ID A0A0M4CZ55_SPHS1 Unreviewed; 270 AA.
AC A0A0M4CZ55;
DT 09-DEC-2015, integrated into UniProtKB/TrEMBL.
DT 09-DEC-2015, sequence version 1.
DT 27-MAR-2024, entry version 37.
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 Synonyms=fpg {ECO:0000256|HAMAP-Rule:MF_00103};
GN ORFNames=LH20_21780 {ECO:0000313|EMBL:ALC14601.1};
OS Sphingopyxis sp. (strain 113P3).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingopyxis.
OX NCBI_TaxID=292913 {ECO:0000313|EMBL:ALC14601.1, ECO:0000313|Proteomes:UP000061305};
RN [1] {ECO:0000313|EMBL:ALC14601.1, ECO:0000313|Proteomes:UP000061305}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=113P3 {ECO:0000313|EMBL:ALC14601.1,
RC ECO:0000313|Proteomes:UP000061305};
RX PubMed=26472829;
RA Ohtsubo Y., Nagata Y., Numata M., Tsuchikane K., Hosoyama A., Yamazoe A.,
RA Tsuda M., Fujita N., Kawai F.;
RT "Complete Genome Sequence of Polyvinyl Alcohol-Degrading Strain
RT Sphingopyxis sp. 113P3 (NBRC 111507).";
RL Genome Announc. 3:e01169-15(2015).
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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00024490, ECO:0000256|HAMAP-
CC 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:0000256|ARBA:ARBA00001668, ECO:0000256|HAMAP-
CC Rule:MF_00103};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00103};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00103};
CC -!- SUBUNIT: Monomer. {ECO:0000256|ARBA:ARBA00011245, ECO:0000256|HAMAP-
CC Rule:MF_00103}.
CC -!- SIMILARITY: Belongs to the FPG family. {ECO:0000256|ARBA:ARBA00009409,
CC ECO:0000256|HAMAP-Rule:MF_00103}.
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DR EMBL; CP009452; ALC14601.1; -; Genomic_DNA.
DR RefSeq; WP_053555970.1; NZ_CP009452.1.
DR AlphaFoldDB; A0A0M4CZ55; -.
DR STRING; 292913.LH20_21780; -.
DR KEGG; sphp:LH20_21780; -.
DR PATRIC; fig|292913.6.peg.4429; -.
DR OrthoDB; 9800855at2; -.
DR Proteomes; UP000061305; 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 CDD; cd08966; EcFpg-like_N; 1.
DR Gene3D; 1.10.8.50; -; 1.
DR Gene3D; 3.20.190.10; MutM-like, N-terminal; 1.
DR HAMAP; MF_00103; Fapy_DNA_glycosyl; 1.
DR InterPro; IPR015886; DNA_glyclase/AP_lyase_DNA-bd.
DR InterPro; IPR020629; Formamido-pyr_DNA_Glyclase.
DR InterPro; IPR012319; FPG_cat.
DR InterPro; IPR035937; MutM-like_N-ter.
DR InterPro; IPR010979; Ribosomal_uS13-like_H2TH.
DR InterPro; IPR000214; Znf_DNA_glyclase/AP_lyase.
DR InterPro; IPR010663; Znf_FPG/IleRS.
DR NCBIfam; TIGR00577; fpg; 1.
DR PANTHER; PTHR22993:SF9; ENDONUCLEASE 8-LIKE 1; 1.
DR PANTHER; PTHR22993; FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE; 1.
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; SSF57716; Glucocorticoid receptor-like (DNA-binding domain); 1.
DR SUPFAM; SSF81624; N-terminal domain of MutM-like DNA repair proteins; 1.
DR SUPFAM; SSF46946; S13-like H2TH domain; 1.
DR PROSITE; PS51068; FPG_CAT; 1.
DR PROSITE; PS51066; ZF_FPG_2; 1.
PE 3: Inferred from homology;
KW DNA damage {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW Rule:MF_00103};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW Rule:MF_00103};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_00103};
KW Glycosidase {ECO:0000256|ARBA:ARBA00023295, ECO:0000256|HAMAP-
KW Rule:MF_00103};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00103};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_00103};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00103};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268, ECO:0000256|HAMAP-
KW Rule:MF_00103}; Reference proteome {ECO:0000313|Proteomes:UP000061305};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_00103};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771, ECO:0000256|HAMAP-
KW Rule:MF_00103}.
FT DOMAIN 2..112
FT /note="Formamidopyrimidine-DNA glycosylase catalytic"
FT /evidence="ECO:0000259|PROSITE:PS51068"
FT DOMAIN 237..270
FT /note="FPG-type"
FT /evidence="ECO:0000259|PROSITE:PS51066"
FT ACT_SITE 2
FT /note="Schiff-base intermediate with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
FT ACT_SITE 3
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
FT ACT_SITE 58
FT /note="Proton donor; for beta-elimination activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
FT ACT_SITE 260
FT /note="Proton donor; for delta-elimination activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
FT BINDING 90
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
FT BINDING 109
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
FT BINDING 152
FT /ligand="DNA"
FT /ligand_id="ChEBI:CHEBI:16991"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00103"
SQ SEQUENCE 270 AA; 29157 MW; 4E6D74BB4A2C677F CRC64;
MPELPEVETT VRGLAPFLEG QQLVAVTTFR PDLRRPFPAD LAQRLTGATV TALSRRAKYG
IVSTDRDDHM IFHLGMSGRW RTEGGAAGKH DHLLIETAGG HRLFLHDPRR FGSVDLVTGD
PLTRFPAFMT LGPEPLSDDF DALYLARVLA GRRAPIKAML LDQAVVAGLG NIYVCEALNM
ARISPLKPAA DVPKARLAAL APAIKAVLAA AIAAGGSTLR DFLSPEGDLG YFAKEWRVYG
REGEACECGG TIARIVQGGR STFHCPKCQR
//