UDGA_SULTO
ID UDGA_SULTO Reviewed; 220 AA.
AC Q96YD0;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Type-4 uracil-DNA glycosylase {ECO:0000305};
DE EC=3.2.2.27 {ECO:0000269|PubMed:26318717};
DE AltName: Full=stoUDG {ECO:0000303|PubMed:26318717};
GN OrderedLocusNames=STK_22380 {ECO:0000312|EMBL:BAB67347.1};
OS Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)
OS (Sulfolobus tokodaii).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Sulfurisphaera.
OX NCBI_TaxID=273063;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 16993 / JCM 10545 / NBRC 100140 / 7;
RX PubMed=11572479; DOI=10.1093/dnares/8.4.123;
RA Kawarabayasi Y., Hino Y., Horikawa H., Jin-no K., Takahashi M., Sekine M.,
RA Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y.,
RA Nishijima K., Otsuka R., Nakazawa H., Takamiya M., Kato Y., Yoshizawa T.,
RA Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K.,
RA Masuda S., Yanagii M., Nishimura M., Yamagishi A., Oshima T., Kikuchi H.;
RT "Complete genome sequence of an aerobic thermoacidophilic Crenarchaeon,
RT Sulfolobus tokodaii strain7.";
RL DNA Res. 8:123-140(2001).
RN [2]
RP CRYSTALLIZATION.
RX PubMed=22949205; DOI=10.1107/s1744309112030278;
RA Kawai A., Higuchi S., Tsunoda M., Nakamura K.T., Miyamoto S.;
RT "Purification, crystallization and preliminary X-ray analysis of uracil-DNA
RT glycosylase from Sulfolobus tokodaii strain 7.";
RL Acta Crystallogr. F 68:1102-1105(2012).
RN [3] {ECO:0007744|PDB:4ZBX, ECO:0007744|PDB:4ZBY, ECO:0007744|PDB:4ZBZ}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 1-194 IN COMPLEX WITH IRON-SULFUR
RP (4FE-4S) AND URACIL, FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF
RP LEU-169; TYR-170 AND ASN-171.
RX PubMed=26318717; DOI=10.1016/j.febslet.2015.08.019;
RA Kawai A., Higuchi S., Tsunoda M., Nakamura K.T., Yamagata Y., Miyamoto S.;
RT "Crystal structure of family 4 uracil-DNA glycosylase from Sulfolobus
RT tokodaii and a function of tyrosine 170 in DNA binding.";
RL FEBS Lett. 589:2675-2682(2015).
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. {ECO:0000269|PubMed:26318717}.
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:26318717};
CC -!- SIMILARITY: Belongs to the uracil-DNA glycosylase (UDG) superfamily.
CC Type 4 (UDGa) family. {ECO:0000305}.
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DR EMBL; BA000023; BAB67347.1; -; Genomic_DNA.
DR RefSeq; WP_010980322.1; NC_003106.2.
DR PDB; 4ZBX; X-ray; 1.70 A; A=1-194.
DR PDB; 4ZBY; X-ray; 1.70 A; A=1-194.
DR PDB; 4ZBZ; X-ray; 1.90 A; A=1-194.
DR PDBsum; 4ZBX; -.
DR PDBsum; 4ZBY; -.
DR PDBsum; 4ZBZ; -.
DR AlphaFoldDB; Q96YD0; -.
DR SMR; Q96YD0; -.
DR STRING; 273063.STK_22380; -.
DR EnsemblBacteria; BAB67347; BAB67347; STK_22380.
DR GeneID; 1460319; -.
DR KEGG; sto:STK_22380; -.
DR PATRIC; fig|273063.9.peg.2538; -.
DR eggNOG; arCOG00905; Archaea.
DR OMA; RPWLIAE; -.
DR OrthoDB; 90493at2157; -.
DR BRENDA; 3.2.2.27; 15396.
DR Proteomes; UP000001015; 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..220
FT /note="Type-4 uracil-DNA glycosylase"
FT /id="PRO_0000439186"
FT BINDING 14
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:26318717,
FT ECO:0007744|PDB:4ZBX, ECO:0007744|PDB:4ZBY,
FT ECO:0007744|PDB:4ZBZ"
FT BINDING 17
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:26318717,
FT ECO:0007744|PDB:4ZBX, ECO:0007744|PDB:4ZBY,
FT ECO:0007744|PDB:4ZBZ"
FT BINDING 41..43
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:26318717"
FT BINDING 55
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:26318717"
FT BINDING 82
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000269|PubMed:26318717"
FT BINDING 86
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:26318717,
FT ECO:0007744|PDB:4ZBX, ECO:0007744|PDB:4ZBY,
FT ECO:0007744|PDB:4ZBZ"
FT BINDING 102
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|PubMed:26318717,
FT ECO:0007744|PDB:4ZBX, ECO:0007744|PDB:4ZBY,
FT ECO:0007744|PDB:4ZBZ"
FT BINDING 164
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000250|UniProtKB:Q5SKC5"
FT MUTAGEN 169
FT /note="L->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:26318717"
FT MUTAGEN 170
FT /note="Y->A: Lack of activity."
FT /evidence="ECO:0000269|PubMed:26318717"
FT MUTAGEN 171
FT /note="N->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:26318717"
FT HELIX 4..12
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 18..22
FT /evidence="ECO:0007829|PDB:4ZBX"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 46..51
FT /evidence="ECO:0007829|PDB:4ZBX"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 58..69
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:4ZBX"
FT STRAND 78..84
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 96..113
FT /evidence="ECO:0007829|PDB:4ZBX"
FT STRAND 116..122
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 123..133
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:4ZBX"
FT STRAND 148..152
FT /evidence="ECO:0007829|PDB:4ZBX"
FT STRAND 155..162
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:4ZBX"
FT HELIX 172..190
FT /evidence="ECO:0007829|PDB:4ZBX"
SQ SEQUENCE 220 AA; 25359 MW; D603F931AC657AAE CRC64;
MDSLEKIKEE VISCKKCKLW QFRTNAVPGE GYPKAEIMFV GEAPGENEDK EGRPFVGAAG
KLLTQMIKEI LGLERDQVFI TNVVKCRPPN NRDPEEDEIT ACSPYLDRQI DIIMPKIIVT
LGRHSTKYIF SKMGENFSSI TKVRGKSYVW KYKEKEIIVF PTYHPAAALY NPNLRKILEE
DFKKIRELAI TPKRYTIDYF LGGKNRSWDK REKSDSNSGK
