(data stored in SCRATCH zone)

SWISSPROT: D3VGW8_XENNA

ID   D3VGW8_XENNA            Unreviewed;       269 AA.
AC   D3VGW8;
DT   20-APR-2010, integrated into UniProtKB/TrEMBL.
DT   20-APR-2010, sequence version 1.
DT   16-JAN-2019, entry version 58.
DE   RecName: Full=Formamidopyrimidine-DNA glycosylase {ECO:0000256|HAMAP-Rule:MF_00103};
DE            Short=Fapy-DNA glycosylase {ECO:0000256|HAMAP-Rule:MF_00103};
DE            EC=3.2.2.23 {ECO:0000256|HAMAP-Rule:MF_00103};
DE   AltName: Full=DNA-(apurinic or apyrimidinic site) lyase MutM {ECO:0000256|HAMAP-Rule:MF_00103};
DE            Short=AP lyase MutM {ECO:0000256|HAMAP-Rule:MF_00103};
DE            EC=4.2.99.18 {ECO:0000256|HAMAP-Rule:MF_00103};
GN   Name=mutM {ECO:0000256|HAMAP-Rule:MF_00103,
GN   ECO:0000313|EMBL:CBJ88253.1};
GN   Synonyms=fpg {ECO:0000256|HAMAP-Rule:MF_00103};
GN   OrderedLocusNames=XNC1_0165 {ECO:0000313|EMBL:CBJ88253.1};
OS   Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 /
OS   NCIB 9965 / AN6).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Morganellaceae; Xenorhabdus.
OX   NCBI_TaxID=406817 {ECO:0000313|EMBL:CBJ88253.1, ECO:0000313|Proteomes:UP000008075};
RN   [1] {ECO:0000313|Proteomes:UP000008075}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6
RC   {ECO:0000313|Proteomes:UP000008075};
RA   Goodrich-Blair H., Barbazuk B., Bode H.B., Darby C., Du Z., Forst S.,
RA   Gaudriault S., Goldman B.S., Goodner B., Henkhaus J., Latreille P.,
RA   Medigue C., Miller N., Norton S., Ogier J.C., Rouy Z., Slater S.,
RA   Suen G.;
RT   "Complete genome sequence of Xenorhabdus nematophila (strain ATCC
RT   19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6).";
RL   Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|EMBL:CBJ88253.1, ECO:0000313|Proteomes:UP000008075}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6
RC   {ECO:0000313|Proteomes:UP000008075};
RX   PubMed=22125637; DOI=10.1371/journal.pone.0027909;
RA   Chaston J.M., Suen G., Tucker S.L., Andersen A.W., Bhasin A., Bode E.,
RA   Bode H.B., Brachmann A.O., Cowles C.E., Cowles K.N., Darby C.,
RA   de Leon L., Drace K., Du Z., Givaudan A., Herbert Tran E.E.,
RA   Jewell K.A., Knack J.J., Krasomil-Osterfeld K.C., Kukor R., Lanois A.,
RA   Latreille P., Leimgruber N.K., Lipke C.M., Liu R., Lu X.,
RA   Martens E.C., Marri P.R., Medigue C., Menard M.L., Miller N.M.,
RA   Morales-Soto N., Norton S., Ogier J.C., Orchard S.S., Park D.,
RA   Park Y., Qurollo B.A., Sugar D.R., Richards G.R., Rouy Z.,
RA   Slominski B., Slominski K., Snyder H., Tjaden B.C., van der Hoeven R.,
RA   Welch R.D., Wheeler C., Xiang B., Barbazuk B., Gaudriault S.,
RA   Goodner B., Slater S.C., Forst S., Goldman B.S., Goodrich-Blair H.;
RT   "The entomopathogenic bacterial endosymbionts xenorhabdus and
RT   photorhabdus: convergent lifestyles from divergent genomes.";
RL   PLoS ONE 6:e27909-e27909(2011).
CC   -!- FUNCTION: Involved in base excision repair of DNA damaged by
CC       oxidation or by mutagenic agents. Acts as DNA glycosylase that
CC       recognizes and removes damaged bases. Has a preference for
CC       oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has
CC       AP (apurinic/apyrimidinic) lyase activity and introduces nicks in
CC       the DNA strand. Cleaves the DNA backbone by beta-delta elimination
CC       to generate a single-strand break at the site of the removed base
CC       with both 3'- and 5'-phosphates. {ECO:0000256|HAMAP-Rule:MF_00103,
CC       ECO:0000256|SAAS:SAAS00020861}.
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:0000256|HAMAP-Rule:MF_00103,
CC         ECO:0000256|SAAS:SAAS01116288};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=The C-O-P bond 3' to the apurinic or apyrimidinic site in
CC         DNA is broken by a beta-elimination reaction, leaving a 3'-
CC         terminal unsaturated sugar and a product with a terminal 5'-
CC         phosphate.; EC=4.2.99.18; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_00103, ECO:0000256|SAAS:SAAS01121890};
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_00103};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-
CC       Rule:MF_00103};
CC   -!- SUBUNIT: Monomer. {ECO:0000256|HAMAP-Rule:MF_00103,
CC       ECO:0000256|SAAS:SAAS00041892}.
CC   -!- SIMILARITY: Belongs to the FPG family. {ECO:0000256|HAMAP-
CC       Rule:MF_00103, ECO:0000256|SAAS:SAAS00557294}.
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DR   EMBL; FN667742; CBJ88253.1; -; Genomic_DNA.
DR   RefSeq; WP_010847623.1; NC_014228.1.
DR   STRING; 406817.XNC1_0165; -.
DR   EnsemblBacteria; CBJ88253; CBJ88253; XNC1_0165.
DR   KEGG; xne:XNC1_0165; -.
DR   eggNOG; ENOG4105ERD; Bacteria.
DR   eggNOG; COG0266; LUCA.
DR   HOGENOM; HOG000020881; -.
DR   KO; K10563; -.
DR   OMA; RNSRLRW; -.
DR   Proteomes; UP000008075; Chromosome.
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   GO; GO:0006289; P:nucleotide-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;
DR   PRODOM; D3VGW8.
DR   SWISS-2DPAGE; D3VGW8.
KW   Complete proteome {ECO:0000313|Proteomes:UP000008075};
KW   DNA damage {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087016};
KW   DNA repair {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087019};
KW   DNA-binding {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087047};
KW   Glycosidase {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087011, ECO:0000313|EMBL:CBJ88253.1};
KW   Hydrolase {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087030, ECO:0000313|EMBL:CBJ88253.1};
KW   Lyase {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087025};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS00551678};
KW   Multifunctional enzyme {ECO:0000256|HAMAP-Rule:MF_00103,
KW   ECO:0000256|SAAS:SAAS01087023};
KW   Reference proteome {ECO:0000313|Proteomes:UP000008075};
KW   Zinc {ECO:0000256|HAMAP-Rule:MF_00103, ECO:0000256|SAAS:SAAS00551670};
KW   Zinc-finger {ECO:0000256|HAMAP-Rule:MF_00103, ECO:0000256|PROSITE-
KW   ProRule:PRU00391, ECO:0000256|SAAS:SAAS00551733}.
FT   DOMAIN        2    112       FPG_CAT. {ECO:0000259|PROSITE:PS51068}.
FT   DOMAIN      235    269       FPG-type. {ECO:0000259|PROSITE:PS51066}.
FT   ACT_SITE      2      2       Schiff-base intermediate with DNA.
FT                                {ECO:0000256|HAMAP-Rule:MF_00103}.
FT   ACT_SITE      3      3       Proton donor. {ECO:0000256|HAMAP-Rule:
FT                                MF_00103}.
FT   ACT_SITE     57     57       Proton donor; for beta-elimination
FT                                activity. {ECO:0000256|HAMAP-Rule:
FT                                MF_00103}.
FT   ACT_SITE    259    259       Proton donor; for delta-elimination
FT                                activity. {ECO:0000256|HAMAP-Rule:
FT                                MF_00103}.
FT   BINDING      90     90       DNA. {ECO:0000256|HAMAP-Rule:MF_00103}.
FT   BINDING     109    109       DNA. {ECO:0000256|HAMAP-Rule:MF_00103}.
FT   BINDING     150    150       DNA. {ECO:0000256|HAMAP-Rule:MF_00103}.
SQ   SEQUENCE   269 AA;  30871 MW;  EF3C024ABB47E83D CRC64;
     MPELPEVETS RRGIEPHLVG NIIQYAEVRN SRLRWPVSEQ IMKLSDRPVL SVQRRAKYLL
     LELPEGWIII HLGMSGSLRI LLEERPPEKH DHVDLIMADG KTLRYTDPRR FGAWLWSDDL
     NKCSVLSHLG PEPLFDQFDG EYLYSLSRNK KTAIKPWLMD NKVVVGVGNI YANEALFVAH
     ILPERPVHSL TQQEAHLLAD IIKQILHRSI EQGGTTLKDF LQSDGKPGYF AQELFVYGKK
     GELCSKCGEK IECIKLGQRS TFFCRQCQH
//

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