MIG_AERPE
ID MIG_AERPE Reviewed; 223 AA.
AC Q9YDP0;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 14-NOV-2006, sequence version 2.
DT 03-AUG-2022, entry version 109.
DE RecName: Full=Thymine-DNA glycosylase {ECO:0000303|PubMed:19825417};
DE EC=3.2.2.29 {ECO:0000269|PubMed:19825417};
DE AltName: Full=ApeTDG {ECO:0000303|PubMed:19825417};
DE AltName: Full=Type II nicking enzyme V.ApeKIP {ECO:0000303|PubMed:12654995};
DE Short=V.ApeKIP {ECO:0000303|PubMed:12654995};
GN OrderedLocusNames=APE_0875.1 {ECO:0000312|EMBL:BAA79857.2};
OS Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 /
OS K1).
OC Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales;
OC Desulfurococcaceae; Aeropyrum.
OX NCBI_TaxID=272557;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1;
RX PubMed=10382966; DOI=10.1093/dnares/6.2.83;
RA Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K.,
RA Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A.,
RA Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S.,
RA Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A.,
RA Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H.;
RT "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon,
RT Aeropyrum pernix K1.";
RL DNA Res. 6:83-101(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K5;
RX PubMed=19825417; DOI=10.1016/j.pep.2009.10.006;
RA Liu X.P., Li C.P., Hou J.L., Liu Y.F., Liang R.B., Liu J.H.;
RT "Expression and characterization of thymine-DNA glycosylase from Aeropyrum
RT pernix.";
RL Protein Expr. Purif. 70:1-6(2010).
RN [3]
RP NOMENCLATURE.
RX PubMed=12654995; DOI=10.1093/nar/gkg274;
RA Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A.,
RA Bitinaite J., Blumenthal R.M., Degtyarev S.K., Dryden D.T., Dybvig K.,
RA Firman K., Gromova E.S., Gumport R.I., Halford S.E., Hattman S.,
RA Heitman J., Hornby D.P., Janulaitis A., Jeltsch A., Josephsen J., Kiss A.,
RA Klaenhammer T.R., Kobayashi I., Kong H., Krueger D.H., Lacks S.,
RA Marinus M.G., Miyahara M., Morgan R.D., Murray N.E., Nagaraja V.,
RA Piekarowicz A., Pingoud A., Raleigh E., Rao D.N., Reich N., Repin V.E.,
RA Selker E.U., Shaw P.C., Stein D.C., Stoddard B.L., Szybalski W.,
RA Trautner T.A., Van Etten J.L., Vitor J.M., Wilson G.G., Xu S.Y.;
RT "A nomenclature for restriction enzymes, DNA methyltransferases, homing
RT endonucleases and their genes.";
RL Nucleic Acids Res. 31:1805-1812(2003).
CC -!- FUNCTION: DNA glycosylase that excises thymine from T/G mismatches.
CC Also has a weak DNA glycosylase activity on uracil paired with various
CC bases. {ECO:0000269|PubMed:19825417}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolyzes mismatched double-stranded DNA and polynucleotides,
CC releasing free thymine.; EC=3.2.2.29;
CC Evidence={ECO:0000269|PubMed:19825417};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:19825417};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster has a structural role.
CC {ECO:0000250|UniProtKB:P83847};
CC -!- ACTIVITY REGULATION: Thymine cleavage is completely inhibited by
CC Ni(2+), Co(2+), Zn(2+), Cu(2+) and Mn(2+). Activity is not affected by
CC Mg(2+) and Ca(2+). {ECO:0000269|PubMed:19825417}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:19825417};
CC Temperature dependence:
CC Optimum temperature is 65-70 degrees Celsius.
CC {ECO:0000269|PubMed:19825417};
CC -!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000305}.
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DR EMBL; BA000002; BAA79857.2; -; Genomic_DNA.
DR PIR; A72682; A72682.
DR AlphaFoldDB; Q9YDP0; -.
DR SMR; Q9YDP0; -.
DR STRING; 272557.APE_0875.1; -.
DR REBASE; 6398; V.ApeKIP.
DR EnsemblBacteria; BAA79857; BAA79857; APE_0875.1.
DR KEGG; ape:APE_0875.1; -.
DR PATRIC; fig|272557.25.peg.628; -.
DR eggNOG; arCOG00462; Archaea.
DR OMA; RNMIRVI; -.
DR Proteomes; UP000002518; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:InterPro.
DR GO; GO:0016798; F:hydrolase activity, acting on glycosyl bonds; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR CDD; cd00056; ENDO3c; 1.
DR Gene3D; 1.10.1670.10; -; 1.
DR InterPro; IPR011257; DNA_glycosylase.
DR InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
DR InterPro; IPR004035; Endouclease-III_FeS-bd_BS.
DR InterPro; IPR003265; HhH-GPD_domain.
DR InterPro; IPR023170; HhH_base_excis_C.
DR InterPro; IPR044298; MIG/MutY.
DR PANTHER; PTHR42944; PTHR42944; 1.
DR Pfam; PF10576; EndIII_4Fe-2S; 1.
DR Pfam; PF00730; HhH-GPD; 1.
DR SMART; SM00478; ENDO3c; 1.
DR SMART; SM00525; FES; 1.
DR SUPFAM; SSF48150; SSF48150; 1.
DR PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; Glycosidase; Hydrolase; Iron; Iron-sulfur;
KW Metal-binding; Reference proteome.
FT CHAIN 1..223
FT /note="Thymine-DNA glycosylase"
FT /id="PRO_0000449118"
FT BINDING 201
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P83847"
FT BINDING 208
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P83847"
FT BINDING 211
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P83847"
FT BINDING 217
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250|UniProtKB:P83847"
SQ SEQUENCE 223 AA; 25882 MW; A77A54EA904CE407 CRC64;
MLFLDKGRIE ALRRRLIEWY RVYGDKDLPW RNTADPWAIL VAAFLLRKTT ARQVVRVYEE
FLRRYPNPKA LASAREDEVR ELIRPLGIEH QRAKHLIELA KHIEARYGGR IPCSKEKLKE
LPGVGDYIAS EVLLAACGSP EPLLDRNMIR ILERVLGVKS AKKRPHTDPK MWSTARRIVP
KDPDMAKEFN YGMLDLARKI CTARKPLCTE CPLNDICIYY NND
