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FPG_VARPS
ID   FPG_VARPS               Reviewed;         270 AA.
AC   C5CYZ1;
DT   22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT   28-JUL-2009, sequence version 1.
DT   03-AUG-2022, entry version 72.
DE   RecName: Full=Formamidopyrimidine-DNA glycosylase {ECO:0000255|HAMAP-Rule:MF_00103};
DE            Short=Fapy-DNA glycosylase {ECO:0000255|HAMAP-Rule:MF_00103};
DE            EC=3.2.2.23 {ECO:0000255|HAMAP-Rule:MF_00103};
DE   AltName: Full=DNA-(apurinic or apyrimidinic site) lyase MutM {ECO:0000255|HAMAP-Rule:MF_00103};
DE            Short=AP lyase MutM {ECO:0000255|HAMAP-Rule:MF_00103};
DE            EC=4.2.99.18 {ECO:0000255|HAMAP-Rule:MF_00103};
GN   Name=mutM {ECO:0000255|HAMAP-Rule:MF_00103};
GN   Synonyms=fpg {ECO:0000255|HAMAP-Rule:MF_00103};
GN   OrderedLocusNames=Vapar_4341;
OS   Variovorax paradoxus (strain S110).
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Variovorax.
OX   NCBI_TaxID=543728;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=S110;
RX   PubMed=21183664; DOI=10.1128/jb.00925-10;
RA   Han J.I., Choi H.K., Lee S.W., Orwin P.M., Kim J., Laroe S.L., Kim T.G.,
RA   O'Neil J., Leadbetter J.R., Lee S.Y., Hur C.G., Spain J.C.,
RA   Ovchinnikova G., Goodwin L., Han C.;
RT   "Complete genome sequence of the metabolically versatile plant growth-
RT   promoting endophyte, Variovorax paradoxus S110.";
RL   J. Bacteriol. 193:1183-1190(2011).
CC   -!- FUNCTION: Involved in base excision repair of DNA damaged by oxidation
CC       or by mutagenic agents. Acts as DNA glycosylase that recognizes and
CC       removes damaged bases. Has a preference for oxidized purines, such as
CC       7,8-dihydro-8-oxoguanine (8-oxoG). Has AP (apurinic/apyrimidinic) lyase
CC       activity and introduces nicks in the DNA strand. Cleaves the DNA
CC       backbone by beta-delta elimination to generate a single-strand break at
CC       the site of the removed base with both 3'- and 5'-phosphates.
CC       {ECO:0000255|HAMAP-Rule:MF_00103}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Hydrolysis of DNA containing ring-opened 7-methylguanine
CC         residues, releasing 2,6-diamino-4-hydroxy-5-(N-
CC         methyl)formamidopyrimidine.; EC=3.2.2.23;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00103};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-
CC         deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-
CC         dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-
CC         2'-deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:66592, Rhea:RHEA-
CC         COMP:13180, Rhea:RHEA-COMP:16897, Rhea:RHEA-COMP:17067,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:136412, ChEBI:CHEBI:157695,
CC         ChEBI:CHEBI:167181; EC=4.2.99.18; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00103};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00103};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00103};
CC   -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00103}.
CC   -!- SIMILARITY: Belongs to the FPG family. {ECO:0000255|HAMAP-
CC       Rule:MF_00103}.
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DR   EMBL; CP001635; ACS20952.1; -; Genomic_DNA.
DR   RefSeq; WP_015867111.1; NC_012791.1.
DR   AlphaFoldDB; C5CYZ1; -.
DR   SMR; C5CYZ1; -.
DR   STRING; 543728.Vapar_4341; -.
DR   EnsemblBacteria; ACS20952; ACS20952; Vapar_4341.
DR   GeneID; 45058597; -.
DR   KEGG; vap:Vapar_4341; -.
DR   eggNOG; COG0266; Bacteria.
DR   HOGENOM; CLU_038423_1_1_4; -.
DR   OMA; GVHLRMT; -.
DR   OrthoDB; 1162346at2; -.
DR   GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR   GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
DR   GO; GO:0008534; F:oxidized purine nucleobase lesion DNA N-glycosylase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR   Gene3D; 3.20.190.10; -; 1.
DR   HAMAP; MF_00103; Fapy_DNA_glycosyl; 1.
DR   InterPro; IPR015886; DNA_glyclase/AP_lyase_DNA-bd.
DR   InterPro; IPR015887; DNA_glyclase_Znf_dom_DNA_BS.
DR   InterPro; IPR020629; Formamido-pyr_DNA_Glyclase.
DR   InterPro; IPR012319; FPG_cat.
DR   InterPro; IPR035937; MutM-like_N-ter.
DR   InterPro; IPR010979; Ribosomal_S13-like_H2TH.
DR   InterPro; IPR000214; Znf_DNA_glyclase/AP_lyase.
DR   InterPro; IPR010663; Znf_FPG/IleRS.
DR   Pfam; PF01149; Fapy_DNA_glyco; 1.
DR   Pfam; PF06831; H2TH; 1.
DR   Pfam; PF06827; zf-FPG_IleRS; 1.
DR   SMART; SM00898; Fapy_DNA_glyco; 1.
DR   SMART; SM01232; H2TH; 1.
DR   SUPFAM; SSF46946; SSF46946; 1.
DR   SUPFAM; SSF81624; SSF81624; 1.
DR   TIGRFAMs; TIGR00577; fpg; 1.
DR   PROSITE; PS51068; FPG_CAT; 1.
DR   PROSITE; PS01242; ZF_FPG_1; 1.
DR   PROSITE; PS51066; ZF_FPG_2; 1.
PE   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA-binding; Glycosidase; Hydrolase; Lyase;
KW   Metal-binding; Multifunctional enzyme; Zinc; Zinc-finger.
FT   INIT_MET        1
FT                   /note="Removed"
FT                   /evidence="ECO:0000250"
FT   CHAIN           2..270
FT                   /note="Formamidopyrimidine-DNA glycosylase"
FT                   /id="PRO_1000202832"
FT   ZN_FING         236..270
FT                   /note="FPG-type"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   ACT_SITE        2
FT                   /note="Schiff-base intermediate with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   ACT_SITE        3
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   ACT_SITE        56
FT                   /note="Proton donor; for beta-elimination activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   ACT_SITE        260
FT                   /note="Proton donor; for delta-elimination activity"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   BINDING         89
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   BINDING         107
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
FT   BINDING         151
FT                   /ligand="DNA"
FT                   /ligand_id="ChEBI:CHEBI:16991"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00103"
SQ   SEQUENCE   270 AA;  29588 MW;  A5FD2F696BDAF7D5 CRC64;
     MPELPEVEVT RRGFAERIAG ARIDAVRIGK PLRWALMVMP EALVGRRVLQ VRRRGKYLLI
     DLDRGLLLLH LGMSGSLRFD AALPAPGVHD HFDLVTELGT LRLNDPRRFG AVVYVEDEAA
     PWAIKLLGGL GMEPLGDAFD LDAFHAGLRK RKAAVKQVLL AGDVVVGVGN IYASEALFLA
     GIRPTLSAAR ISRPRAARLH AAVREILARA VEKGGSTLRD FSNVEGQSGY FQLEATVYGR
     AGEPCRVCAT PIRLLRQGQR STYYCPNCQK
 
 
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