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Conserved domains on  [gi|266618604|pdb|3GQ4|A]
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Chain A, DNA glycosylase

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;
1-273 7.41e-152

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


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 424.49  E-value: 7.41e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHprDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:PRK01103   2 PELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWP--VPEDFAERLSGQTILAVGRRGKYLLLDLDDGgTLISHLGMSGS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVK 159
Cdd:PRK01103  80 LRLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       160 ALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLY 239
Cdd:PRK01103 160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                        250       260       270
                 ....*....|....*....|....*....|....
3GQ4_A       240 VYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK01103 240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-273 7.41e-152

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 424.49  E-value: 7.41e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHprDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:PRK01103   2 PELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWP--VPEDFAERLSGQTILAVGRRGKYLLLDLDDGgTLISHLGMSGS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVK 159
Cdd:PRK01103  80 LRLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       160 ALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLY 239
Cdd:PRK01103 160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                        250       260       270
                 ....*....|....*....|....*....|....
3GQ4_A       240 VYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK01103 240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
1-273 7.03e-136

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 384.09  E-value: 7.03e-136
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIiRHPrDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPRL-RFP-VPEDFAARLTGRRITAVERRGKYLLLELDGGlTLLIHLGMSGR 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVK 159
Cdd:COG0266  79 LRVVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVHPLLARLGPEPLDPDFDPEYLAARLRRRRRPIK 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A      160 ALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLY 239
Cdd:COG0266 159 ALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLY 238

                       250       260       270
                ....*....|....*....|....*....|....
3GQ4_A      240 VYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:COG0266 239 VYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 1-272 1.56e-128

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: 365.47  E-value: 1.56e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A          1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRDALISHLRMEGRY 80
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGALVSHLRMEGKY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         81 AVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKA 160
Cdd:TIGR00577  81 RLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLSEDFTAEYLFEKLAKSKRKIKT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        161 LLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLYV 240
Cdd:TIGR00577 161 ALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQELQV 240

                         250       260       270
                  ....*....|....*....|....*....|..
3GQ4_A        241 YGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQ 272
Cdd:TIGR00577 241 YGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 1-120 5.27e-55

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: 173.45  E-value: 5.27e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:cd08966   1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPP-DPEEFAERLVGRRITGVERRGKYLLFELDDGlVLVIHLGMTGR 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
3GQ4_A       80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYA 120
Cdd:cd08966  80 LLVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 2.07e-43

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: 143.42  E-value: 2.07e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A          1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:pfam01149   2 PELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGP-SPEEFAAALTGRKVTSVGRRGKYLLLELDSGgHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
3GQ4_A         80 YAVASALEPlEPHTHVVFCFTDGSELRYRDVRKFGTM 116
Cdd:pfam01149  81 LLIKTEEWP-PKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 1-117 1.34e-42

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: 141.55  E-value: 1.34e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A           1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDseaFAARMIGQTVRGLERRGKFLKF-LLDRDALISHLRMEGR 79
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRFPDE---FAAALSGRTITSVRRRGKYLLLrLLGGLTLVVHLGMSGS 77

                           90       100       110
                   ....*....|....*....|....*....|....*...
3GQ4_A          80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMH 117
Cdd:smart00898  78 LRVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-273 7.41e-152

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 424.49  E-value: 7.41e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHprDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:PRK01103   2 PELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWP--VPEDFAERLSGQTILAVGRRGKYLLLDLDDGgTLISHLGMSGS 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVK 159
Cdd:PRK01103  80 LRLLPEDTPPEKHDHVDFVLDDGTVLRYNDPRRFGAMLLTPKGDLEAHPLLAHLGPEPLSDAFDGEYLAAKLRKKKTAIK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       160 ALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLY 239
Cdd:PRK01103 160 PALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRDYVNADGKPGYFQQSLQ 239

                        250       260       270
                 ....*....|....*....|....*....|....
3GQ4_A       240 VYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK01103 240 VYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
1-273 7.03e-136

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 384.09  E-value: 7.03e-136
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIiRHPrDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:COG0266   1 PELPEVETVRRGLAPALVGRTITRVEVRSPRL-RFP-VPEDFAARLTGRRITAVERRGKYLLLELDGGlTLLIHLGMSGR 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVK 159
Cdd:COG0266  79 LRVVPPGEPPEKHDHVRLVLDDGTELRFADPRRFGALELLTPDELEVHPLLARLGPEPLDPDFDPEYLAARLRRRRRPIK 158

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A      160 ALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLY 239
Cdd:COG0266 159 ALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRDYVNADGEPGYFQQRLY 238

                       250       260       270
                ....*....|....*....|....*....|....
3GQ4_A      240 VYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:COG0266 239 VYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 1-272 1.56e-128

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: 365.47  E-value: 1.56e-128
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A          1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRDALISHLRMEGRY 80
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLRPAGSEDLQKRLLGQTILSIQRRGKYLLFELDDGALVSHLRMEGKY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         81 AVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKA 160
Cdd:TIGR00577  81 RLEAVPDAPDKHDHVDFLFDDGTELRYHDPRRFGTWLLLDRGQVENIPLLAKLGPEPLSEDFTAEYLFEKLAKSKRKIKT 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        161 LLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGTFQHHLYV 240
Cdd:TIGR00577 161 ALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRDFSQSDGHNGYFQQELQV 240

                         250       260       270
                  ....*....|....*....|....*....|..
3GQ4_A        241 YGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQ 272
Cdd:TIGR00577 241 YGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-273 3.15e-90

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 268.72  E-value: 3.15e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRDA------LISHL 74
Cdd:PRK13945   2 PELPEVETVRRGLEQLLLNFIIKGVEVLLERTIASPGGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEGsenagwLGVHL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        75 RMEGRYAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTM-HVYAKEEADRR-PPLAELGPEPLSPAFSPAVLAERAV 152
Cdd:PRK13945  82 RMTGQFLWVEQSTPPCKHTRVRLFFEKNQELRFVDIRSFGQMwWVPPGVSPESIiTGLQKLGPEPFSPEFSVEYLKKKLK 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       153 KTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAG 232
Cdd:PRK13945 162 KRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKTSIGAGGTTFSDFRDLEGVNG 241

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
3GQ4_A       233 TFQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK13945 242 NYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQK 282
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-273 1.87e-75

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 230.84  E-value: 1.87e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHprdseafAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:PRK14811   2 PELPEVETTRRKLEPLLLGQTIQQVVHDDPARYRN-------TELAEGRRVLGLSRRGKYLLLHLPHDlELIVHLGMTGG 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        80 YAvasaLEPlEPHTHVVFCfTDGSELRYRDVRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLaERAVKTKRSVK 159
Cdd:PRK14811  75 FR----LEP-GPHTRVTLE-LPGRTLYFTDPRRFGKWWVVRAGDYREIPLLARMGPEPLSDDFTEPEF-VRALATARPVK 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       160 ALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTV--RTYVNTQGEAGTFQHH 237
Cdd:PRK14811 148 PWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKAPEARRLYRAIREVMAEAVEAGGSTLsdGSYRQPDGEPGGFQFQ 227

                        250       260       270
                 ....*....|....*....|....*....|....*.
3GQ4_A       238 LYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK14811 228 HAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-273 6.55e-68

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 211.69  E-value: 6.55e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         1 PQLPEVETIRRTLLPLIVGKTIEDVrifWPNIIRHPR--DSEAFAARMIGQTVRGLERRGKFLKFLLD-----RDALISH 73
Cdd:PRK14810   2 PELPEVETVARGLAPRAAGRRIATA---EFRNLRIPRkgDPDLMAARLAGRKILSVKRVGKHIVADLEgpgepRGQWIIH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        74 LRMEGRYAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYAKeeadRRPPLAELGPEPLSpaFSPAVLAERAVK 153
Cdd:PRK14810  79 LGMTGKLLLGGPDTPSPKHTHAVLTLSSGKELRFVDSRQFGCIEYSEA----FPKRFARPGPEPLE--ISFEDFAALFRG 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       154 TKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGEAVMKGGSTVRTYVNTQGEAGT 233
Cdd:PRK14810 153 RKTRIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSDYVDAEGRSGF 232

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
3GQ4_A       234 FQHHLYVYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK14810 233 FQLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 1-120 5.27e-55

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: 173.45  E-value: 5.27e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:cd08966   1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPKLRRPP-DPEEFAERLVGRRITGVERRGKYLLFELDDGlVLVIHLGMTGR 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
3GQ4_A       80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHVYA 120
Cdd:cd08966  80 LLVVPPDEPPEKHDHVIFELDDGRELRFNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-116 2.07e-43

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: 143.42  E-value: 2.07e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A          1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:pfam01149   2 PELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRGP-SPEEFAAALTGRKVTSVGRRGKYLLLELDSGgHLVVHLGMTGW 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
3GQ4_A         80 YAVASALEPlEPHTHVVFCFTDGSELRYRDVRKFGTM 116
Cdd:pfam01149  81 LLIKTEEWP-PKHDHVRLELDDGRELRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 1-117 1.34e-42

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: 141.55  E-value: 1.34e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A           1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDseaFAARMIGQTVRGLERRGKFLKF-LLDRDALISHLRMEGR 79
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRFPDE---FAAALSGRTITSVRRRGKYLLLrLLGGLTLVVHLGMSGS 77

                           90       100       110
                   ....*....|....*....|....*....|....*...
3GQ4_A          80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMH 117
Cdd:smart00898  78 LRVVPAGTPPPKHDHVRLVLDDGTELRFNDPRRFGAVR 115
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 1-118 4.83e-38

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: 129.79  E-value: 4.83e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrdSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR 79
Cdd:cd08773   1 PELPEVELLRRKLRRALKGKRVTRVEVSDPRRLFTP--AAELAAALIGRRVRGAERRGKYLLLELSGGpWLVIHLGMTGR 78

                        90       100       110
                ....*....|....*....|....*....|....*....
3GQ4_A       80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHV 118
Cdd:cd08773  79 LRVCPEGEPPPKHDRLVLRLANGSQLRFTDPRKFGRVEL 117
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 133-221 4.84e-34

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: 118.55  E-value: 4.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        133 LGPEPLSPAFSPAVLAERAVKTKRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATIGE 212
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*....
3GQ4_A        213 AVMKGGSTV 221
Cdd:pfam06831  81 AIEMGGGGI 89
PRK10445 PRK10445
endonuclease VIII; Provisional
 3-273 3.44e-31

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 116.67  E-value: 3.44e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A         3 LPEVETIRRT---LLPLIVGKTIEDVRIFWPNIirhprdsEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEG 78
Cdd:PRK10445   1 MPEGPEIRRAadnLEAAIKGKPLTDVWFAFPQL-------KPYESQLIGQRVTHIETRGKALLTHFSNGlTLYSHNQLYG 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        79 RYAVASALEplEPHT----HVVFCFTDGSELRYR--DVRkfgtmhVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAV 152
Cdd:PRK10445  74 VWRVVDTGE--EPQTtrvlRVRLQTADKTILLYSasDIE------MLTPEQLTTHPFLQRVGPDVLDPNLTPEQVKERLL 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A       153 KTK---RSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVATigeavmkggstVRTYVNTQG 229
Cdd:PRK10445 146 SPRfrnRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDI-----------PRLSYATRG 214

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
3GQ4_A       230 EAGTFQHH--LY---VYGRQGNPCKRCGTPIEKTVVAGRGTHYCPRCQR 273
Cdd:PRK10445 215 QVDENKHHgaLFrfkVFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-118 3.75e-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: 3.75e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrdSEAFAARMIGQTVRGLERRGKFLKFLLDRDA-LISHLRMEGR 79
Cdd:cd08976   1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGEP--KATLREVLEGRTFTETHRIGKYLFLKTKEGGwLVMHFGMTGK 78

                        90       100       110
                ....*....|....*....|....*....|....*....
3GQ4_A       80 YAVASALEPLEPHTHVVFCFTDGSELRYRDVRKFGTMHV 118
Cdd:cd08976  79 LDYYPDDEDPPKHARLLLHFEDGFRLAFECPRKFGRVRL 117
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 245-272 7.52e-11

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: 55.67  E-value: 7.52e-11
                          10        20
                  ....*....|....*....|....*...
3GQ4_A        245 GNPCKRCGTPIEKTVVAGRGTHYCPRCQ 272
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 28
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-102 8.79e-11

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: 58.03  E-value: 8.79e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPrdsEAFAARMIGQTVRGLERRGKFLKFLLDRDA-LISHLRMEGR 79
Cdd:cd08973   2 PELPEVEVYAENLERRLTGKTITRVELASKSLLVTP---DPPLEALEGRTVTGVRRHGKRLDFEFDNGLhLVLHLMLAGW 78

                        90       100
                ....*....|....*....|....*
3GQ4_A       80 --YAVASALEPLePHTHVVFCFTDG 102
Cdd:cd08973  79 lyWTEAGALLPG-KKGPIALRFEDY 102
RqcH COG1293
Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) ...
 128-234 5.76e-05

Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440904 [Multi-domain]  Cd Length: 578  Bit Score: 44.06  E-value: 5.76e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A      128 PPLAELGPEPLSpaFSPAVLAER-AVKTKRSVKALLldcTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEM 206
Cdd:COG1293 163 PPPSQDKLNPLE--LSEEEFAELlSESDGDLVRTLA---TNFLGLSPLLAEEICYRAGLDKDTPTDELSEEDLEALYEAL 237

                        90       100
                ....*....|....*....|....*...
3GQ4_A      207 vATIGEAVMKGGSTVRTYVNTQGEAGTF 234
Cdd:COG1293 238 -QELLEELENGEFKPTIYYEEDGKPVDF 264
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 4-82 2.58e-04

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: 39.49  E-value: 2.58e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        4 PEVETIRRT---LLPLIVGKTIEDVRIfwpniiRHPRDSeafAARMIGQTVRGLERRGKFLKFLLDRDA-LISHLRMEGR 79
Cdd:cd08971   2 PEGDTVHRAarrLRRALAGRVLTRADL------RVPRLA---TADLAGRTVEEVVARGKHLLIRFDGGLtLHTHLRMDGS 72


                ...
3GQ4_A       80 YAV 82
Cdd:cd08971  73 WHV 75
BaFpgNei_N_3 cd08975
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-108 5.12e-04

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. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In this family the N-terminal proline is replaced by an isoleucine or valine. 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_3 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif.


Pssm-ID: 176809  Cd Length: 117  Bit Score: 38.84  E-value: 5.12e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQ4_A        2 QLPEVETIRRTLLPLIVGKTIEDVrifWPNIIRHP-----RDSEAFAARMIGQTVRGLERRGKFLKFLLDRDALishlrm 76
Cdd:cd08975   2 ELPESATLSKQLNETLKGKRITDV---FPATSPHKftwynGDPNEYDELLVGKRITSAEGFGGFVEIIFEDKRL------ 72

                        90       100       110
                ....*....|....*....|....*....|..
3GQ4_A       77 egryavasaleplephthvvfCFTDGSELRYR 108
Cdd:cd08975  73 ---------------------LFNDGVNVRYY 83
NFACT_N pfam05833
NFACT N-terminal and middle domains; This family contains the N-terminal and middle domains of ...
 127-205 3.89e-03

NFACT N-terminal and middle domains; This family contains the N-terminal and middle domains of NFACT (NEMF, FbpA, Caliban, and Tae2) proteins from eukaryotes, archaea and bacteria. Many members of this family act in ribosome quality control (RQC), including RqcH, which are involved in the addition of a poly-Ala tail to defective translated proteins to tag them for degradation. This process is analogous to the ssrA/tmRNA bacterial system. However, some other NFACT family members, such as bacterial proteins FbpA in Listeria or PavA in Streptococcus, are exported (despite lack of a classical signal peptide) and behave as fibronectin-binding adhesins associated with virulence.


Pssm-ID: 428644 [Multi-domain]  Cd Length: 451  Bit Score: 38.37  E-value: 3.89e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
3GQ4_A        127 RPPlAELGPEPLSpaFSPAVLAERAVKTKRSVKALLldcTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEE 205
Cdd:pfam05833 160 LPP-SQDKLNPLT--AEEFEEFKELLNDGKLAKALV---KAFQGLSPLLAEELCYRAGLDKETPAEELSDEDWERLYEA 232
 
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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