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Conserved domains on  [gi|55925237|ref|NP_001007336|]
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endonuclease 8-like 3 [Danio rerio]

Protein Classification

MeNeil3_N and zf-GRF domain-containing protein( domain architecture ID 12963224)

protein containing domains MeNeil3_N, Nei, zf-RanBP, and zf-GRF

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 ...
 1-129 5.18e-70

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: 221.13  E-value: 5.18e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   1 MVEGPGCTLNGEKIRARVQKRQKVLHIQGNETKTTSDDGSRSS----------FQSFTGGEFTGVETLGKELFMYFGVRA 70
Cdd:cd08969   1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGagskdershvLDSLTGQVYTGVETLGKELFMYFGDKA 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  71 LRLHFGMNGSMRINPL-KKDLHGKPPVLVIQLTNDAICFFDTTVEIRLSEDCEQKVRAME 129
Cdd:cd08969  81 LRIHFGMNGSMRINPLeSKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
Nei super family cl33822
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
45-258 8.32e-27

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: 109.44  E-value: 8.32e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  45 QSFTGGEFTGVETLGKELFMYF-GVRALRLHFGMNGSMRI----NPLKKDLHgkppvLVIQLTNDAICFF-D----TTVE 114
Cdd:COG0266  42 ARLTGRRITAVERRGKYLLLELdGGLTLLIHLGMSGRLRVvppgEPPEKHDH-----VRLVLDDGTELRFaDprrfGALE 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237 115 IrLSEDCEQKVRAMEAL--DICSPKFSFSRAVEAVKTeRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLT 192
Cdd:COG0266 117 L-LTPDELEVHPLLARLgpEPLDPDFDPEYLAARLRR-RRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLS 194

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237 193 DEQVHHLVK---------------MTRDFTllfykcRKNGSPLY--KHYKVYKR---PnCGQCSGTVTVCRLGdnGRMTY 252
Cdd:COG0266 195 RAELERLAAairevlreaieaggtTLRDYV------NADGEPGYfqQRLYVYGRegeP-CPRCGTPIERIVLG--GRSTY 265


                ....*.
gi 55925237 253 YCQRCQ 258
Cdd:COG0266 266 YCPRCQ 271
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 497-541 5.20e-16

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


:

Pssm-ID: 462017  Cd Length: 45  Bit Score: 72.05  E-value: 5.20e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 55925237   497 PMCHHGKRTVMKTVLKLGPNNGRNFYTCPVKMGKQCNFFQWAENG 541
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 455-493 6.32e-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: 68.97  E-value: 6.32e-15
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 55925237   455 HHRPCTQRVVTKEGENKGRQFYTCSLPRETQCNFFEWAD 493
Cdd:pfam06839   5 CGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWAD 43
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
296-324 4.34e-05

Zn-finger in Ran binding protein and others;


:

Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 40.41  E-value: 4.34e-05
                          10        20
                  ....*....|....*....|....*....
gi 55925237   296 EEEWACSLCTLINRPFNKHCDACMSPRPD 324
Cdd:pfam00641   2 EGDWDCSKCLVQNFATSTKCVACQAPKPD 30
 
Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-129 5.18e-70

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: 221.13  E-value: 5.18e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   1 MVEGPGCTLNGEKIRARVQKRQKVLHIQGNETKTTSDDGSRSS----------FQSFTGGEFTGVETLGKELFMYFGVRA 70
Cdd:cd08969   1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGagskdershvLDSLTGQVYTGVETLGKELFMYFGDKA 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  71 LRLHFGMNGSMRINPL-KKDLHGKPPVLVIQLTNDAICFFDTTVEIRLSEDCEQKVRAME 129
Cdd:cd08969  81 LRIHFGMNGSMRINPLeSKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
45-258 8.32e-27

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 109.44  E-value: 8.32e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  45 QSFTGGEFTGVETLGKELFMYF-GVRALRLHFGMNGSMRI----NPLKKDLHgkppvLVIQLTNDAICFF-D----TTVE 114
Cdd:COG0266  42 ARLTGRRITAVERRGKYLLLELdGGLTLLIHLGMSGRLRVvppgEPPEKHDH-----VRLVLDDGTELRFaDprrfGALE 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237 115 IrLSEDCEQKVRAMEAL--DICSPKFSFSRAVEAVKTeRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLT 192
Cdd:COG0266 117 L-LTPDELEVHPLLARLgpEPLDPDFDPEYLAARLRR-RRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLS 194

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237 193 DEQVHHLVK---------------MTRDFTllfykcRKNGSPLY--KHYKVYKR---PnCGQCSGTVTVCRLGdnGRMTY 252
Cdd:COG0266 195 RAELERLAAairevlreaieaggtTLRDYV------NADGEPGYfqQRLYVYGRegeP-CPRCGTPIERIVLG--GRSTY 265


                ....*.
gi 55925237 253 YCQRCQ 258
Cdd:COG0266 266 YCPRCQ 271
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
48-258 1.27e-18

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 85.90  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   48 TGGEFTGVETLGKELFMYFGVR-ALRLHFGMNGSMRI----NPLKKDLHgkppvLVIQLTNDAICFF-DT----TVEIRL 117
Cdd:PRK01103  46 SGQTILAVGRRGKYLLLDLDDGgTLISHLGMSGSLRLlpedTPPEKHDH-----VDFVLDDGTVLRYnDPrrfgAMLLTP 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  118 SEDCEQKVR----AMEALDicsPKFSFSRAVEAVKTeRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTD 193
Cdd:PRK01103 121 KGDLEAHPLlahlGPEPLS---DAFDGEYLAAKLRK-KKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSR 196

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  194 EQVHHLVK-----MT----------RDFTllfykcRKNGSPLY--KHYKVYKRPN--CGQCSGTVTVCRLGdnGRMTYYC 254
Cdd:PRK01103 197 AEAERLVDaikavLAeaieqggttlRDYV------NADGKPGYfqQSLQVYGREGepCRRCGTPIEKIKQG--GRSTFFC 268


                 ....
gi 55925237  255 QRCQ 258
Cdd:PRK01103 269 PRCQ 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 497-541 5.20e-16

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


Pssm-ID: 462017  Cd Length: 45  Bit Score: 72.05  E-value: 5.20e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 55925237   497 PMCHHGKRTVMKTVLKLGPNNGRNFYTCPVKMGKQCNFFQWAENG 541
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 11-258 8.61e-16

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: 77.72  E-value: 8.61e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237    11 GEKI-RARVQKRQKVLHIQGNETKTTSddgsrssfqsFTGGEFTGVETLGKELFMYFGVRALRLHFGMNGSMRINPLKkd 89
Cdd:TIGR00577  19 GKTIkSVEVVLRNPVLRPAGSEDLQKR----------LLGQTILSIQRRGKYLLFELDDGALVSHLRMEGKYRLEAVP-- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237    90 lHGKPP-VLVIQLTNDA--ICFFDT----TVE-IRLSEDCEQKVRAMEALDICSPKFSFsRAVEAVKTERARMLCDVLLD 161
Cdd:TIGR00577  87 -DAPDKhDHVDFLFDDGteLRYHDPrrfgTWLlLDRGQVENIPLLAKLGPEPLSEDFTA-EYLFEKLAKSKRKIKTALLD 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   162 QTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHLVKMTRDF----------TLLFYKcRKNGSPLYKH--YKVYKR 229
Cdd:TIGR00577 165 QRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVlrkaiemggtTIRDFS-QSDGHNGYFQqeLQVYGR 243

                         250       260       270
                  ....*....|....*....|....*....|.
gi 55925237   230 PN--CGQCSGTVTVCRLGdnGRMTYYCQRCQ 258
Cdd:TIGR00577 244 KGepCRRCGTTIEKEKVG--GRGTHFCPQCQ 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 455-493 6.32e-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: 68.97  E-value: 6.32e-15
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 55925237   455 HHRPCTQRVVTKEGENKGRQFYTCSLPRETQCNFFEWAD 493
Cdd:pfam06839   5 CGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWAD 43
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 130-205 2.98e-09

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 54.22  E-value: 2.98e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 55925237   130 ALDICSPKFSFSRAVEAVKtERARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHLVKMTRD 205
Cdd:pfam06831   2 GPEPLSEDFTVDYFAERLA-KKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 9-111 1.23e-05

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: 44.48  E-value: 1.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237      9 LNGEKIRARVQKRQKVLhiqgnetkTTSDDgsrssFQSF-TGGEFTGVETLGKELFMYF-GVRALRLHFGMNGSMRIN-- 84
Cdd:smart00898  17 LAGRTITRVEVVRPPQL--------RFPDE-----FAAAlSGRTITSVRRRGKYLLLRLlGGLTLVVHLGMSGSLRVVpa 83

                           90       100       110
                   ....*....|....*....|....*....|
gi 55925237     85 --PLKKDLHgkppvLVIQLTND-AICFFDT 111
Cdd:smart00898  84 gtPPPKHDH-----VRLVLDDGtELRFNDP 108
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
296-324 4.34e-05

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 40.41  E-value: 4.34e-05
                          10        20
                  ....*....|....*....|....*....
gi 55925237   296 EEEWACSLCTLINRPFNKHCDACMSPRPD 324
Cdd:pfam00641   2 EGDWDCSKCLVQNFATSTKCVACQAPKPD 30
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 45-111 8.16e-03

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: 36.33  E-value: 8.16e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 55925237    45 QSFTGGEFTGVETLGKELFMYFGVR-ALRLHFGMNGSMRINPlkkdlHGKPPV---LVIQLTND-AICFFDT 111
Cdd:pfam01149  44 AALTGRKVTSVGRRGKYLLLELDSGgHLVVHLGMTGWLLIKT-----EEWPPKhdhVRLELDDGrELRFTDP 110
 
Name Accession Description Interval E-value
MeNeil3_N cd08969
N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3); This family contains the ...
 1-129 5.18e-70

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: 221.13  E-value: 5.18e-70
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   1 MVEGPGCTLNGEKIRARVQKRQKVLHIQGNETKTTSDDGSRSS----------FQSFTGGEFTGVETLGKELFMYFGVRA 70
Cdd:cd08969   1 MVEGPGCTLNGEKIRARVEKGQRVVHVRGSAPSSPSGAASRNGagskdershvLDSLTGQVYTGVETLGKELFMYFGDKA 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  71 LRLHFGMNGSMRINPL-KKDLHGKPPVLVIQLTNDAICFFDTTVEIRLSEDCEQKVRAME 129
Cdd:cd08969  81 LRIHFGMNGSMRINPLeSKDRSGASPVLEVQLTKDLICFFDSTVEIRNAAECQQKIRMME 140
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
45-258 8.32e-27

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 109.44  E-value: 8.32e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  45 QSFTGGEFTGVETLGKELFMYF-GVRALRLHFGMNGSMRI----NPLKKDLHgkppvLVIQLTNDAICFF-D----TTVE 114
Cdd:COG0266  42 ARLTGRRITAVERRGKYLLLELdGGLTLLIHLGMSGRLRVvppgEPPEKHDH-----VRLVLDDGTELRFaDprrfGALE 116

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237 115 IrLSEDCEQKVRAMEAL--DICSPKFSFSRAVEAVKTeRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLT 192
Cdd:COG0266 117 L-LTPDELEVHPLLARLgpEPLDPDFDPEYLAARLRR-RRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLS 194

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237 193 DEQVHHLVK---------------MTRDFTllfykcRKNGSPLY--KHYKVYKR---PnCGQCSGTVTVCRLGdnGRMTY 252
Cdd:COG0266 195 RAELERLAAairevlreaieaggtTLRDYV------NADGEPGYfqQRLYVYGRegeP-CPRCGTPIERIVLG--GRSTY 265


                ....*.
gi 55925237 253 YCQRCQ 258
Cdd:COG0266 266 YCPRCQ 271
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
48-258 1.27e-18

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 85.90  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   48 TGGEFTGVETLGKELFMYFGVR-ALRLHFGMNGSMRI----NPLKKDLHgkppvLVIQLTNDAICFF-DT----TVEIRL 117
Cdd:PRK01103  46 SGQTILAVGRRGKYLLLDLDDGgTLISHLGMSGSLRLlpedTPPEKHDH-----VDFVLDDGTVLRYnDPrrfgAMLLTP 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  118 SEDCEQKVR----AMEALDicsPKFSFSRAVEAVKTeRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTD 193
Cdd:PRK01103 121 KGDLEAHPLlahlGPEPLS---DAFDGEYLAAKLRK-KKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSR 196

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  194 EQVHHLVK-----MT----------RDFTllfykcRKNGSPLY--KHYKVYKRPN--CGQCSGTVTVCRLGdnGRMTYYC 254
Cdd:PRK01103 197 AEAERLVDaikavLAeaieqggttlRDYV------NADGKPGYfqQSLQVYGREGepCRRCGTPIEKIKQG--GRSTFFC 268


                 ....
gi 55925237  255 QRCQ 258
Cdd:PRK01103 269 PRCQ 272
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 497-541 5.20e-16

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


Pssm-ID: 462017  Cd Length: 45  Bit Score: 72.05  E-value: 5.20e-16
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 55925237   497 PMCHHGKRTVMKTVLKLGPNNGRNFYTCPVKMGKQCNFFQWAENG 541
Cdd:pfam06839   1 PLCPCGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWADEV 45
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 11-258 8.61e-16

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: 77.72  E-value: 8.61e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237    11 GEKI-RARVQKRQKVLHIQGNETKTTSddgsrssfqsFTGGEFTGVETLGKELFMYFGVRALRLHFGMNGSMRINPLKkd 89
Cdd:TIGR00577  19 GKTIkSVEVVLRNPVLRPAGSEDLQKR----------LLGQTILSIQRRGKYLLFELDDGALVSHLRMEGKYRLEAVP-- 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237    90 lHGKPP-VLVIQLTNDA--ICFFDT----TVE-IRLSEDCEQKVRAMEALDICSPKFSFsRAVEAVKTERARMLCDVLLD 161
Cdd:TIGR00577  87 -DAPDKhDHVDFLFDDGteLRYHDPrrfgTWLlLDRGQVENIPLLAKLGPEPLSEDFTA-EYLFEKLAKSKRKIKTALLD 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   162 QTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHLVKMTRDF----------TLLFYKcRKNGSPLYKH--YKVYKR 229
Cdd:TIGR00577 165 QRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVlrkaiemggtTIRDFS-QSDGHNGYFQqeLQVYGR 243

                         250       260       270
                  ....*....|....*....|....*....|.
gi 55925237   230 PN--CGQCSGTVTVCRLGdnGRMTYYCQRCQ 258
Cdd:TIGR00577 244 KGepCRRCGTTIEKEKVG--GRGTHFCPQCQ 272
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-111 4.72e-15

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: 71.63  E-value: 4.72e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   2 VEGPGCTLNGEKIRARVqKRQKVLHIQGNETKTTSDDGSRSSFQsFTGGEFTGVETLGKELFMYF-GVRALRLHFGMNGS 80
Cdd:cd08773   1 PELPEVELLRRKLRRAL-KGKRVTRVEVSDPRRLFTPAAELAAA-LIGRRVRGAERRGKYLLLELsGGPWLVIHLGMTGR 78

                        90       100       110
                ....*....|....*....|....*....|..
gi 55925237  81 MRINPLKKDLhGKPPVLVIQLTND-AICFFDT 111
Cdd:cd08773  79 LRVCPEGEPP-PKHDRLVLRLANGsQLRFTDP 109
zf-GRF pfam06839
GRF zinc finger; This presumed zinc binding domain is found in a variety of DNA-binding ...
 455-493 6.32e-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: 68.97  E-value: 6.32e-15
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 55925237   455 HHRPCTQRVVTKEGENKGRQFYTCSLPRETQCNFFEWAD 493
Cdd:pfam06839   5 CGQRAVLLTVRKTGPNPGRQFYKCPVGREKQCGFFQWAD 43
PRK10445 PRK10445
endonuclease VIII; Provisional
 133-258 2.06e-12

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 67.36  E-value: 2.06e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  133 ICSPKFsfsraveavkteRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHLVKMTRDFTLLFYK 212
Cdd:PRK10445 144 LLSPRF------------RNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYA 211

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 55925237  213 CR------KNGSPLYKHyKVYKRPN--CGQCSGTVTVCRLGdnGRMTYYCQRCQ 258
Cdd:PRK10445 212 TRgqvdenKHHGALFRF-KVFHRDGeaCERCGGIIEKTTLS--SRPFYWCPGCQ 262
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 130-205 2.98e-09

Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.


Pssm-ID: 399664 [Multi-domain]  Cd Length: 89  Bit Score: 54.22  E-value: 2.98e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 55925237   130 ALDICSPKFSFSRAVEAVKtERARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHLVKMTRD 205
Cdd:pfam06831   2 GPEPLSEDFTVDYFAERLA-KKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKA 76
BaFpgNei_N_2 cd08974
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-113 9.21e-08

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: 50.02  E-value: 9.21e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   1 MVEGPGCTLNGEKIRARvqKRQKVLHIQGNetkTTSDDgsrssfQSFTGGEFTGVETLGKELFMYFGVRALRLHFGMNGS 80
Cdd:cd08974   1 MPEGPSIVILREAAAAF--KGQTVIRASGN---AKIDK------DRLAGQKVLAIRSWGKHFLLEFEDFTVRIHLLLFGS 69

                        90       100       110
                ....*....|....*....|....*....|...
gi 55925237  81 MRINPLKKdlhgKPPVLVIQLTNDAICFFDTTV 113
Cdd:cd08974  70 YRINERKD----APPRLSLGFDNGELNFYTCSV 98
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 135-259 1.63e-07

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 53.01  E-value: 1.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  135 SPKFSFSRAVEAVKTeRARMLCDVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHL-------VKMT---- 203
Cdd:PRK13945 148 SPEFSVEYLKKKLKK-RTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLreaiievLKTSigag 226

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 55925237  204 -------RDFTLLfykcrkNGSplykhYK----VYKRPN--CGQCSGTVTVCRLGdnGRMTYYCQRCQT 259
Cdd:PRK13945 227 gttfsdfRDLEGV------NGN-----YGgqawVYRRTGkpCRKCGTPIERIKLA--GRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 73-258 1.17e-05

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 47.21  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237   73 LHFGMNGSMRI----NPLKKDLHGkppvlVIQLTNDAICFFDTTVE---IRLSEDCEQKVRA--MEALDICSPKFS--FS 141
Cdd:PRK14810  77 IHLGMTGKLLLggpdTPSPKHTHA-----VLTLSSGKELRFVDSRQfgcIEYSEAFPKRFARpgPEPLEISFEDFAalFR 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237  142 RAVEAVKTerarmlcdVLLDQTVLPGVGNIIKNEALFDSGLNPAVKVSQLTDEQVHHLVKMTRDftLLFYKCRKNGSPLY 221
Cdd:PRK14810 152 GRKTRIKS--------ALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGE--VLREAIELGGSSVS 221

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 55925237  222 KH-------------YKVYKRPN--CGQCSGTVTvcRLGDNGRMTYYCQRCQ 258
Cdd:PRK14810 222 DYvdaegrsgffqlsHRVYQRTGepCLNCKTPIR--RVVVAGRSSHYCPHCQ 271
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 9-111 1.23e-05

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: 44.48  E-value: 1.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 55925237      9 LNGEKIRARVQKRQKVLhiqgnetkTTSDDgsrssFQSF-TGGEFTGVETLGKELFMYF-GVRALRLHFGMNGSMRIN-- 84
Cdd:smart00898  17 LAGRTITRVEVVRPPQL--------RFPDE-----FAAAlSGRTITSVRRRGKYLLLRLlGGLTLVVHLGMSGSLRVVpa 83

                           90       100       110
                   ....*....|....*....|....*....|
gi 55925237     85 --PLKKDLHgkppvLVIQLTND-AICFFDT 111
Cdd:smart00898  84 gtPPPKHDH-----VRLVLDDGtELRFNDP 108
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
296-324 4.34e-05

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 40.41  E-value: 4.34e-05
                          10        20
                  ....*....|....*....|....*....
gi 55925237   296 EEEWACSLCTLINRPFNKHCDACMSPRPD 324
Cdd:pfam00641   2 EGDWDCSKCLVQNFATSTKCVACQAPKPD 30
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 45-111 8.16e-03

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: 36.33  E-value: 8.16e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 55925237    45 QSFTGGEFTGVETLGKELFMYFGVR-ALRLHFGMNGSMRINPlkkdlHGKPPV---LVIQLTND-AICFFDT 111
Cdd:pfam01149  44 AALTGRKVTSVGRRGKYLLLELDSGgHLVVHLGMTGWLLIKT-----EEWPPKhdhVRLELDDGrELRFTDP 110
 
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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