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Conserved domains on  [gi|24475412|dbj|BAC22661|]
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putative DNA glycosylase [Mus musculus]

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 ...
 1-152 2.53e-65

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: 210.35  E-value: 2.53e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   1 MVEGPGCTLNGEKIRARVLPGQAVTGVRGTALQSLLGpamspaasladvATSAAPMNAKDSGWKLLRLFNGYVYSGVETL 80
Cdd:cd08969   1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSG------------AASRNGAGSKDERSHVLDSLTGQVYTGVETL 68

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24475412  81 GKELFMYFGPRALRIHFGMKGSILINPREGENRAGASPALAVQLTRDLICFYDSSVELRNSVESQQRVRVME 152
Cdd:cd08969  69 GKELFMYFGDKALRIHFGMNGSMRINPLESKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
76-282 6.43e-20

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: 89.80  E-value: 6.43e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  76 GVETLGKELFMYFGP-RALRIHFGMKGSILINPregenrAGASPALAVQL-----TRDLICFYD----SSVELRnSVESQ 145
Cdd:COG0266  51 AVERRGKYLLLELDGgLTLLIHLGMSGRLRVVP------PGEPPEKHDHVrlvldDGTELRFADprrfGALELL-TPDEL 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412 146 QRVRVMEEL--DICSPKFSFSRAESEVKKQGdRMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLV 223
Cdd:COG0266 124 EVHPLLARLgpEPLDPDFDPEYLAARLRRRR-RPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLA 202

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24475412 224 KMTRD---FSIlfyrccKA-GSAIS-------------KHCKVYKR---PnCDQCHSKITVCRFGenSRMTYFCPHCQK 282
Cdd:COG0266 203 AAIREvlrEAI------EAgGTTLRdyvnadgepgyfqQRLYVYGRegeP-CPRCGTPIERIVLG--GRSTYYCPRCQR 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 506-551 2.32e-17

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: 75.90  E-value: 2.32e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 24475412   506 PLCKmHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADLS 551
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 553-597 1.25e-15

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: 70.90  E-value: 1.25e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 24475412   553 PFCRHGKRSIMKTVLKIGPNNGKNFFVCPLEKKKQCNFFQWAENG 597
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
318-347 4.85e-04

Zn-finger in Ran binding protein and others;


:

Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 37.72  E-value: 4.85e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 24475412   318 SEEQWSCVVCTLINRPSAKACDACLTTRPL 347
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQAPKPD 30
 
Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-152 2.53e-65

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: 210.35  E-value: 2.53e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   1 MVEGPGCTLNGEKIRARVLPGQAVTGVRGTALQSLLGpamspaasladvATSAAPMNAKDSGWKLLRLFNGYVYSGVETL 80
Cdd:cd08969   1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSG------------AASRNGAGSKDERSHVLDSLTGQVYTGVETL 68

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24475412  81 GKELFMYFGPRALRIHFGMKGSILINPREGENRAGASPALAVQLTRDLICFYDSSVELRNSVESQQRVRVME 152
Cdd:cd08969  69 GKELFMYFGDKALRIHFGMNGSMRINPLESKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
76-282 6.43e-20

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 89.80  E-value: 6.43e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  76 GVETLGKELFMYFGP-RALRIHFGMKGSILINPregenrAGASPALAVQL-----TRDLICFYD----SSVELRnSVESQ 145
Cdd:COG0266  51 AVERRGKYLLLELDGgLTLLIHLGMSGRLRVVP------PGEPPEKHDHVrlvldDGTELRFADprrfGALELL-TPDEL 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412 146 QRVRVMEEL--DICSPKFSFSRAESEVKKQGdRMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLV 223
Cdd:COG0266 124 EVHPLLARLgpEPLDPDFDPEYLAARLRRRR-RPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLA 202

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24475412 224 KMTRD---FSIlfyrccKA-GSAIS-------------KHCKVYKR---PnCDQCHSKITVCRFGenSRMTYFCPHCQK 282
Cdd:COG0266 203 AAIREvlrEAI------EAgGTTLRdyvnadgepgyfqQRLYVYGRegeP-CPRCGTPIERIVLG--GRSTYYCPRCQR 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 506-551 2.32e-17

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: 75.90  E-value: 2.32e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 24475412   506 PLCKmHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADLS 551
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 553-597 1.25e-15

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: 70.90  E-value: 1.25e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 24475412   553 PFCRHGKRSIMKTVLKIGPNNGKNFFVCPLEKKKQCNFFQWAENG 597
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
181-282 4.80e-14

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 72.81  E-value: 4.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  181 VLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDfsILfyrcCKA----GSAI------------- 243
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA--VL----AEAieqgGTTLrdyvnadgkpgyf 234

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 24475412  244 SKHCKVYKRPN--CDQCHSKITVCRFGEnsRMTYFCPHCQK 282
Cdd:PRK01103 235 QQSLQVYGREGepCRRCGTPIEKIKQGG--RSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 182-281 9.52e-13

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


Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 68.87  E-value: 9.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   182 LLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDfsILFYRCCKAGSAIS------------KHC-K 248
Cdd:TIGR00577 162 LLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKE--VLRKAIEMGGTTIRdfsqsdghngyfQQElQ 239

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 24475412   249 VYKRPN--CDQCHSKITVCRFGenSRMTYFCPHCQ 281
Cdd:TIGR00577 240 VYGRKGepCRRCGTTIEKEKVG--GRGTHFCPQCQ 272
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 182-223 1.75e-08

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: 51.91  E-value: 1.75e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 24475412   182 LLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQaCHLV 223
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEE-CELL 70
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
318-347 4.85e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 37.72  E-value: 4.85e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 24475412   318 SEEQWSCVVCTLINRPSAKACDACLTTRPL 347
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQAPKPD 30
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 65-109 2.76e-03

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: 37.93  E-value: 2.76e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 24475412     65 LLRLFNGYVYSGVETLGKELFMYF-GPRALRIHFGMKGSILINPRE 109
Cdd:smart00898  39 FAAALSGRTITSVRRRGKYLLLRLlGGLTLVVHLGMSGSLRVVPAG 84
 
Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-152 2.53e-65

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: 210.35  E-value: 2.53e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   1 MVEGPGCTLNGEKIRARVLPGQAVTGVRGTALQSLLGpamspaasladvATSAAPMNAKDSGWKLLRLFNGYVYSGVETL 80
Cdd:cd08969   1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSG------------AASRNGAGSKDERSHVLDSLTGQVYTGVETL 68

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24475412  81 GKELFMYFGPRALRIHFGMKGSILINPREGENRAGASPALAVQLTRDLICFYDSSVELRNSVESQQRVRVME 152
Cdd:cd08969  69 GKELFMYFGDKALRIHFGMNGSMRINPLESKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-142 1.18e-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: 87.42  E-value: 1.18e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   2 VEGPGCTLNGEKIRARvLPGQAVTGVRGTALQSLLGPAMSPAASLadvatsaapmnakdsgwkllrlfNGYVYSGVETLG 81
Cdd:cd08773   1 PELPEVELLRRKLRRA-LKGKRVTRVEVSDPRRLFTPAAELAAAL-----------------------IGRRVRGAERRG 56

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24475412  82 KELFMYF-GPRALRIHFGMKGSILINPREGEnrAGASPALAVQLT-RDLICFYDSSVELRNSV 142
Cdd:cd08773  57 KYLLLELsGGPWLVIHLGMTGRLRVCPEGEP--PPKHDRLVLRLAnGSQLRFTDPRKFGRVEL 117
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
76-282 6.43e-20

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 89.80  E-value: 6.43e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  76 GVETLGKELFMYFGP-RALRIHFGMKGSILINPregenrAGASPALAVQL-----TRDLICFYD----SSVELRnSVESQ 145
Cdd:COG0266  51 AVERRGKYLLLELDGgLTLLIHLGMSGRLRVVP------PGEPPEKHDHVrlvldDGTELRFADprrfGALELL-TPDEL 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412 146 QRVRVMEEL--DICSPKFSFSRAESEVKKQGdRMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLV 223
Cdd:COG0266 124 EVHPLLARLgpEPLDPDFDPEYLAARLRRRR-RPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLA 202

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24475412 224 KMTRD---FSIlfyrccKA-GSAIS-------------KHCKVYKR---PnCDQCHSKITVCRFGenSRMTYFCPHCQK 282
Cdd:COG0266 203 AAIREvlrEAI------EAgGTTLRdyvnadgepgyfqQRLYVYGRegeP-CPRCGTPIERIVLG--GRSTYYCPRCQR 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 506-551 2.32e-17

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: 75.90  E-value: 2.32e-17
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 24475412   506 PLCKmHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADLS 551
Cdd:pfam06839   1 PLCP-CGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 553-597 1.25e-15

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: 70.90  E-value: 1.25e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 24475412   553 PFCRHGKRSIMKTVLKIGPNNGKNFFVCPLEKKKQCNFFQWAENG 597
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
181-282 4.80e-14

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 72.81  E-value: 4.80e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  181 VLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDfsILfyrcCKA----GSAI------------- 243
Cdd:PRK01103 161 ALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKA--VL----AEAieqgGTTLrdyvnadgkpgyf 234

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 24475412  244 SKHCKVYKRPN--CDQCHSKITVCRFGEnsRMTYFCPHCQK 282
Cdd:PRK01103 235 QQSLQVYGREGepCRRCGTPIEKIKQGG--RSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 182-281 9.52e-13

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


Pssm-ID: 273150 [Multi-domain]  Cd Length: 272  Bit Score: 68.87  E-value: 9.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   182 LLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDfsILFYRCCKAGSAIS------------KHC-K 248
Cdd:TIGR00577 162 LLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKE--VLRKAIEMGGTTIRdfsqsdghngyfQQElQ 239

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 24475412   249 VYKRPN--CDQCHSKITVCRFGenSRMTYFCPHCQ 281
Cdd:TIGR00577 240 VYGRKGepCRRCGTTIEKEKVG--GRGTHFCPQCQ 272
PRK10445 PRK10445
endonuclease VIII; Provisional
 176-282 6.02e-11

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 63.12  E-value: 6.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  176 RMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDFSILFYRC------CKAGSAISKHcKV 249
Cdd:PRK10445 152 RQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATrgqvdeNKHHGALFRF-KV 230

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 24475412  250 YKRPN--CDQCHSKITvcRFGENSRMTYFCPHCQK 282
Cdd:PRK10445 231 FHRDGeaCERCGGIIE--KTTLSSRPFYWCPGCQK 263
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 176-285 3.96e-10

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 60.97  E-value: 3.96e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  176 RMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDfsILFYRCCKAGSAIS----------- 244
Cdd:PRK14811 144 RPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIRE--VMAEAVEAGGSTLSdgsyrqpdgep 221

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 24475412  245 -----KHcKVYKRPN--CDQCHSKITVCRFGEnsRMTYFCPHCQKENP 285
Cdd:PRK14811 222 ggfqfQH-AVYGREGqpCPRCGTPIEKIVVGG--RGTHFCPQCQPLRP 266
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 182-223 1.75e-08

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: 51.91  E-value: 1.75e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 24475412   182 LLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQaCHLV 223
Cdd:pfam06831  30 LLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEE-CELL 70
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 158-282 2.00e-08

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 55.70  E-value: 2.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  158 SPKFSFSRAESEVKKQgDRMLCDVLLDQRVLPGVGNIIKNEALFDSGLHPAVKVCQLSDKQA-------CHLVKMT---- 226
Cdd:PRK13945 148 SPEFSVEYLKKKLKKR-TRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLerlreaiIEVLKTSigag 226

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24475412  227 ----RDFSILF-----YrcckAGSAiskhcKVYKRPN--CDQCHSKITVCRFGenSRMTYFCPHCQK 282
Cdd:PRK13945 227 gttfSDFRDLEgvngnY----GGQA-----WVYRRTGkpCRKCGTPIERIKLA--GRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 51-282 9.16e-08

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 53.76  E-value: 9.16e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   51 TSAAPMNAKDSGWKLLRlfngyvysgVETLGKEL-FMYFGPRALR----IHFGMKGSILInpregenragASPALAVQLT 125
Cdd:PRK14810  37 GDPDLMAARLAGRKILS---------VKRVGKHIvADLEGPGEPRgqwiIHLGMTGKLLL----------GGPDTPSPKH 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  126 RDLICFYDSSVELRnSVESQQRVRV--------------MEELDICSPKFS--FSRAESEVKKqgdrmlcdVLLDQRVLP 189
Cdd:PRK14810  98 THAVLTLSSGKELR-FVDSRQFGCIeyseafpkrfarpgPEPLEISFEDFAalFRGRKTRIKS--------ALLNQTLLR 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412  190 GVGNIIKNEALFDSGLHPAVKVCQLSDKQACHLVKMTRDfsILFYRCCKAGSAISKHC-------------KVYKRPN-- 254
Cdd:PRK14810 169 GVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE--VLREAIELGGSSVSDYVdaegrsgffqlshRVYQRTGep 246

                        250       260
                 ....*....|....*....|....*...
gi 24475412  255 CDQCHSKITvcRFGENSRMTYFCPHCQK 282
Cdd:PRK14810 247 CLNCKTPIR--RVVVAGRSSHYCPHCQK 272
AcNei1_N cd08970
N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases; This family contains ...
 67-116 5.16e-05

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: 42.63  E-value: 5.16e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 24475412  67 RLFNGYVYSGVETLGKELFMYFGP-RALRIHFGMKGSILINPREGENRAGA 116
Cdd:cd08970  37 ALLDGRVLADAEAHGKHLFLGFEGdRILHVHLGLYGKFRFGGDPPPPPRGQ 87
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
318-347 4.85e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 37.72  E-value: 4.85e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 24475412   318 SEEQWSCVVCTLINRPSAKACDACLTTRPL 347
Cdd:pfam00641   1 REGDWDCSKCLVQNFATSTKCVACQAPKPD 30
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-136 1.73e-03

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


Pssm-ID: 176808  Cd Length: 98  Bit Score: 38.07  E-value: 1.73e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24475412   1 MVEGPGCTLNGEKIRArvLPGQAVTGVRGTALQsllgpAMSPAAsladvatsaapmnakdsGWKLLrlfngyvysGVETL 80
Cdd:cd08974   1 MPEGPSIVILREAAAA--FKGQTVIRASGNAKI-----DKDRLA-----------------GQKVL---------AIRSW 47

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 24475412  81 GKELFMYFGPRALRIHFGMKGSILINpregeNRAGASPALAVQLTRDLICFYDSSV 136
Cdd:cd08974  48 GKHFLLEFEDFTVRIHLLLFGSYRIN-----ERKDAPPRLSLGFDNGELNFYTCSV 98
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 65-109 2.76e-03

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: 37.93  E-value: 2.76e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 24475412     65 LLRLFNGYVYSGVETLGKELFMYF-GPRALRIHFGMKGSILINPRE 109
Cdd:smart00898  39 FAAALSGRTITSVRRRGKYLLLRLlGGLTLVVHLGMSGSLRVVPAG 84
 
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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