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Conserved domains on  [gi|896176768|ref|WP_049189533|]
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MULTISPECIES: bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase [Corynebacterium]

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;
1-287 1.04e-118

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


:

Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 341.29  E-value: 1.04e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpgGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWP---VPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  81 GQLRVEAPYTPdtlPGRHTRaaFDIALPDGARhlINFNDQRTFG-WVWACE-MVESHgrfvpEPAAKIAPDLLEPTVDVV 158
Cdd:PRK01103  78 GSLRLLPEDTP---PEKHDH--VDFVLDDGTV--LRYNDPRRFGaMLLTPKgDLEAH-----PLLAHLGPEPLSDAFDGE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 159 ALAHRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlY 238
Cdd:PRK01103 146 YLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRD-Y 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 896176768 239 VHVNGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK01103 225 VNADGKPGYFQQSLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-287 1.04e-118

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 341.29  E-value: 1.04e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpgGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWP---VPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  81 GQLRVEAPYTPdtlPGRHTRaaFDIALPDGARhlINFNDQRTFG-WVWACE-MVESHgrfvpEPAAKIAPDLLEPTVDVV 158
Cdd:PRK01103  78 GSLRLLPEDTP---PEKHDH--VDFVLDDGTV--LRYNDPRRFGaMLLTPKgDLEAH-----PLLAHLGPEPLSDAFDGE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 159 ALAHRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlY 238
Cdd:PRK01103 146 YLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRD-Y 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 896176768 239 VHVNGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK01103 225 VNADGKPGYFQQSLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-287 3.63e-111

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 322.07  E-value: 3.63e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARaVRRQPGgaAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPR-LRFPVP--EDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  82 QLRVEAPYTPdtlPGRHTRaaFDIALPDGARhlINFNDQRTFGwvwACEMVESHGRFVPEPAAKIAPDLLEPTVDVVALA 161
Cdd:COG0266   78 RLRVVPPGEP---PEKHDH--VRLVLDDGTE--LRFADPRRFG---ALELLTPDELEVHPLLARLGPEPLDPDFDPEYLA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 162 HRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlYVHV 241
Cdd:COG0266  148 ARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRD-YVNA 226

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 896176768 242 NGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:COG0266  227 DGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-286 1.13e-89

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: 267.63  E-value: 1.13e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768    2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqPGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDsAIAIHLGMSG 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLR-PAGSEDLQKRLLGQTILSIQRRGKYLLFELDDG-ALVSHLRMEG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   82 QLRVEAPytpDTLPGRHTRaaFDIALPDGArhLINFNDQRTFGWVWACEMVESHGRFvpePAAKIAPDLLEPTVDVVALA 161
Cdd:TIGR00577  79 KYRLEAV---PDAPDKHDH--VDFLFDDGT--ELRYHDPRRFGTWLLLDRGQVENIP---LLAKLGPEPLSEDFTAEYLF 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  162 HRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlYVHV 241
Cdd:TIGR00577 149 EKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRD-FSQS 227

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 896176768  242 NGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQ 286
Cdd:TIGR00577 228 DGHNGYFQQELQVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-130 1.17e-43

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


Pssm-ID: 176800  Cd Length: 120  Bit Score: 144.56  E-value: 1.17e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARavRRQPGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPK--LRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 896176768  82 QLRVEAPYTPdtlPGRHTRAAFDIalpDGARHLInFNDQRTFGWVWACE 130
Cdd:cd08966   79 RLLVVPPDEP---PEKHDHVIFEL---DDGRELR-FNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-126 1.14e-37

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: 129.16  E-value: 1.14e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768    1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRG--PSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMT 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 896176768   81 GQLRVEAPYTPDtlpgRHTRaaFDIALPDGARhlINFNDQRTFGWV 126
Cdd:pfam01149  79 GWLLIKTEEWPP----KHDH--VRLELDDGRE--LRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-127 1.29e-33

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: 118.83  E-value: 1.29e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768     2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpggAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRF----PDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSG 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 896176768    82 QLRVEAPYTPdtlPGRHTRAAFDIalpDGARHLInFNDQRTFGWVW 127
Cdd:smart00898  77 SLRVVPAGTP---PPKHDHVRLVL---DDGTELR-FNDPRRFGAVR 115
 
Name Accession Description Interval E-value
PRK01103 PRK01103
bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
1-287 1.04e-118

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


Pssm-ID: 234899 [Multi-domain]  Cd Length: 274  Bit Score: 341.29  E-value: 1.04e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpgGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:PRK01103   1 MPELPEVETVRRGLEPHLVGKTITRVEVRRPKLRWP---VPEDFAERLSGQTILAVGRRGKYLLLDLDDGGTLISHLGMS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  81 GQLRVEAPYTPdtlPGRHTRaaFDIALPDGARhlINFNDQRTFG-WVWACE-MVESHgrfvpEPAAKIAPDLLEPTVDVV 158
Cdd:PRK01103  78 GSLRLLPEDTP---PEKHDH--VDFVLDDGTV--LRYNDPRRFGaMLLTPKgDLEAH-----PLLAHLGPEPLSDAFDGE 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 159 ALAHRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlY 238
Cdd:PRK01103 146 YLAAKLRKKKTAIKPALLDQTVVVGVGNIYADEALFRAGIHPERPAGSLSRAEAERLVDAIKAVLAEAIEQGGTTLRD-Y 224

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 896176768 239 VHVNGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK01103 225 VNADGKPGYFQQSLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273
Nei COG0266
Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair];
2-287 3.63e-111

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


Pssm-ID: 440036 [Multi-domain]  Cd Length: 272  Bit Score: 322.07  E-value: 3.63e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARaVRRQPGgaAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:COG0266    1 PELPEVETVRRGLAPALVGRTITRVEVRSPR-LRFPVP--EDFAARLTGRRITAVERRGKYLLLELDGGLTLLIHLGMSG 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  82 QLRVEAPYTPdtlPGRHTRaaFDIALPDGARhlINFNDQRTFGwvwACEMVESHGRFVPEPAAKIAPDLLEPTVDVVALA 161
Cdd:COG0266   78 RLRVVPPGEP---PEKHDH--VRLVLDDGTE--LRFADPRRFG---ALELLTPDELEVHPLLARLGPEPLDPDFDPEYLA 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 162 HRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlYVHV 241
Cdd:COG0266  148 ARLRRRRRPIKALLLDQSVVAGVGNIYADEALFRAGIHPLRPAGSLSRAELERLAAAIREVLREAIEAGGTTLRD-YVNA 226

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 896176768 242 NGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:COG0266  227 DGEPGYFQQRLYVYGREGEPCPRCGTPIERIVLGGRSTYYCPRCQR 272
fpg TIGR00577
DNA-formamidopyrimidine glycosylase; All proteins in the FPG family with known functions are ...
 2-286 1.13e-89

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: 267.63  E-value: 1.13e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768    2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqPGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDsAIAIHLGMSG 81
Cdd:TIGR00577   1 PELPEVETVRRGLEPLVLGKTIKSVEVVLRNPVLR-PAGSEDLQKRLLGQTILSIQRRGKYLLFELDDG-ALVSHLRMEG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   82 QLRVEAPytpDTLPGRHTRaaFDIALPDGArhLINFNDQRTFGWVWACEMVESHGRFvpePAAKIAPDLLEPTVDVVALA 161
Cdd:TIGR00577  79 KYRLEAV---PDAPDKHDH--VDFLFDDGT--ELRYHDPRRFGTWLLLDRGQVENIP---LLAKLGPEPLSEDFTAEYLF 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  162 HRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDAlYVHV 241
Cdd:TIGR00577 149 EKLAKSKRKIKTALLDQRLVAGIGNIYADEVLFRAGIHPERLASSLSKEECELLHRAIKEVLRKAIEMGGTTIRD-FSQS 227

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 896176768  242 NGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQ 286
Cdd:TIGR00577 228 DGHNGYFQQELQVYGRKGEPCRRCGTTIEKEKVGGRGTHFCPQCQ 272
PRK14811 PRK14811
formamidopyrimidine-DNA glycosylase; Provisional
 1-287 1.04e-62

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184831 [Multi-domain]  Cd Length: 269  Bit Score: 198.87  E-value: 1.04e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDtFVYNARAVRRQpggaaefIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:PRK14811   1 MPELPEVETTRRKLEPLLLGQTIQQ-VVHDDPARYRN-------TELAEGRRVLGLSRRGKYLLLHLPHDLELIVHLGMT 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  81 GQLRVEapytpdtlPGRHTRAAFDiaLPDGARHlinFNDQRTFGWVWACEMveshGRFVPEPA-AKIAPdllEPTVDVVA 159
Cdd:PRK14811  73 GGFRLE--------PGPHTRVTLE--LPGRTLY---FTDPRRFGKWWVVRA----GDYREIPLlARMGP---EPLSDDFT 132

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 160 LAH--RMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLS---VRRLAKLLREgqaVLQRALAAGGTSF 234
Cdd:PRK14811 133 EPEfvRALATARPVKPWLLSQKPVAGVGNIYADESLWRARIHPARPATSLKapeARRLYRAIRE---VMAEAVEAGGSTL 209

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 896176768 235 -DALYVHVNGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK14811 210 sDGSYRQPDGEPGGFQFQHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263
PRK13945 PRK13945
formamidopyrimidine-DNA glycosylase; Provisional
 1-287 1.34e-60

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 184410 [Multi-domain]  Cd Length: 282  Bit Score: 193.61  E-value: 1.34e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRrQPGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIA-----I 75
Cdd:PRK13945   1 MPELPEVETVRRGLEQLLLNFIIKGVEVLLERTIA-SPGGVEEFIKGLKGSLIGQWQRRGKYLLASLKKEGSENagwlgV 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  76 HLGMSGQLR-VEapytPDTLPGRHTRaafdIALPDGARHLINFNDQRTFGWVWacemveshgrFVPEPAA---------K 145
Cdd:PRK13945  80 HLRMTGQFLwVE----QSTPPCKHTR----VRLFFEKNQELRFVDIRSFGQMW----------WVPPGVSpesiitglqK 141

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 146 IAPDLLEPTVDVVALAHRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQR 225
Cdd:PRK13945 142 LGPEPFSPEFSVEYLKKKLKKRTRSIKTALLDQSIVAGIGNIYADESLFKAGIHPTTPAGQLKKKQLERLREAIIEVLKT 221

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 896176768 226 ALAAGGTSF-DalYVHVNGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK13945 222 SIGAGGTTFsD--FRDLEGVNGNYGGQAWVYRRTGKPCRKCGTPIERIKLAGRSTHWCPNCQK 282
PRK14810 PRK14810
formamidopyrimidine-DNA glycosylase; Provisional
 1-287 4.40e-46

formamidopyrimidine-DNA glycosylase; Provisional


Pssm-ID: 173271 [Multi-domain]  Cd Length: 272  Bit Score: 156.22  E-value: 4.40e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpGGAAEFIGRTRGRTVIATDRRGKFMWLTLDD----DSAIAIH 76
Cdd:PRK14810   1 MPELPEVETVARGLAPRAAGRRIATAEFRNLRIPRK--GDPDLMAARLAGRKILSVKRVGKHIVADLEGpgepRGQWIIH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  77 LGMSGQLRVEAPYTPdTLPGRHTRAAFDialpdgARHLINFNDQRTFGwvwaceMVESHGRFvPEPAAKIAPDLLEPTVD 156
Cdd:PRK14810  79 LGMTGKLLLGGPDTP-SPKHTHAVLTLS------SGKELRFVDSRQFG------CIEYSEAF-PKRFARPGPEPLEISFE 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 157 VVALAHRMMKSrsPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFDA 236
Cdd:PRK14810 145 DFAALFRGRKT--RIKSALLNQTLLRGVGNIYADEALFRAGIRPQRLASSLSRERLRKLHDAIGEVLREAIELGGSSVSD 222

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 896176768 237 lYVHVNGESGYFERSLNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK14810 223 -YVDAEGRSGFFQLSHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHCQK 272
EcFpg-like_N cd08966
N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases; This ...
 2-130 1.17e-43

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


Pssm-ID: 176800  Cd Length: 120  Bit Score: 144.56  E-value: 1.17e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARavRRQPGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:cd08966    1 PELPEVETVRRGLAPHLVGRRIEDVEVRRPK--LRRPPDPEEFAERLVGRRITGVERRGKYLLFELDDGLVLVIHLGMTG 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 896176768  82 QLRVEAPYTPdtlPGRHTRAAFDIalpDGARHLInFNDQRTFGWVWACE 130
Cdd:cd08966   79 RLLVVPPDEP---PEKHDHVIFEL---DDGRELR-FNDPRRFGTLLLVP 120
Fapy_DNA_glyco pfam01149
Formamidopyrimidine-DNA glycosylase N-terminal domain; Formamidopyrimidine-DNA glycosylase ...
 1-126 1.14e-37

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: 129.16  E-value: 1.14e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768    1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:pfam01149   1 MPELPEVETVRRGLRRHLVGKTIASVEVLDDKNLRG--PSPEEFAAALTGRKVTSVGRRGKYLLLELDSGGHLVVHLGMT 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 896176768   81 GQLRVEAPYTPDtlpgRHTRaaFDIALPDGARhlINFNDQRTFGWV 126
Cdd:pfam01149  79 GWLLIKTEEWPP----KHDH--VRLELDDGRE--LRFTDPRRFGRV 116
Fapy_DNA_glyco smart00898
Formamidopyrimidine-DNA glycosylase N-terminal domain; This entry represents the catalytic ...
 2-127 1.29e-33

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: 118.83  E-value: 1.29e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768     2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpggAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:smart00898   1 PELPEVETVRRGLAPALAGRTITRVEVVRPPQLRF----PDEFAAALSGRTITSVRRRGKYLLLRLLGGLTLVVHLGMSG 76

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 896176768    82 QLRVEAPYTPdtlPGRHTRAAFDIalpDGARHLInFNDQRTFGWVW 127
Cdd:smart00898  77 SLRVVPAGTP---PPKHDHVRLVL---DDGTELR-FNDPRRFGAVR 115
FpgNei_N cd08773
N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) ...
 2-127 4.51e-25

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: 96.66  E-value: 4.51e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   2 PELPEVESVRRGLDAYVVGGRIEDTfvyNARAVRRQPGGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:cd08773    1 PELPEVELLRRKLRRALKGKRVTRV---EVSDPRRLFTPAAELAAALIGRRVRGAERRGKYLLLELSGGPWLVIHLGMTG 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 896176768  82 QLRVEApytPDTLPGRHTRAAFDIALpdgaRHLINFNDQRTFGWVW 127
Cdd:cd08773   78 RLRVCP---EGEPPPKHDRLVLRLAN----GSQLRFTDPRKFGRVE 116
H2TH pfam06831
Formamidopyrimidine-DNA glycosylase H2TH domain; Formamidopyrimidine-DNA glycosylase (Fpg) is ...
 146-233 1.19e-23

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: 91.97  E-value: 1.19e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  146 IAPDLLEPTVDVVALAHRMMKSRSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQR 225
Cdd:pfam06831   1 LGPEPLSEDFTVDYFAERLAKKKRPIKTALLDQTLVAGLGNIYADEVLFRAGIHPERLANSLSKEECELLHQAIKAVLQE 80


                  ....*...
gi 896176768  226 ALAAGGTS 233
Cdd:pfam06831  81 AIEMGGGG 88
PF_Nei_N cd08972
N-terminal domain of the plant and fungal Nei and related proteins; This family contains the ...
 1-126 9.43e-19

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: 80.43  E-value: 9.43e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqPGGAAEFIGRTRGRTVIATDRRGKFMWLTLD-DDSAIAIHLGM 79
Cdd:cd08972    1 MPELPEVERARRLLEEHCLGKKITKVDAQDDDKVFG-GVTPGAFQKALLGRTITSAHRKGKYFWLTLDgDAPVPVMHFGM 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 896176768  80 SG--QLR-VEAPYT---------PDTLPGRHTRaaFDIALPDGARhlINFNDQRTFGWV 126
Cdd:cd08972   80 TGaiSIKgVKTIYYkmlrppkeeDQTWPPRFYK--FVLTLEDGTE--LAFTDPRRLGRV 134
PRK10445 PRK10445
endonuclease VIII; Provisional
 1-287 1.78e-16

endonuclease VIII; Provisional


Pssm-ID: 182467 [Multi-domain]  Cd Length: 263  Bit Score: 76.99  E-value: 1.78e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRQpggaAEFIGRTrgrtVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:PRK10445   1 MPEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKPYE----SQLIGQR----VTHIETRGKALLTHFSNGLTLYSHNQLY 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768  81 GQLRVEAPYT-PDTlpGRHTRAAFDIAlpDGARHLINFNDQRtfgwVWACEMVESHGrFVpepaAKIAPDLLEPTVDVVA 159
Cdd:PRK10445  73 GVWRVVDTGEePQT--TRVLRVRLQTA--DKTILLYSASDIE----MLTPEQLTTHP-FL----QRVGPDVLDPNLTPEQ 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768 160 LAHRMMKS---RSPIKAVLLNQNIVSGIGNIYADEMLWAAKVDGRVPACDLSVRRLAKLLREGQAVLQRALAAGGTSFD- 235
Cdd:PRK10445 140 VKERLLSPrfrNRQFSGLLLDQAFLAGLGNYLRVEILWQAGLTPQHKAKDLNEAQLDALAHALLDIPRLSYATRGQVDEn 219

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896176768 236 ----ALYVHvngesgyferslNAYGQAGEPCSRCGRAIVRLPFGNRSSYLCPTCQR 287
Cdd:PRK10445 220 khhgALFRF------------KVFHRDGEACERCGGIIEKTTLSSRPFYWCPGCQK 263
BaFpgNei_N_1 cd08973
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 1-110 1.13e-14

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: 68.81  E-value: 1.13e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRrqpgGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:cd08973    1 MPELPEVEVYAENLERRLTGKTITRVELASKSLLV----TPDPPLEALEGRTVTGVRRHGKRLDFEFDNGLHLVLHLMLA 76

                         90       100       110
                 ....*....|....*....|....*....|
gi 896176768  81 GQLRVEAPytPDTLPGRHTRAAFDIALPDG 110
Cdd:cd08973   77 GWLYWTEA--GALLPGKKGPIALRFEDYGG 104
BaFpgNei_N_4 cd08976
Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA ...
 2-126 7.16e-14

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: 66.60  E-value: 7.16e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   2 PELPEVESVRRGLDAYVVGGRIEDTFVYNARAVRRqpgGAAEFIGRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMSG 81
Cdd:cd08976    1 PELPEVEVQKQYLERTSLHRKIVEVEVGDDKILGE---PKATLREVLEGRTFTETHRIGKYLFLKTKEGGWLVMHFGMTG 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 896176768  82 QLRveapYTPDTL-PGRHTRAAFDIalpDGARHLiNFNDQRTFGWV 126
Cdd:cd08976   78 KLD----YYPDDEdPPKHARLLLHF---EDGFRL-AFECPRKFGRV 115
zf-FPG_IleRS pfam06827
Zinc finger found in FPG and IleRS; This zinc binding domain is found at the C-terminus of ...
 259-286 4.23e-08

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: 48.35  E-value: 4.23e-08
                          10        20
                  ....*....|....*....|....*...
gi 896176768  259 GEPCSRCGRAIVRLPFGNRSSYLCPTCQ 286
Cdd:pfam06827   1 GEKCPRCWTYIEKVGVGGRSTYFCPRCQ 28
AcNei2_N cd08971
N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases; This family contains ...
 1-101 2.50e-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: 39.88  E-value: 2.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896176768   1 MPELPEVESVRRGLDAYVVGGRIEdtfvynaRAVRRQPGGAAEfigRTRGRTVIATDRRGKFMWLTLDDDSAIAIHLGMS 80
Cdd:cd08971    1 MPEGDTVHRAARRLRRALAGRVLT-------RADLRVPRLATA---DLAGRTVEEVVARGKHLLIRFDGGLTLHTHLRMD 70

                         90       100
                 ....*....|....*....|.
gi 896176768  81 GQLRVEAPYTPDTLPGRHTRA 101
Cdd:cd08971   71 GSWHVYRPGERWRRPAHQARA 91
 
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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