UDGA_THET8
ID UDGA_THET8 Reviewed; 205 AA.
AC Q5SKC5; Q7WYV4;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 81.
DE RecName: Full=Type-4 uracil-DNA glycosylase {ECO:0000305};
DE EC=3.2.2.27 {ECO:0000269|PubMed:12000829, ECO:0000269|PubMed:14556741};
DE AltName: Full=TTUDGA {ECO:0000303|PubMed:12000829};
DE AltName: Full=TthUDG {ECO:0000303|PubMed:14556741};
GN Name=udg {ECO:0000312|EMBL:BAC79245.1};
GN OrderedLocusNames=TTHA0718 {ECO:0000312|EMBL:BAD70541.1};
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1] {ECO:0007744|PDB:1UI0, ECO:0007744|PDB:1UI1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY,
RP IRON-SULFUR CLUSTER, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, AND X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH
RP IRON-SULFUR (4FE-4S) AND URACIL.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=14556741; DOI=10.1016/j.jmb.2003.08.030;
RA Hoseki J., Okamoto A., Masui R., Shibata T., Inoue Y., Yokoyama S.,
RA Kuramitsu S.;
RT "Crystal structure of a family 4 uracil-DNA glycosylase from Thermus
RT thermophilus HB8.";
RL J. Mol. Biol. 333:515-526(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=HB27 / ATCC BAA-163 / DSM 7039;
RX PubMed=12000829; DOI=10.1093/nar/30.10.2097;
RA Starkuviene V., Fritz H.J.;
RT "A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA
RT damage in the extremely thermophilic eubacterium Thermus thermophilus.";
RL Nucleic Acids Res. 30:2097-2102(2002).
CC -!- FUNCTION: Removes uracil bases that are present in DNA as a result of
CC either deamination of cytosine or misincorporation of dUMP instead of
CC dTMP. Can remove uracil from double-stranded DNA containing either a
CC U/G, U/A, U/C or U/T base pair as well as from single-stranded DNA
CC (PubMed:12000829, PubMed:14556741). Specifically recognizes uracil that
CC is flipped out from double-stranded DNA (PubMed:14556741).
CC {ECO:0000269|PubMed:12000829, ECO:0000269|PubMed:14556741}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolyzes single-stranded DNA or mismatched double-stranded
CC DNA and polynucleotides, releasing free uracil.; EC=3.2.2.27;
CC Evidence={ECO:0000269|PubMed:12000829, ECO:0000269|PubMed:14556741};
CC -!- ACTIVITY REGULATION: Product-inhibited by apurinic/apyrimidinic sites.
CC {ECO:0000269|PubMed:14556741}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.0 uM for G/U dsDNA {ECO:0000269|PubMed:14556741};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:14556741}.
CC -!- MISCELLANEOUS: The 4Fe-4S cluster may have a structural rather than a
CC catalytic role. Does not appear to be essential for enzyme activity.
CC {ECO:0000269|PubMed:14556741}.
CC -!- SIMILARITY: Belongs to the uracil-DNA glycosylase (UDG) superfamily.
CC Type 4 (UDGa) family. {ECO:0000305}.
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DR EMBL; AB109239; BAC79245.1; -; Genomic_DNA.
DR EMBL; AP008226; BAD70541.1; -; Genomic_DNA.
DR RefSeq; WP_011228142.1; NC_006461.1.
DR RefSeq; YP_143984.1; NC_006461.1.
DR PDB; 1UI0; X-ray; 1.50 A; A=1-205.
DR PDB; 1UI1; X-ray; 2.80 A; A=1-205.
DR PDBsum; 1UI0; -.
DR PDBsum; 1UI1; -.
DR AlphaFoldDB; Q5SKC5; -.
DR SMR; Q5SKC5; -.
DR STRING; 300852.55772100; -.
DR DrugBank; DB03419; Uracil.
DR EnsemblBacteria; BAD70541; BAD70541; BAD70541.
DR GeneID; 3169183; -.
DR KEGG; ttj:TTHA0718; -.
DR PATRIC; fig|300852.9.peg.711; -.
DR eggNOG; COG1573; Bacteria.
DR HOGENOM; CLU_044815_1_3_0; -.
DR OMA; RPWLIAE; -.
DR PhylomeDB; Q5SKC5; -.
DR BRENDA; 3.2.2.27; 2305.
DR SABIO-RK; Q5SKC5; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004844; F:uracil DNA N-glycosylase activity; IDA:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IDA:UniProtKB.
DR Gene3D; 3.40.470.10; -; 1.
DR InterPro; IPR005273; Ura-DNA_glyco_family4.
DR InterPro; IPR005122; Uracil-DNA_glycosylase-like.
DR InterPro; IPR036895; Uracil-DNA_glycosylase-like_sf.
DR Pfam; PF03167; UDG; 1.
DR SMART; SM00986; UDG; 1.
DR SUPFAM; SSF52141; SSF52141; 1.
DR TIGRFAMs; TIGR00758; UDG_fam4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; DNA damage; DNA repair; Hydrolase; Iron; Iron-sulfur;
KW Metal-binding; Reference proteome.
FT CHAIN 1..205
FT /note="Type-4 uracil-DNA glycosylase"
FT /id="PRO_0000439182"
FT BINDING 13
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:14556741,
FT ECO:0007744|PDB:1UI0, ECO:0007744|PDB:1UI1"
FT BINDING 16
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:14556741,
FT ECO:0007744|PDB:1UI0, ECO:0007744|PDB:1UI1"
FT BINDING 40..42
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:14556741"
FT BINDING 54
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:14556741"
FT BINDING 80
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:14556741"
FT BINDING 84
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:14556741,
FT ECO:0007744|PDB:1UI0, ECO:0007744|PDB:1UI1"
FT BINDING 100
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:14556741,
FT ECO:0007744|PDB:1UI0, ECO:0007744|PDB:1UI1"
FT BINDING 155
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:14556741"
FT HELIX 3..10
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:1UI0"
FT STRAND 35..41
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 45..50
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 57..69
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:1UI0"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 94..103
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 105..112
FT /evidence="ECO:0007829|PDB:1UI0"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 122..129
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:1UI0"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:1UI0"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 156..161
FT /evidence="ECO:0007829|PDB:1UI0"
FT HELIX 170..187
FT /evidence="ECO:0007829|PDB:1UI0"
SQ SEQUENCE 205 AA; 22966 MW; 74720211D889806F CRC64;
MTLELLQAQA QNCTACRLME GRTRVVFGEG NPDAKLMIVG EGPGEEEDKT GRPFVGKAGQ
LLNRILEAAG IPREEVYITN IVKCRPPQNR APLPDEAKIC TDKWLLKQIE LIAPQIIVPL
GAVAAEFFLG EKVSITKVRG KWYEWHGIKV FPMFHPAYLL RNPSRAPGSP KHLTWLDIQE
VKRALDALPP KERRPVKAVS QEPLF
