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Formamidopyrimidine-DNA glycosylase (Fapy-DNA glycosylase) (EC 3.2.2.23) (DNA-(apurinic or apyrimidinic site) lyase MutM) (AP lyase MutM) (EC 4.2.99.18)

 FPG_LACLC               Reviewed;         273 AA.
P42371;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
23-MAY-2018, entry version 123.
RecName: Full=Formamidopyrimidine-DNA glycosylase;
Short=Fapy-DNA glycosylase;
EC=3.2.2.23;
AltName: Full=DNA-(apurinic or apyrimidinic site) lyase MutM;
Short=AP lyase MutM;
EC=4.2.99.18;
Name=mutM; Synonyms=fpg;
Lactococcus lactis subsp. cremoris (Streptococcus cremoris).
Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
Lactococcus.
NCBI_TaxID=1359;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-22, AND
FUNCTION.
STRAIN=NCDO 763 / ML3;
PubMed=7704272; DOI=10.1099/13500872-141-2-411;
Duwat P., de Oliveira R., Ehrlich S.D., Boiteux S.;
"Repair of oxidative DNA damage in Gram-positive bacteria: the
Lactococcus lactis Fpg protein.";
Microbiology 141:411-417(1995).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 194-273.
STRAIN=NCDO 763 / ML3;
PubMed=1514816;
Duwat P., Ehrlich S.D., Gruss A.;
"Use of degenerate primers for polymerase chain reaction cloning and
sequencing of the Lactococcus lactis subsp. lactis recA gene.";
Appl. Environ. Microbiol. 58:2674-2678(1992).
[3]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-273 OF MUTANT GLY-2 IN
COMPLEX WITH SUBSTRATE ANALOG.
PubMed=12065399; DOI=10.1093/emboj/cdf304;
Serre L., Pereira de Jesus K., Boiteux S., Zelwer C., Castaing B.;
"Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA
glycosylase bound to an abasic site analogue-containing DNA.";
EMBO J. 21:2854-2865(2002).
-!- FUNCTION: Involved in base excision repair of DNA damaged by
oxidation or by mutagenic agents. Acts as DNA glycosylase that
recognizes and removes damaged bases. Has a preference for
oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Has
AP (apurinic/apyrimidinic) lyase activity and introduces nicks in
the DNA strand. Cleaves 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. {ECO:0000269|PubMed:7704272}.
-!- CATALYTIC ACTIVITY: Hydrolysis of DNA containing ring-opened 7-
methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-
methyl)formamidopyrimidine.
-!- CATALYTIC ACTIVITY: The C-O-P bond 3' to the apurinic or
apyrimidinic site in DNA is broken by a beta-elimination reaction,
leaving a 3'-terminal unsaturated sugar and a product with a
terminal 5'-phosphate.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Note=Binds 1 zinc ion per subunit.;
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12065399}.
-!- MISCELLANEOUS: The zinc finger is important for DNA binding.
-!- SIMILARITY: Belongs to the FPG family. {ECO:0000305}.
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EMBL; X74298; CAA52351.1; -; Genomic_DNA.
EMBL; M88106; -; NOT_ANNOTATED_CDS; Genomic_DNA.
PIR; S39200; S39200.
PDB; 1KFV; X-ray; 2.55 A; A/B=2-273.
PDB; 1NNJ; X-ray; 1.90 A; A=2-273.
PDB; 1PJI; X-ray; 1.90 A; A=2-273.
PDB; 1PJJ; X-ray; 1.90 A; A=2-273.
PDB; 1PM5; X-ray; 1.95 A; A=2-273.
PDB; 1TDZ; X-ray; 1.80 A; A=1-273.
PDB; 1XC8; X-ray; 1.95 A; A=2-273.
PDB; 2XZF; X-ray; 1.80 A; A=2-273.
PDB; 2XZU; X-ray; 1.82 A; A=2-273.
PDB; 3C58; X-ray; 1.90 A; A=2-273.
PDB; 4PCZ; X-ray; 1.70 A; A=2-273.
PDB; 4PD2; X-ray; 1.65 A; A=2-273.
PDB; 4PDG; X-ray; 2.40 A; A=2-273.
PDB; 4PDI; X-ray; 2.10 A; A=2-273.
PDBsum; 1KFV; -.
PDBsum; 1NNJ; -.
PDBsum; 1PJI; -.
PDBsum; 1PJJ; -.
PDBsum; 1PM5; -.
PDBsum; 1TDZ; -.
PDBsum; 1XC8; -.
PDBsum; 2XZF; -.
PDBsum; 2XZU; -.
PDBsum; 3C58; -.
PDBsum; 4PCZ; -.
PDBsum; 4PD2; -.
PDBsum; 4PDG; -.
PDBsum; 4PDI; -.
ProteinModelPortal; P42371; -.
SMR; P42371; -.
PRIDE; P42371; -.
eggNOG; ENOG4105ERD; Bacteria.
eggNOG; COG0266; LUCA.
BRENDA; 3.2.2.23; 2903.
EvolutionaryTrace; P42371; -.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
GO; GO:0003684; F:damaged DNA binding; IEA:InterPro.
GO; GO:0008534; F:oxidized purine nucleobase lesion DNA N-glycosylase activity; IEA:UniProtKB-EC.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0006284; P:base-excision repair; IEA:InterPro.
GO; GO:0006289; P:nucleotide-excision repair; IEA:InterPro.
Gene3D; 3.20.190.10; -; 1.
HAMAP; MF_00103; Fapy_DNA_glycosyl; 1.
InterPro; IPR015886; DNA_glyclase/AP_lyase_DNA-bd.
InterPro; IPR015887; DNA_glyclase_Znf_dom_DNA_BS.
InterPro; IPR020629; Formamido-pyr_DNA_Glyclase.
InterPro; IPR012319; FPG_cat.
InterPro; IPR035937; MutM-like_N-ter.
InterPro; IPR010979; Ribosomal_S13-like_H2TH.
InterPro; IPR000214; Znf_DNA_glyclase/AP_lyase.
InterPro; IPR010663; Znf_FPG/IleRS.
Pfam; PF01149; Fapy_DNA_glyco; 1.
Pfam; PF06831; H2TH; 1.
Pfam; PF06827; zf-FPG_IleRS; 1.
SMART; SM00898; Fapy_DNA_glyco; 1.
SMART; SM01232; H2TH; 1.
SUPFAM; SSF46946; SSF46946; 1.
SUPFAM; SSF81624; SSF81624; 1.
TIGRFAMs; TIGR00577; fpg; 1.
PROSITE; PS51068; FPG_CAT; 1.
PROSITE; PS01242; ZF_FPG_1; 1.
PROSITE; PS51066; ZF_FPG_2; 1.
1: Evidence at protein level;
3D-structure; Direct protein sequencing; DNA damage; DNA repair;
DNA-binding; Glycosidase; Hydrolase; Lyase; Metal-binding;
Multifunctional enzyme; Zinc; Zinc-finger.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:7704272}.
CHAIN 2 273 Formamidopyrimidine-DNA glycosylase.
/FTId=PRO_0000170830.
ZN_FING 238 272 FPG-type.
REGION 58 76 DNA binding.
REGION 162 172 DNA binding.
ACT_SITE 2 2 Schiff-base intermediate with DNA.
{ECO:0000305}.
ACT_SITE 3 3 Proton donor. {ECO:0000305}.
ACT_SITE 58 58 Proton donor; for beta-elimination
activity. {ECO:0000305}.
ACT_SITE 262 262 Proton donor; for delta-elimination
activity. {ECO:0000305}.
BINDING 92 92 DNA.
BINDING 110 110 DNA.
MUTAGEN 2 2 P->G: Loss of activity.
HELIX 4 18 {ECO:0000244|PDB:4PD2}.
STRAND 25 29 {ECO:0000244|PDB:4PD2}.
HELIX 31 33 {ECO:0000244|PDB:4PD2}.
HELIX 38 45 {ECO:0000244|PDB:4PD2}.
STRAND 49 56 {ECO:0000244|PDB:4PD2}.
STRAND 59 64 {ECO:0000244|PDB:4PD2}.
TURN 65 67 {ECO:0000244|PDB:4PD2}.
STRAND 68 73 {ECO:0000244|PDB:4PD2}.
TURN 75 77 {ECO:0000244|PDB:4PD2}.
STRAND 79 83 {ECO:0000244|PDB:4PD2}.
STRAND 93 98 {ECO:0000244|PDB:4PD2}.
STRAND 103 107 {ECO:0000244|PDB:4PD2}.
STRAND 114 119 {ECO:0000244|PDB:4PD2}.
HELIX 120 122 {ECO:0000244|PDB:4PD2}.
HELIX 123 129 {ECO:0000244|PDB:4PD2}.
HELIX 144 153 {ECO:0000244|PDB:4PD2}.
HELIX 158 163 {ECO:0000244|PDB:4PD2}.
STRAND 165 169 {ECO:0000244|PDB:4PD2}.
HELIX 173 182 {ECO:0000244|PDB:4PD2}.
HELIX 191 193 {ECO:0000244|PDB:4PD2}.
HELIX 196 215 {ECO:0000244|PDB:4PD2}.
STRAND 221 223 {ECO:0000244|PDB:1XC8}.
TURN 227 230 {ECO:0000244|PDB:4PD2}.
HELIX 233 236 {ECO:0000244|PDB:4PD2}.
TURN 248 250 {ECO:0000244|PDB:4PCZ}.
STRAND 255 259 {ECO:0000244|PDB:4PD2}.
STRAND 262 266 {ECO:0000244|PDB:4PD2}.
TURN 268 270 {ECO:0000244|PDB:4PD2}.
SEQUENCE 273 AA; 31310 MW; EB16055C5E09840F CRC64;
MPELPEVETV RRELEKRIVG QKIISIEATY PRMVLTGFEQ LKKELTGKTI QGISRRGKYL
IFEIGDDFRL ISHLRMEGKY RLATLDAPRE KHDHLTMKFA DGQLIYADVR KFGTWELIST
DQVLPYFLKK KIGPEPTYDE DFDEKLFREK LRKSTKKIKP YLLEQTLVAG LGNIYVDEVL
WLAKIHPEKE TNQLIESSIH LLHDSIIEIL QKAIKLGGSS IRTYSALGST GKMQNELQVY
GKTGEKCSRC GAEIQKIKVA GRGTHFCPVC QQK


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