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Conserved domains on  [gi|88195496|ref|YP_500300|]
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formamidopyrimidine-DNA glycosylase [Staphylococcus aureus subsp. aureus NCTC 8325]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 11415887)

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

CATH:  1.10.8.50|3.20.190.10
EC:  3.2.2.-|4.2.99.-
Gene Ontology:  GO:0140078|GO:0003684|GO:0008534|GO:0008270|GO:0006284|GO:0003906|GO:0006281
PubMed:  21486746|14607836
SCOP:  4000303

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-290 5.34e-106

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


:

Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 308.98  E-value: 5.34e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIegkaqgketiiKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkreQ 81
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPRL-----------RFPVPEDFAARLTGRRITAVERRGKYLLLELDG---G 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  82 RTLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFGEIR--NVASVASYPSFLEIAPEPFSNEA 159
Cdd:COG0266  67 LTLLIHLGMSGRLRVVPPGEPP-----EKHDHVRLVLDDGTELRFADPRRFGALEllTPDELEVHPLLARLGPEPLDPDF 141

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496 160 LTYYL-NRIhqqSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGGT 238
Cdd:COG0266 142 DPEYLaARL---RRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGT 218

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496 239 SISDYRHADGKTGEMQLHLNVYK---QPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:COG0266 219 TLRDYVNADGEPGYFQQRLYVYGregEP-CPRCGTPIERIVLGGRSTYYCPRCQR 272
 
Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-290 5.34e-106

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 308.98  E-value: 5.34e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIegkaqgketiiKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkreQ 81
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPRL-----------RFPVPEDFAARLTGRRITAVERRGKYLLLELDG---G 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  82 RTLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFGEIR--NVASVASYPSFLEIAPEPFSNEA 159
Cdd:COG0266  67 LTLLIHLGMSGRLRVVPPGEPP-----EKHDHVRLVLDDGTELRFADPRRFGALEllTPDELEVHPLLARLGPEPLDPDF 141

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496 160 LTYYL-NRIhqqSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGGT 238
Cdd:COG0266 142 DPEYLaARL---RRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGT 218

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496 239 SISDYRHADGKTGEMQLHLNVYK---QPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:COG0266 219 TLRDYVNADGEPGYFQQRLYVYGregEP-CPRCGTPIERIVLGGRSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-290 1.46e-98

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 290.44  E-value: 1.46e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    1 MPELPEVEHVKRGIEPYVINQKIEHVIfsdkVIEGKaqgketIIKGIeLDTFKTLSEGYTITNVERRSKYIVFQLDNkre 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVE----VRRPK------LRWPV-PEDFAERLSGQTILAVGRRGKYLLLDLDD--- 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   81 QRTLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFG--EIRNVASVASYPSFLEIAPEPFSNE 158
Cdd:PRK01103  67 GGTLISHLGMSGSLRLLPEDTPP-----EKHDHVDFVLDDGTVLRYNDPRRFGamLLTPKGDLEAHPLLAHLGPEPLSDA 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  159 -ALTYYLNRIHqqsNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGG 237
Cdd:PRK01103 142 fDGEYLAAKLR---KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGG 218

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496  238 TSISDYRHADGKTGEMQLHLNVY---KQPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:PRK01103 219 TTLRDYVNADGKPGYFQQSLQVYgreGEP-CRRCGTPIEKIKQGGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-289 1.57e-75

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: 231.80  E-value: 1.57e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496     2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIegkaqgketIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNKReq 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNP---------VLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    82 rtLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFGEIRNVA--SVASYPSFLEIAPEPFSNEA 159
Cdd:TIGR00577  70 --LVSHLRMEGKYRLEAVPDAP-----DKHDHVDFLFDDGTELRYHDPRRFGTWLLLDrgQVENIPLLAKLGPEPLSEDF 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   160 LTYYL-NRIHQqsnKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGGT 238
Cdd:TIGR00577 143 TAEYLfEKLAK---SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGT 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 88195496   239 SISDYRHADGKTGEMQLHLNVY--KQPVCKVCGSQIETKIIATRNSHYCPVCQ 289
Cdd:TIGR00577 220 TIRDFSQSDGHNGYFQQELQVYgrKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-136 1.07e-43

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 144.95  E-value: 1.07e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDkviegkaqgkETIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkreQ 81
Cdd:cd08966   1 PELPEVETVRRGLAPHLVGRRIEDVEVRR----------PKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDD---G 67

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496  82 RTLISHLGMAGGFFIVDELEdimipNYRKHWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:cd08966  68 LVLVIHLGMTGRLLVVPPDE-----PPEKHDHVIFELDDGRELRFNDPRRFGTLL 117
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-135 3.55e-39

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: 133.02  E-value: 3.55e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496     1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDkviegkaqgkETIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkre 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLD----------DKNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDS--- 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496    81 QRTLISHLGMAGGFFIVDELEDimiPnyrKHWHVIFELSNDKKLIYSDIRRFGEI 135
Cdd:pfam01149  68 GGHLVVHLGMTGWLLIKTEEWP---P---KHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-136 1.09e-38

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: 131.92  E-value: 1.09e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496      2 PELPEVEHVKRGIEPYVINQKIEHV-IFSDKVIEGKaqgketiikgielDTFKTLSEGYTITNVERRSKYIVFQLDNkre 80
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVeVVRPPQLRFP-------------DEFAAALSGRTITSVRRRGKYLLLRLLG--- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496     81 QRTLISHLGMAGGFFIVDELEdimipNYRKHWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:smart00898  65 GLTLVVHLGMSGSLRVVPAGT-----PPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
 
Name Accession Description Interval E-value
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-290 5.34e-106

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 308.98  E-value: 5.34e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIegkaqgketiiKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkreQ 81
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPRL-----------RFPVPEDFAARLTGRRITAVERRGKYLLLELDG---G 66

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  82 RTLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFGEIR--NVASVASYPSFLEIAPEPFSNEA 159
Cdd:COG0266  67 LTLLIHLGMSGRLRVVPPGEPP-----EKHDHVRLVLDDGTELRFADPRRFGALEllTPDELEVHPLLARLGPEPLDPDF 141

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496 160 LTYYL-NRIhqqSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGGT 238
Cdd:COG0266 142 DPEYLaARL---RRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGT 218

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496 239 SISDYRHADGKTGEMQLHLNVYK---QPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:COG0266 219 TLRDYVNADGEPGYFQQRLYVYGregEP-CPRCGTPIERIVLGGRSTYYCPRCQR 272
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-290 1.46e-98

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 290.44  E-value: 1.46e-98
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    1 MPELPEVEHVKRGIEPYVINQKIEHVIfsdkVIEGKaqgketIIKGIeLDTFKTLSEGYTITNVERRSKYIVFQLDNkre 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVE----VRRPK------LRWPV-PEDFAERLSGQTILAVGRRGKYLLLDLDD--- 66

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   81 QRTLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFG--EIRNVASVASYPSFLEIAPEPFSNE 158
Cdd:PRK01103  67 GGTLISHLGMSGSLRLLPEDTPP-----EKHDHVDFVLDDGTVLRYNDPRRFGamLLTPKGDLEAHPLLAHLGPEPLSDA 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  159 -ALTYYLNRIHqqsNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGG 237
Cdd:PRK01103 142 fDGEYLAAKLR---KKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGG 218

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496  238 TSISDYRHADGKTGEMQLHLNVY---KQPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:PRK01103 219 TTLRDYVNADGKPGYFQQSLQVYgreGEP-CRRCGTPIEKIKQGGRSTFFCPRCQK 273
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-289 1.57e-75

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: 231.80  E-value: 1.57e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496     2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIegkaqgketIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNKReq 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNP---------VLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    82 rtLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFGEIRNVA--SVASYPSFLEIAPEPFSNEA 159
Cdd:TIGR00577  70 --LVSHLRMEGKYRLEAVPDAP-----DKHDHVDFLFDDGTELRYHDPRRFGTWLLLDrgQVENIPLLAKLGPEPLSEDF 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   160 LTYYL-NRIHQqsnKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGGT 238
Cdd:TIGR00577 143 TAEYLfEKLAK---SKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGT 219

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 88195496   239 SISDYRHADGKTGEMQLHLNVY--KQPVCKVCGSQIETKIIATRNSHYCPVCQ 289
Cdd:TIGR00577 220 TIRDFSQSDGHNGYFQQELQVYgrKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-290 8.47e-59

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 189.37  E-value: 8.47e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    1 MPELPEVEHVKRGIEPYVINQKIEHV-IFSDKVIeGKAQGKETIIKGIEldtfktlseGYTITNVERRSKYIVFQLDNKR 79
Cdd:PRK13945   1 MPELPEVETVRRGLEQLLLNFIIKGVeVLLERTI-ASPGGVEEFIKGLK---------GSLIGQWQRRGKYLLASLKKEG 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   80 EQR--TLISHLGMAGGFFIVDELEdimipNYRKHWHVIFELSNDKKLIYSDIRRFGEIRNVASVASYPSFL----EIAPE 153
Cdd:PRK13945  71 SENagWLGVHLRMTGQFLWVEQST-----PPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESIItglqKLGPE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  154 PFSNEALTYYLNriHQQSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGI 233
Cdd:PRK13945 146 PFSPEFSVEYLK--KKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSI 223

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  234 KYGGTSISDYRHADGKTGEMQLHLNVYK---QPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:PRK13945 224 GAGGTTFSDFRDLEGVNGNYGGQAWVYRrtgKP-CRKCGTPIERIKLAGRSTHWCPNCQK 282
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-290 3.81e-57

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 184.61  E-value: 3.81e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDKviegkAQGKETiikgieldtfkTLSEGYTITNVERRSKYIVFQLDNKRE 80
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQQVVHDDP-----ARYRNT-----------ELAEGRRVLGLSRRGKYLLLHLPHDLE 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   81 qrtLISHLGMAGGFfivdELEDimipnyRKHWHVIFELSNdKKLIYSDIRRFGEIRNVAS--VASYPSFLEIAPEPFSNE 158
Cdd:PRK14811  65 ---LIVHLGMTGGF----RLEP------GPHTRVTLELPG-RTLYFTDPRRFGKWWVVRAgdYREIPLLARMGPEPLSDD 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  159 altYYLNRIHQQSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYGGT 238
Cdd:PRK14811 131 ---FTEPEFVRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGS 207

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496  239 SISD--YRHADGKTGEMQLHLNVYKQP--VCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:PRK14811 208 TLSDgsYRQPDGEPGGFQFQHAVYGREgqPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-290 2.07e-56

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 182.80  E-value: 2.07e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDKviegkaqgkeTIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNKRE 80
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRNL----------RIPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGPGE 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   81 QRT-LISHLGMAGGFFIVDEleDIMIPnyrKHWHVIFELSNDKKLIYSDIRRFGEI-------RNVASVASYPsfLEIAP 152
Cdd:PRK14810  71 PRGqWIIHLGMTGKLLLGGP--DTPSP---KHTHAVLTLSSGKELRFVDSRQFGCIeyseafpKRFARPGPEP--LEISF 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  153 EPFSNEAltyylnrihqqSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEG 232
Cdd:PRK14810 144 EDFAALF-----------RGRKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREA 212

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 88195496  233 IKYGGTSISDYRHADGKTGEMQLHLNVYK---QPvCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:PRK14810 213 IELGGSSVSDYVDAEGRSGFFQLSHRVYQrtgEP-CLNCKTPIRRVVVAGRSSHYCPHCQK 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-136 1.07e-43

N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site.


Pssm-ID: 176800  Cd Length: 120  Bit Score: 144.95  E-value: 1.07e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDkviegkaqgkETIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkreQ 81
Cdd:cd08966   1 PELPEVETVRRGLAPHLVGRRIEDVEVRR----------PKLRRPPDPEEFAERLVGRRITGVERRGKYLLFELDD---G 67

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496  82 RTLISHLGMAGGFFIVDELEdimipNYRKHWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:cd08966  68 LVLVIHLGMTGRLLVVPPDE-----PPEKHDHVIFELDDGRELRFNDPRRFGTLL 117
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-135 3.55e-39

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: 133.02  E-value: 3.55e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496     1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDkviegkaqgkETIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNkre 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLD----------DKNLRGPSPEEFAAALTGRKVTSVGRRGKYLLLELDS--- 67

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496    81 QRTLISHLGMAGGFFIVDELEDimiPnyrKHWHVIFELSNDKKLIYSDIRRFGEI 135
Cdd:pfam01149  68 GGHLVVHLGMTGWLLIKTEEWP---P---KHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-136 1.09e-38

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: 131.92  E-value: 1.09e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496      2 PELPEVEHVKRGIEPYVINQKIEHV-IFSDKVIEGKaqgketiikgielDTFKTLSEGYTITNVERRSKYIVFQLDNkre 80
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVeVVRPPQLRFP-------------DEFAAALSGRTITSVRRRGKYLLLRLLG--- 64

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496     81 QRTLISHLGMAGGFFIVDELEdimipNYRKHWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:smart00898  65 GLTLVVHLGMSGSLRVVPAGT-----PPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-136 1.22e-24

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: 95.51  E-value: 1.22e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIEGKaqgketiikgiELDTFKTLSEGYTITNVERRSKYIVFQLDNKreq 81
Cdd:cd08773   1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFT-----------PAAELAAALIGRRVRGAERRGKYLLLELSGG--- 66

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496  82 RTLISHLGMAGGFFIVDELEDImipnyRKHWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:cd08773  67 PWLVIHLGMTGRLRVCPEGEPP-----PKHDRLVLRLANGSQLRFTDPRKFGRVE 116
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 150-240 2.59e-20

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: 83.11  E-value: 2.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   150 IAPEPFSNEALTYYLNRIHQQsnKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVL 229
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAK--KKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVL 78

                          90
                  ....*....|.
gi 88195496   230 EEGIKYGGTSI 240
Cdd:pfam06831  79 QEAIEMGGGGI 89
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-290 1.43e-17

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 80.07  E-value: 1.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496    1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDKviegkaqgketiikgiELDTFKTLSEGYTITNVERRSKYIVFQLDNKRe 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFP----------------QLKPYESQLIGQRVTHIETRGKALLTHFSNGL- 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   81 qrTLISHLGMAGGFFIVDELEdimIPNYRKHWHVIFELSNDKKLIYS--DIrrfgEIRNVASVASYPSFLEIAPEPFSnE 158
Cdd:PRK10445  64 --TLYSHNQLYGVWRVVDTGE---EPQTTRVLRVRLQTADKTILLYSasDI----EMLTPEQLTTHPFLQRVGPDVLD-P 133

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496  159 ALTY--YLNRIHQQSNKNKPIKQVILDHKVIAGCGNIYACEALFRAGVLPDKKVKDLTHQQQEMVFYYVREVLEEGIKYG 236
Cdd:PRK10445 134 NLTPeqVKERLLSPRFRNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATR 213

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496  237 GTsISDYRHAdgktGEMQLHlNVY--KQPVCKVCGSQIETKIIATRNSHYCPVCQK 290
Cdd:PRK10445 214 GQ-VDENKHH----GALFRF-KVFhrDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-136 3.10e-15

N-terminal domain of the plant and fungal Nei and related proteins; This family contains the N-terminal domain of plant and Fungi Nei and related proteins. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. The plant and fungal FpgNei glycosylases prefer the oxidized pyrimidines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh) over 8-oxoguanine in double stranded oligonucleotides and also show weak activity on single stranded DNA. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a characteristic zincless finger motif. They share a common ancestor not shared with other eukaryotic members of the FpgNei family.


Pssm-ID: 176806  Cd Length: 137  Bit Score: 70.80  E-value: 3.10e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDKVIegkaqgketIIKGIELDTFKTLSEGYTITNVERRSKYIVFQLDNKre 80
Cdd:cd08972   1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDK---------VFGGVTPGAFQKALLGRTITSAHRKGKYFWLTLDGD-- 69

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 88195496  81 QRTLISHLGMAGGFFI-------------VDELEDIMIPNYrkhWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:cd08972  70 APVPVMHFGMTGAISIkgvktiyykmlrpPKEEDQTWPPRF---YKFVLTLEDGTELAFTDPRRLGRVR 135
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-136 5.71e-12

Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases; This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176810  Cd Length: 117  Bit Score: 61.60  E-value: 5.71e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   2 PELPEVEHVKRGIEPYVINQKIEHVIFSDKVIEGKAQGketiikgieldTFKTLSEGYTITNVERRSKYIVFQLDnkrEQ 81
Cdd:cd08976   1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEPKA-----------TLREVLEGRTFTETHRIGKYLFLKTK---EG 66

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 88195496  82 RTLISHLGMAGGFFIVDELEDimIPnyrKHWHVIFELSNDKKLIYSDIRRFGEIR 136
Cdd:cd08976  67 GWLVMHFGMTGKLDYYPDDED--PP---KHARLLLHFEDGFRLAFECPRKFGRVR 116
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-94 2.23e-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_1 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176807  Cd Length: 122  Bit Score: 51.48  E-value: 2.23e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   1 MPELPEVEHVKRGIEPYVINQKIEHVIFSDKviegkaqgkeTIIKGIelDTFKTLSEGYTITNVERRSKYIVFQLDNKRE 80
Cdd:cd08973   1 MPELPEVEVYAENLERRLTGKTITRVELASK----------SLLVTP--DPPLEALEGRTVTGVRRHGKRLDFEFDNGLH 68

                        90
                ....*....|....
gi 88195496  81 qrtLISHLGMAGGF 94
Cdd:cd08973  69 ---LVLHLMLAGWL 79
MeNeil1_N cd08967
N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1); This family contains the ...
 1-133 1.31e-05

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: 43.99  E-value: 1.31e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 88195496   1 MPELPEVEhvkrgIEPYVINQKIEHVIFSDKVIegkaqgKETIIKGIELdTFKtlSEGYTITNVER-----------RSK 69
Cdd:cd08967   1 MPEGPELH-----LASLFVNKMCKGLIFTGAVE------KSSVSKNPEV-PFA--CKAYTISAESRgkelrlilsplPAA 66

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 88195496  70 YIVFQLDNKREQRTLIsHLGMAGGFFIVDELEdimIPnyrKHWHVIFELSNDKKLIYS--DIRRFG 133
Cdd:cd08967  67 NGKKECKSQEEMRIVF-RFGMSGSFQFTPVDE---IP---KHAHLRFYTKEEPKRVLSfvDIRRFG 125
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 264-289 9.54e-04

Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23.


Pssm-ID: 429140 [Multi-domain]  Cd Length: 28  Bit Score: 36.03  E-value: 9.54e-04
                          10        20
                  ....*....|....*....|....*.
gi 88195496   264 VCKVCGSQIETKIIATRNSHYCPVCQ 289
Cdd:pfam06827   3 KCPRCWTYIEKVGVGGRSTYFCPRCQ 28
 
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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