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Conserved domains on  [gi|1270530335|ref|NP_001344338|]
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endonuclease 8-like 1 isoform 2 [Mus musculus]

Protein Classification

FpgNei_N and Neil1-DNA_bind domain-containing protein( domain architecture ID 13069084)

protein containing domains FpgNei_N, Nei, and Neil1-DNA_bind

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) ...
 1-52 2.64e-26

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 cd08967:

Pssm-ID: 470740  Cd Length: 131  Bit Score: 101.00  E-value: 2.64e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1270530335   1 MPEGPELHLASHFVNETCKGLVFGGCVEKSSVSRNPEVPFESSAYHISALAR 52
Cdd:cd08967     1 MPEGPELHLASLFVNKMCKGLIFTGAVEKSSVSKNPEVPFACKAYTISAESR 52
Neil1-DNA_bind pfam09292
Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in ...
 189-227 1.54e-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: 90.94  E-value: 1.54e-23
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1270530335 189 DFAAFRAWLRCYGVPGMSSLRDRHGRTIWFQGDPGPLAP 227
Cdd:pfam09292   1 DYAAFQAWLQCYNVPGMNSLRDHNGRTIWFQGDPGPLAP 39
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
52-134 1.50e-08

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: 54.75  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270530335  52 RDIRRFGHW---DPGGEWQPGR----GPCVLLEyeRFRENVLRNLSDKAfDRPICEALLDQRFFNGIGNYLRAEILYRLK 124
Cdd:COG0266   107 ADPRRFGALellTPDELEVHPLlarlGPEPLDP--DFDPEYLAARLRRR-RRPIKALLLDQSVVAGVGNIYADEALFRAG 183

                          90
                  ....*....|
gi 1270530335 125 IPPFEKARTV 134
Cdd:COG0266   184 IHPLRPAGSL 193
 
Name Accession Description Interval E-value
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-52 2.64e-26

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: 101.00  E-value: 2.64e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1270530335   1 MPEGPELHLASHFVNETCKGLVFGGCVEKSSVSRNPEVPFESSAYHISALAR 52
Cdd:cd08967     1 MPEGPELHLASLFVNKMCKGLIFTGAVEKSSVSKNPEVPFACKAYTISAESR 52
Neil1-DNA_bind pfam09292
Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in ...
 189-227 1.54e-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: 90.94  E-value: 1.54e-23
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1270530335 189 DFAAFRAWLRCYGVPGMSSLRDRHGRTIWFQGDPGPLAP 227
Cdd:pfam09292   1 DYAAFQAWLQCYNVPGMNSLRDHNGRTIWFQGDPGPLAP 39
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
52-134 1.50e-08

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 54.75  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270530335  52 RDIRRFGHW---DPGGEWQPGR----GPCVLLEyeRFRENVLRNLSDKAfDRPICEALLDQRFFNGIGNYLRAEILYRLK 124
Cdd:COG0266   107 ADPRRFGALellTPDELEVHPLlarlGPEPLDP--DFDPEYLAARLRRR-RRPIKALLLDQSVVAGVGNIYADEALFRAG 183

                          90
                  ....*....|
gi 1270530335 125 IPPFEKARTV 134
Cdd:COG0266   184 IHPLRPAGSL 193
PRK10445 PRK10445
endonuclease VIII; Provisional
 71-131 1.33e-07

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 51.95  E-value: 1.33e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1270530335  71 GPCVL---LEYERFREnvlRNLSDKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 131
Cdd:PRK10445  127 GPDVLdpnLTPEQVKE---RLLSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKA 187
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 96-158 4.25e-06

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: 44.21  E-value: 4.25e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1270530335  96 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARTVleALQQCRpspelTLSQKIKAKLQ 158
Cdd:pfam06831  24 RPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSL--SKEECE-----LLHQAIKAVLQ 79
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 52-158 1.53e-05

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: 45.75  E-value: 1.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270530335  52 RDIRRFGHWDPGGEWQpGRGPCVLLEY------ERFRENVLRNLSdKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKI 125
Cdd:TIGR00577 108 HDPRRFGTWLLLDRGQ-VENIPLLAKLgpeplsEDFTAEYLFEKL-AKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGI 185

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1270530335 126 PPFEKARTVleALQQCRpspelTLSQKIKAKLQ 158
Cdd:TIGR00577 186 HPERLASSL--SKEECE-----LLHRAIKEVLR 211
 
Name Accession Description Interval E-value
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-52 2.64e-26

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: 101.00  E-value: 2.64e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1270530335   1 MPEGPELHLASHFVNETCKGLVFGGCVEKSSVSRNPEVPFESSAYHISALAR 52
Cdd:cd08967     1 MPEGPELHLASLFVNKMCKGLIFTGAVEKSSVSKNPEVPFACKAYTISAESR 52
Neil1-DNA_bind pfam09292
Endonuclease VIII-like 1, DNA bind; Members of this family are predominantly found in ...
 189-227 1.54e-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: 90.94  E-value: 1.54e-23
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1270530335 189 DFAAFRAWLRCYGVPGMSSLRDRHGRTIWFQGDPGPLAP 227
Cdd:pfam09292   1 DYAAFQAWLQCYNVPGMNSLRDHNGRTIWFQGDPGPLAP 39
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
52-134 1.50e-08

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 54.75  E-value: 1.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270530335  52 RDIRRFGHW---DPGGEWQPGR----GPCVLLEyeRFRENVLRNLSDKAfDRPICEALLDQRFFNGIGNYLRAEILYRLK 124
Cdd:COG0266   107 ADPRRFGALellTPDELEVHPLlarlGPEPLDP--DFDPEYLAARLRRR-RRPIKALLLDQSVVAGVGNIYADEALFRAG 183

                          90
                  ....*....|
gi 1270530335 125 IPPFEKARTV 134
Cdd:COG0266   184 IHPLRPAGSL 193
PRK10445 PRK10445
endonuclease VIII; Provisional
 71-131 1.33e-07

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 51.95  E-value: 1.33e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1270530335  71 GPCVL---LEYERFREnvlRNLSDKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKA 131
Cdd:PRK10445  127 GPDVLdpnLTPEQVKE---RLLSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKA 187
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 96-158 4.25e-06

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: 44.21  E-value: 4.25e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1270530335  96 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARTVleALQQCRpspelTLSQKIKAKLQ 158
Cdd:pfam06831  24 RPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSL--SKEECE-----LLHQAIKAVLQ 79
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 52-158 1.53e-05

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: 45.75  E-value: 1.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1270530335  52 RDIRRFGHWDPGGEWQpGRGPCVLLEY------ERFRENVLRNLSdKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKI 125
Cdd:TIGR00577 108 HDPRRFGTWLLLDRGQ-VENIPLLAKLgpeplsEDFTAEYLFEKL-AKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGI 185

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1270530335 126 PPFEKARTVleALQQCRpspelTLSQKIKAKLQ 158
Cdd:TIGR00577 186 HPERLASSL--SKEECE-----LLHRAIKEVLR 211
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-60 2.82e-03

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: 36.96  E-value: 2.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1270530335   2 PEGPELHLASHFVNETCKGLVFgGCVEKSSVSRNPEVPFESSAYHISALARDIRRFGHW 60
Cdd:cd08773     1 PELPEVELLRRKLRRALKGKRV-TRVEVSDPRRLFTPAAELAAALIGRRVRGAERRGKY 58
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 96-144 9.83e-03

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 37.22  E-value: 9.83e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1270530335  96 RPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARTV-LEALQQCRPS 144
Cdd:PRK13945  165 RSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLkKKQLERLREA 214
 
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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