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Conserved domains on  [gi|488909072|ref|WP_002820147|]
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bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase [Oenococcus oeni]

Protein Classification

Fpg/Nei family DNA glycosylase( domain architecture ID 11479425)

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:  3.20.190.10
EC:  3.2.2.23
Gene Ontology:  GO:0140078|GO:0003684|GO:0008534|GO:0008270|GO:0006284
PubMed:  21486746|14607836
SCOP:  4000303

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-274 2.17e-135

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


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 382.89  E-value: 2.17e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRY 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  81 SVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAvEVKSIGSMGPEPVESDLTFDYFYNRLQKSKKAVK 160
Cdd:PRK01103  81 RLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLE-AHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 161 ALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKLH 240
Cdd:PRK01103 160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488909072 241 AYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:PRK01103 240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-274 2.17e-135

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 382.89  E-value: 2.17e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRY 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  81 SVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAvEVKSIGSMGPEPVESDLTFDYFYNRLQKSKKAVK 160
Cdd:PRK01103  81 RLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLE-AHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 161 ALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKLH 240
Cdd:PRK01103 160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488909072 241 AYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:PRK01103 240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-274 1.19e-126

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 360.98  E-value: 1.19e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRYS 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  82 VEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAVEvKSIGSMGPEPVESDLTFDYFYNRLQKSKKAVKA 161
Cdd:COG0266   81 VVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVH-PLLARLGPEPLDPDFDPEYLAARLRRRRRPIKA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 162 LLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKLHA 241
Cdd:COG0266  160 LLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLYV 239

                        250       260       270
                 ....*....|....*....|....*....|...
gi 488909072 242 YGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:COG0266  240 YGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-273 4.98e-105

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: 306.15  E-value: 4.98e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072    2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLL--DSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLtIVSHLRMEGR 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVlrPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   80 YSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAVEVkSIGSMGPEPVESDLTFDYFYNRLQKSKKAV 159
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIP-LLAKLGPEPLSEDFTAEYLFEKLAKSKRKI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  160 KALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKL 239
Cdd:TIGR00577 159 KTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQEL 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 488909072  240 HAYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQ 273
Cdd:TIGR00577 239 QVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-119 1.30e-51

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: 164.59  E-value: 1.30e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLL-DSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRY 80
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRrPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 488909072  81 SVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLV 119
Cdd:cd08966   81 LVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLV 119
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 3.35e-44

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: 145.73  E-value: 3.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072    1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLL-DSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGR 79
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLrGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 488909072   80 YSVEAAQEAPhKHTEMIFELENGKQVFYDDTRKFGKM 116
Cdd:pfam01149  81 LLIKTEEWPP-KHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-116 1.02e-43

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: 144.25  E-value: 1.02e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072     2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLLdsdRT--EFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGR 79
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQL---RFpdEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGS 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 488909072    80 YSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKM 116
Cdd:smart00898  78 LRVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAV 114
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-274 2.17e-135

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 382.89  E-value: 2.17e-135
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRY 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWPVPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMSGSL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  81 SVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAvEVKSIGSMGPEPVESDLTFDYFYNRLQKSKKAVK 160
Cdd:PRK01103  81 RLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLE-AHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 161 ALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKLH 240
Cdd:PRK01103 160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                        250       260       270
                 ....*....|....*....|....*....|....
gi 488909072 241 AYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:PRK01103 240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-274 1.19e-126

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 360.98  E-value: 1.19e-126
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRYS 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPRLRFPVPEDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSGRLR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  82 VEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAVEvKSIGSMGPEPVESDLTFDYFYNRLQKSKKAVKA 161
Cdd:COG0266   81 VVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVH-PLLARLGPEPLDPDFDPEYLAARLRRRRRPIKA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 162 LLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKLHA 241
Cdd:COG0266  160 LLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLYV 239

                        250       260       270
                 ....*....|....*....|....*....|...
gi 488909072 242 YGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:COG0266  240 YGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-273 4.98e-105

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: 306.15  E-value: 4.98e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072    2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLL--DSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLtIVSHLRMEGR 79
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVlrPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGA-LVSHLRMEGK 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   80 YSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAVEVkSIGSMGPEPVESDLTFDYFYNRLQKSKKAV 159
Cdd:TIGR00577  80 YRLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIP-LLAKLGPEPLSEDFTAEYLFEKLAKSKRKI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  160 KALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRMQDKL 239
Cdd:TIGR00577 159 KTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQEL 238

                         250       260       270
                  ....*....|....*....|....*....|....
gi 488909072  240 HAYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQ 273
Cdd:TIGR00577 239 QVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-274 1.31e-82

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 249.46  E-value: 1.31e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDS--DRTEFIEKVVGSTVSRIDRRGKFLLFRLD-----NNLTIVSH 73
Cdd:PRK13945   1 MPELPEVETVRRGLEQLLLNFIIKGVEVLLERTIASpgGVEEFIKGLKGSLIGQWQRRGKYLLASLKkegseNAGWLGVH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  74 LRMEGRYSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLVKSGNEAVEV-KSIGSMGPEPVESDLTFDYFYNRL 152
Cdd:PRK13945  81 LRMTGQFLWVEQSTPPCKHTRVRLFFEKNQELRFVDIRSFGQMWWVPPGVSPESIiTGLQKLGPEPFSPEFSVEYLKKKL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 153 QKSKKAVKALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHT 232
Cdd:PRK13945 161 KKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSIGAGGTTFSDFRDLEGVN 240

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 488909072 233 GRMQDKLHAYGRAGQPCeRDGGELI-KIRVAQRGTTYCPKCQK 274
Cdd:PRK13945 241 GNYGGQAWVYRRTGKPC-RKCGTPIeRIKLAGRSTHWCPNCQK 282
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-274 2.55e-78

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 238.16  E-value: 2.55e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKdlkiiypKLLDSDRTEF--IEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEG 78
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQ-------QVVHDDPARYrnTELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMTG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  79 RYSVEaaqeaPHKHTEMIFELEnGKQVFYDDTRKFGKMKLVKSGNEAvEVKSIGSMGPEPVESDLTFDYFYNRLqKSKKA 158
Cdd:PRK14811  74 GFRLE-----PGPHTRVTLELP-GRTLYFTDPRRFGKWWVVRAGDYR-EIPLLARMGPEPLSDDFTEPEFVRAL-ATARP 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 159 VKALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTV--HSFIDASGHTGRMQ 236
Cdd:PRK14811 146 VKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGSTLsdGSYRQPDGEPGGFQ 225

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 488909072 237 DKLHAYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:PRK14811 226 FQHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-274 7.39e-53

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 173.17  E-value: 7.39e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPK-LLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDN----NLTIVSHLR 75
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRiPRKGDPDLMAARLAGRKILSVKRVGKHIVADLEGpgepRGQWIIHLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  76 MEGRYSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLvksgnEAVEVKSIGSMGPEPVEsdLTFDYFYNRLQKS 155
Cdd:PRK14810  81 MTGKLLLGGPDTPSPKHTHAVLTLSSGKELRFVDSRQFGCIEY-----SEAFPKRFARPGPEPLE--ISFEDFAALFRGR 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 156 KKAVKALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTVHSFIDASGHTGRM 235
Cdd:PRK14810 154 KTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSDYVDAEGRSGFF 233

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 488909072 236 QDKLHAYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:PRK14810 234 QLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-119 1.30e-51

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: 164.59  E-value: 1.30e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLL-DSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRY 80
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRrPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTGRL 80

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 488909072  81 SVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLV 119
Cdd:cd08966   81 LVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLV 119
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 3.35e-44

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: 145.73  E-value: 3.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072    1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLL-DSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGR 79
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLrGPSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 488909072   80 YSVEAAQEAPhKHTEMIFELENGKQVFYDDTRKFGKM 116
Cdd:pfam01149  81 LLIKTEEWPP-KHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-116 1.02e-43

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: 144.25  E-value: 1.02e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072     2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLLdsdRT--EFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGR 79
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQL---RFpdEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSGS 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 488909072    80 YSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKM 116
Cdd:smart00898  78 LRVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAV 114
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 134-222 6.88e-33

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: 115.47  E-value: 6.88e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  134 MGPEPVESDLTFDYFYNRLQKSKKAVKALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAF 213
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*....
gi 488909072  214 AIENGGSTV 222
Cdd:pfam06831  81 AIEMGGGGI 89
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-274 2.01e-29

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 112.04  E-value: 2.01e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLldsdrTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRY 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQL-----KPYESQLIGQRVTHIETRGKALLTHFSNGLTLYSHNQLYGVW 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  81 SVEAAQEAPHKHTEMIFELENGKqvfyddtrkfgKMKLVKSGNEaVEV------------KSIG------SMGPEPVESD 142
Cdd:PRK10445  76 RVVDTGEEPQTTRVLRVRLQTAD-----------KTILLYSASD-IEMltpeqltthpflQRVGpdvldpNLTPEQVKER 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072 143 LTFDYFYNRlQKSkkavkALLLDQNNVAGIGNIYADEVLWLSEISPLRPTNEISEEEADNLRENIIRELAFAIENGGSTv 222
Cdd:PRK10445 144 LLSPRFRNR-QFS-----GLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQV- 216

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 488909072 223 hsfiDASGHTGRMQdKLHAYGRAGQPCERDGGELIKIRVAQRGTTYCPKCQK 274
Cdd:PRK10445 217 ----DENKHHGALF-RFKVFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-118 4.86e-29

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: 106.68  E-value: 4.86e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRYS 81
Cdd:cd08773    1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTPAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTGRLR 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 488909072  82 VEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKL 118
Cdd:cd08773   81 VCPEGEPPPKHDRLVLRLANGSQLRFTDPRKFGRVEL 117
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-118 3.22e-16

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: 72.77  E-value: 3.22e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVEtvrrGLKKYFENE----KIKDLKIIYPKLLDSDRTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRME 77
Cdd:cd08976    1 PELPEVE----VQKQYLERTslhrKIVEVEVGDDKILGEPKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMT 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 488909072  78 GRYSVEAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKL 118
Cdd:cd08976   77 GKLDYYPDDEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-119 2.86e-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: 2.86e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDL-----KIIYPKLLDSDrteFIEKVVGSTVSRIDRRGKFLLFRLDNN-LTIVSHL 74
Cdd:cd08972    1 MPELPEVERARRLLEEHCLGKKITKVdaqddDKVFGGVTPGA---FQKALLGRTITSAHRKGKYFWLTLDGDaPVPVMHF 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072  75 RMEGRYSV---------------EAAQEAPHKHTEMIFELENGKQVFYDDTRKFGKMKLV 119
Cdd:cd08972   78 GMTGAISIkgvktiyykmlrppkEEDQTWPPRFYKFVLTLEDGTELAFTDPRRLGRVRLV 137
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-79 3.92e-15

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: 69.97  E-value: 3.92e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488909072   1 MPELPEVETVRRGLKKYFENEKIKDLKIIYPKLLDSDrTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGR 79
Cdd:cd08973    1 MPELPEVEVYAENLERRLTGKTITRVELASKSLLVTP-DPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLAGW 78
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 45-91 6.10e-09

N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains the N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei2 (MtuNei2). Complementation experiments in repair-deficient Escherichia coli (fpg mutY nei triple and nei nth double mutants), support that MtuNei2 is functionally active in vivo and recognizes both guanine and cytosine oxidation products. In addition to this AcNei2_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176805  Cd Length: 114  Bit Score: 52.59  E-value: 6.10e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 488909072  45 VVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRYSVEAAQEAPHK 91
Cdd:cd08971   38 LAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMDGSWHVYRPGERWRR 84
EcNei-like_N cd08965
N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This ...
 2-103 1.27e-08

N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases; This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and 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 Nei has been well studied, it is a DNA glycosylase/AP lyase that excises damaged pyrimidines, including 5-hydroxycytosine, 5-hydroxyuracil, and uracil glycol. In addition to this EcNei-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a canonical zinc-finger motif.


Pssm-ID: 176799  Cd Length: 115  Bit Score: 51.98  E-value: 1.27e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488909072   2 PELPEVETVRRGLKKYFENEKIKDLKIIYPKLldsdrTEFIEKVVGSTVSRIDRRGKFLLFRLDNNLTIVSHLRMEGRYS 81
Cdd:cd08965    1 PEGPEIRRAADRIEAAIKGRPLEEVWFAFPHL-----KEYEAQLKGQNVTRVETRGKALLTHFDNGLSIYSHNQLYGVWR 75

                         90       100
                 ....*....|....*....|..
gi 488909072  82 VEAAQEAPHKHTEMIFELENGK 103
Cdd:cd08965   76 VRKRGNYPKTNRQLRVALHTAK 97
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 246-273 1.70e-06

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: 43.73  E-value: 1.70e-06
                          10        20
                  ....*....|....*....|....*...
gi 488909072  246 GQPCERDGGELIKIRVAQRGTTYCPKCQ 273
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 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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