains on  [gi|22004053|dbj|BAC06476|]
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endonuclease VIII [Homo sapiens]

Protein Classification

endonuclease VIII( domain architecture ID 12963177)

endonuclease VIII is a DNA-(apurinic or apyrimidinic site) lyase involved in base excision repair of DNA damaged by oxidation or by mutagenic agents; acts as DNA glycosylase that recognizes and removes damaged bases with a preference for oxidized pyrimidines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-127 5.98e-77

N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the N-terminal domain of metazoan NEIL1. 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. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), thymine glycol (Tg) and 5-hydroxyuracil (5-OHU). However, even though it has weak activity on 8-oxo-7,8-dihydroguanine (8-oxoG), it does show strong preference for the products of its further oxidation: spiroiminodihydantoin and guanidinohydantoin. In addition to this MeNeil1_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zincless finger motif. This characteristic "zincless finger" motif, is a structural equivalent of the zinc finger common to other members of the Fpg/Nei family. Neil1 is one of three homologs found in eukaryotes and its lineage extends back as far as early metazoans.


:

Pssm-ID: 176801  Cd Length: 131  Bit Score: 233.89  E-value: 5.98e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   1 MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGA-----QPQQEPLAL 75
Cdd:cd08967   1 MPEGPELHLASLFVNKMCKGLIFTGAVEKSSVSKNPEVPFACKAYTISAESRGKELRLILSPLPAAngkkeCKSQEEMRI 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 22004053  76 VFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRlALCFVDIRRFGRWDLGG 127
Cdd:cd08967  81 VFRFGMSGSFQFTPVDEIPKHAHLRFYTKEEPKR-VLSFVDIRRFGTWQVGG 131
Neil1-DNA_bind pfam09292
Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in ...
 252-290 7.20e-23

Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding.


:

Pssm-ID: 462745  Cd Length: 39  Bit Score: 90.17  E-value: 7.20e-23
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 22004053   252 DFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
Cdd:pfam09292   1 DYAAFQAWLQCYNVPGMNSLRDHNGRTIWFQGDPGPLAP 39
PRK10445 super family cl32516
endonuclease VIII; Provisional
 134-194 4.36e-07

endonuclease VIII; Provisional


The actual alignment was detected with superfamily member PRK10445:

Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 50.80  E-value: 4.36e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22004053  134 GPCVLQEyQQFRENVLRNLADKAF-DRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 194
Cdd:PRK10445 127 GPDVLDP-NLTPEQVKERLLSPRFrNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKA 187
 
Name Accession Description Interval E-value
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-127 5.98e-77

N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the N-terminal domain of metazoan NEIL1. 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. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), thymine glycol (Tg) and 5-hydroxyuracil (5-OHU). However, even though it has weak activity on 8-oxo-7,8-dihydroguanine (8-oxoG), it does show strong preference for the products of its further oxidation: spiroiminodihydantoin and guanidinohydantoin. In addition to this MeNeil1_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zincless finger motif. This characteristic "zincless finger" motif, is a structural equivalent of the zinc finger common to other members of the Fpg/Nei family. Neil1 is one of three homologs found in eukaryotes and its lineage extends back as far as early metazoans.


Pssm-ID: 176801  Cd Length: 131  Bit Score: 233.89  E-value: 5.98e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   1 MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGA-----QPQQEPLAL 75
Cdd:cd08967   1 MPEGPELHLASLFVNKMCKGLIFTGAVEKSSVSKNPEVPFACKAYTISAESRGKELRLILSPLPAAngkkeCKSQEEMRI 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 22004053  76 VFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRlALCFVDIRRFGRWDLGG 127
Cdd:cd08967  81 VFRFGMSGSFQFTPVDEIPKHAHLRFYTKEEPKR-VLSFVDIRRFGTWQVGG 131
Neil1-DNA_bind pfam09292
Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in ...
 252-290 7.20e-23

Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding.


Pssm-ID: 462745  Cd Length: 39  Bit Score: 90.17  E-value: 7.20e-23
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 22004053   252 DFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
Cdd:pfam09292   1 DYAAFQAWLQCYNVPGMNSLRDHNGRTIWFQGDPGPLAP 39
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-123 5.92e-22

Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.


Pssm-ID: 460082  Cd Length: 116  Bit Score: 89.87  E-value: 5.92e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053     1 MPEGPELHLASQFVNEacraLVFGGCVEKSSVSRNPEVPFESSA--------YRI-SASARGKELRLILSplpgaqpqqE 71
Cdd:pfam01149   1 MPELPEVETVRRGLRR----HLVGKTIASVEVLDDKNLRGPSPEefaaaltgRKVtSVGRRGKYLLLELD---------S 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 22004053    72 PLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGprlALCFVDIRRFGRW 123
Cdd:pfam01149  68 GGHLVVHLGMTGWLLIKTEEWPPKHDHVRLELDDGR---ELRFTDPRRFGRV 116
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-197 9.31e-20

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 88.26  E-value: 9.31e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   2 PEGPELH-----LASQFVNEACRALVFGgcvekSSVSRNPeVPFESSA----YRI-SASARGKELRLILSPlpgaqpqqe 71
Cdd:COG0266   1 PELPEVEtvrrgLAPALVGRTITRVEVR-----SPRLRFP-VPEDFAArltgRRItAVERRGKYLLLELDG--------- 65

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053  72 PLALVFRFGMSGSFQLV-PREELPRHAHLRFYTAPpGPRLAlcFVDIRRFGRWDLGGKWQPGRGPcvlqeyqqfrenVLR 150
Cdd:COG0266  66 GLTLLIHLGMSGRLRVVpPGEPPEKHDHVRLVLDD-GTELR--FADPRRFGALELLTPDELEVHP------------LLA 130

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22004053 151 NLA----DKAFD------------RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:COG0266 131 RLGpeplDPDFDpeylaarlrrrrRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSL 193
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-124 1.04e-19

Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger.


Pssm-ID: 214895 [Multi-domain]  Cd Length: 115  Bit Score: 83.77  E-value: 1.04e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053      2 PEGPELHLASQFVNEACRALVFGGCVEKSS-VSRNPEvPFE---SSAYRISASARGKELRLILSplpgaqpqqEPLALVF 77
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPpQLRFPD-EFAaalSGRTITSVRRRGKYLLLRLL---------GGLTLVV 70

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 22004053     78 RFGMSGSFQLVPREE-LPRHAHLRFYTAPPGprlALCFVDIRRFGRWD 124
Cdd:smart00898  71 HLGMSGSLRVVPAGTpPPKHDHVRLVLDDGT---ELRFNDPRRFGAVR 115
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
52-197 2.66e-11

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 63.56  E-value: 2.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   52 RGKELRLILSplpgaqpqqEPLALVFRFGMSGSFQLVPREELPR-HAHLRFYTAPpgpRLALCFVDIRRFGRWDLGGKWQ 130
Cdd:PRK01103  56 RGKYLLLDLD---------DGGTLISHLGMSGSLRLLPEDTPPEkHDHVDFVLDD---GTVLRYNDPRRFGAMLLTPKGD 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053  131 PGRGPcvlqeyqqfrenVLRNLA----DKAFD------------RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 194
Cdd:PRK01103 124 LEAHP------------LLAHLGpeplSDAFDgeylaaklrkkkTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPA 191


                 ...
gi 22004053  195 RSV 197
Cdd:PRK01103 192 GSL 194
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 47-197 1.28e-10

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: 61.55  E-value: 1.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053    47 ISASARGKELRLILsplpgaqpqqEPLALVFRFGMSGSFQLVPR-EELPRHAHLRFYTAPpgpRLALCFVDIRRFGRWDL 125
Cdd:TIGR00577  52 LSIQRRGKYLLFEL----------DDGALVSHLRMEGKYRLEAVpDAPDKHDHVDFLFDD---GTELRYHDPRRFGTWLL 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 22004053   126 GGKWQpGRGPCVLQEY------QQFRENVLRN-LADKAfdRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:TIGR00577 119 LDRGQ-VENIPLLAKLgpeplsEDFTAEYLFEkLAKSK--RKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSL 194
PRK10445 PRK10445
endonuclease VIII; Provisional
 134-194 4.36e-07

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 50.80  E-value: 4.36e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22004053  134 GPCVLQEyQQFRENVLRNLADKAF-DRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 194
Cdd:PRK10445 127 GPDVLDP-NLTPEQVKERLLSPRFrNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKA 187
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 159-197 2.34e-05

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: 42.66  E-value: 2.34e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 22004053   159 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:pfam06831  24 RPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSL 62
 
Name Accession Description Interval E-value
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-127 5.98e-77

N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the N-terminal domain of metazoan NEIL1. 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. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), thymine glycol (Tg) and 5-hydroxyuracil (5-OHU). However, even though it has weak activity on 8-oxo-7,8-dihydroguanine (8-oxoG), it does show strong preference for the products of its further oxidation: spiroiminodihydantoin and guanidinohydantoin. In addition to this MeNeil1_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zincless finger motif. This characteristic "zincless finger" motif, is a structural equivalent of the zinc finger common to other members of the Fpg/Nei family. Neil1 is one of three homologs found in eukaryotes and its lineage extends back as far as early metazoans.


Pssm-ID: 176801  Cd Length: 131  Bit Score: 233.89  E-value: 5.98e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   1 MPEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGA-----QPQQEPLAL 75
Cdd:cd08967   1 MPEGPELHLASLFVNKMCKGLIFTGAVEKSSVSKNPEVPFACKAYTISAESRGKELRLILSPLPAAngkkeCKSQEEMRI 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 22004053  76 VFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRlALCFVDIRRFGRWDLGG 127
Cdd:cd08967  81 VFRFGMSGSFQFTPVDEIPKHAHLRFYTKEEPKR-VLSFVDIRRFGTWQVGG 131
Neil1-DNA_bind pfam09292
Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in ...
 252-290 7.20e-23

Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding.


Pssm-ID: 462745  Cd Length: 39  Bit Score: 90.17  E-value: 7.20e-23
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 22004053   252 DFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
Cdd:pfam09292   1 DYAAFQAWLQCYNVPGMNSLRDHNGRTIWFQGDPGPLAP 39
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-123 5.92e-22

Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges.


Pssm-ID: 460082  Cd Length: 116  Bit Score: 89.87  E-value: 5.92e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053     1 MPEGPELHLASQFVNEacraLVFGGCVEKSSVSRNPEVPFESSA--------YRI-SASARGKELRLILSplpgaqpqqE 71
Cdd:pfam01149   1 MPELPEVETVRRGLRR----HLVGKTIASVEVLDDKNLRGPSPEefaaaltgRKVtSVGRRGKYLLLELD---------S 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 22004053    72 PLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGprlALCFVDIRRFGRW 123
Cdd:pfam01149  68 GGHLVVHLGMTGWLLIKTEEWPPKHDHVRLELDDGR---ELRFTDPRRFGRV 116
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-125 2.57e-20

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: 85.49  E-value: 2.57e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   2 PEGPELHLASQFVNEACRALVFGgCVEKSSVSRN----PEVPFESSAYRI-SASARGKELRLILSPlpgaqpqqePLALV 76
Cdd:cd08773   1 PELPEVELLRRKLRRALKGKRVT-RVEVSDPRRLftpaAELAAALIGRRVrGAERRGKYLLLELSG---------GPWLV 70

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 22004053  77 FRFGMSGSFQLVPRE-ELPRHAHLRFYTAPpgpRLALCFVDIRRFGRWDL 125
Cdd:cd08773  71 IHLGMTGRLRVCPEGePPPKHDRLVLRLAN---GSQLRFTDPRKFGRVEL 117
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-197 9.31e-20

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 88.26  E-value: 9.31e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   2 PEGPELH-----LASQFVNEACRALVFGgcvekSSVSRNPeVPFESSA----YRI-SASARGKELRLILSPlpgaqpqqe 71
Cdd:COG0266   1 PELPEVEtvrrgLAPALVGRTITRVEVR-----SPRLRFP-VPEDFAArltgRRItAVERRGKYLLLELDG--------- 65

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053  72 PLALVFRFGMSGSFQLV-PREELPRHAHLRFYTAPpGPRLAlcFVDIRRFGRWDLGGKWQPGRGPcvlqeyqqfrenVLR 150
Cdd:COG0266  66 GLTLLIHLGMSGRLRVVpPGEPPEKHDHVRLVLDD-GTELR--FADPRRFGALELLTPDELEVHP------------LLA 130

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 22004053 151 NLA----DKAFD------------RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:COG0266 131 RLGpeplDPDFDpeylaarlrrrrRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSL 193
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-124 1.04e-19

Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger.


Pssm-ID: 214895 [Multi-domain]  Cd Length: 115  Bit Score: 83.77  E-value: 1.04e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053      2 PEGPELHLASQFVNEACRALVFGGCVEKSS-VSRNPEvPFE---SSAYRISASARGKELRLILSplpgaqpqqEPLALVF 77
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPpQLRFPD-EFAaalSGRTITSVRRRGKYLLLRLL---------GGLTLVV 70

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 22004053     78 RFGMSGSFQLVPREE-LPRHAHLRFYTAPPGprlALCFVDIRRFGRWD 124
Cdd:smart00898  71 HLGMSGSLRVVPAGTpPPKHDHVRLVLDDGT---ELRFNDPRRFGAVR 115
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
52-197 2.66e-11

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 63.56  E-value: 2.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   52 RGKELRLILSplpgaqpqqEPLALVFRFGMSGSFQLVPREELPR-HAHLRFYTAPpgpRLALCFVDIRRFGRWDLGGKWQ 130
Cdd:PRK01103  56 RGKYLLLDLD---------DGGTLISHLGMSGSLRLLPEDTPPEkHDHVDFVLDD---GTVLRYNDPRRFGAMLLTPKGD 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053  131 PGRGPcvlqeyqqfrenVLRNLA----DKAFD------------RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 194
Cdd:PRK01103 124 LEAHP------------LLAHLGpeplSDAFDgeylaaklrkkkTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPA 191


                 ...
gi 22004053  195 RSV 197
Cdd:PRK01103 192 GSL 194
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 47-197 1.28e-10

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: 61.55  E-value: 1.28e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053    47 ISASARGKELRLILsplpgaqpqqEPLALVFRFGMSGSFQLVPR-EELPRHAHLRFYTAPpgpRLALCFVDIRRFGRWDL 125
Cdd:TIGR00577  52 LSIQRRGKYLLFEL----------DDGALVSHLRMEGKYRLEAVpDAPDKHDHVDFLFDD---GTELRYHDPRRFGTWLL 118

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 22004053   126 GGKWQpGRGPCVLQEY------QQFRENVLRN-LADKAfdRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:TIGR00577 119 LDRGQ-VENIPLLAKLgpeplsEDFTAEYLFEkLAKSK--RKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSL 194
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 52-125 2.21e-09

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial 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. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 54.81  E-value: 2.21e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 22004053  52 RGKELRLILSplpgaqpqqEPLALVFRFGMSGSFQLV-PREELPRHAHLRFYTAPPGprlALCFVDIRRFGRWDL 125
Cdd:cd08966  56 RGKYLLFELD---------DGLVLVIHLGMTGRLLVVpPDEPPEKHDHVIFELDDGR---ELRFNDPRRFGTLLL 118
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-197 1.88e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 51.83  E-value: 1.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053    1 MPEGPELHLASQFVNEacraLVFGGCVEKSSVsRNPEVPFESSAYRISASARGKEL-------RLILSPLpgAQPQQEPL 73
Cdd:PRK14810   1 MPELPEVETVARGLAP----RAAGRRIATAEF-RNLRIPRKGDPDLMAARLAGRKIlsvkrvgKHIVADL--EGPGEPRG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   74 ALVFRFGMSGSFQLV-PREELPRHAHLRFyTAPPGPRLAlcFVDIRRFGRWDL-GGKWQPGRGP------CVLQEYQQ-F 144
Cdd:PRK14810  74 QWIIHLGMTGKLLLGgPDTPSPKHTHAVL-TLSSGKELR--FVDSRQFGCIEYsEAFPKRFARPgpepleISFEDFAAlF 150

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 22004053  145 REnvlRNLadkafdrPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:PRK14810 151 RG---RKT-------RIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSL 193
PRK10445 PRK10445
endonuclease VIII; Provisional
 134-194 4.36e-07

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 50.80  E-value: 4.36e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 22004053  134 GPCVLQEyQQFRENVLRNLADKAF-DRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 194
Cdd:PRK10445 127 GPDVLDP-NLTPEQVKERLLSPRFrNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKA 187
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 50-200 1.82e-06

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 49.02  E-value: 1.82e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   50 SARGKELRLILsplpgaqpqQEPLALVFRFGMSGSFQLVPreelprHAHLRFYTAPPGPRLAlcFVDIRRFGRW------ 123
Cdd:PRK14811  49 SRRGKYLLLHL---------PHDLELIVHLGMTGGFRLEP------GPHTRVTLELPGRTLY--FTDPRRFGKWwvvrag 111

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 22004053  124 DLGGKWQPGR-GPCVLQEyqQFRENVLRNLADKAfdRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEA 200
Cdd:PRK14811 112 DYREIPLLARmGPEPLSD--DFTEPEFVRALATA--RPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAP 185
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 81-217 2.16e-06

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 48.77  E-value: 2.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   81 MSGSFQLVPREE-LPRHAHLRFYTappGPRLALCFVDIRRFGR-WdlggkW-QPGRGPcvlqeyqqfrENVLRNLA---- 153
Cdd:PRK13945  83 MTGQFLWVEQSTpPCKHTRVRLFF---EKNQELRFVDIRSFGQmW-----WvPPGVSP----------ESIITGLQklgp 144

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 22004053  154 ---DKAFD------------RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFekarsvlealqqhRPSPELTLSQKIR 217
Cdd:PRK13945 145 epfSPEFSveylkkklkkrtRSIKTALLDQSIVAGIGNIYADESLFKAGIHPT-------------TPAGQLKKKQLER 210
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 159-197 2.34e-05

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: 42.66  E-value: 2.34e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 22004053   159 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSV 197
Cdd:pfam06831  24 RPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSL 62
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-122 2.42e-05

N-terminal domain of the plant and fungal Nei and related proteins; This family contains the N-terminal domain of plant and Fungi Nei and related proteins. 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. The plant and fungal FpgNei glycosylases prefer the oxidized pyrimidines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh) over 8-oxoguanine in double stranded oligonucleotides and also show weak activity on single stranded DNA. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a characteristic zincless finger motif. They share a common ancestor not shared with other eukaryotic members of the FpgNei family.


Pssm-ID: 176806  Cd Length: 137  Bit Score: 43.83  E-value: 2.42e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053   1 MPEGPELHLASQFVNEACralvFGGCVEKSSVSRNPEV--PFESSAYR--------ISASARGKELRLILSplpgaqpqQ 70
Cdd:cd08972   1 MPELPEVERARRLLEEHC----LGKKITKVDAQDDDKVfgGVTPGAFQkallgrtiTSAHRKGKYFWLTLD--------G 68

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 22004053  71 EPLALVFRFGMSGSFQLvpREElprHAHLRFYTAPPG-------PRLA-----------LCFVDIRRFGR 122
Cdd:cd08972  69 DAPVPVMHFGMTGAISI--KGV---KTIYYKMLRPPKeedqtwpPRFYkfvltledgteLAFTDPRRLGR 133
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 75-125 1.42e-04

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_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176810  Cd Length: 117  Bit Score: 41.18  E-value: 1.42e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 22004053  75 LVFRFGMSGSFQLVP-REELPRHAHLRFYTAPpGPRLAlcFVDIRRFGRWDL 125
Cdd:cd08976  69 LVMHFGMTGKLDYYPdDEDPPKHARLLLHFED-GFRLA--FECPRKFGRVRL 117
 
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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