UDGB_THET8
ID UDGB_THET8 Reviewed; 219 AA.
AC Q5SJ65;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Type-5 uracil-DNA glycosylase {ECO:0000305};
DE EC=3.2.2.- {ECO:0000269|PubMed:12000829, ECO:0000269|PubMed:17870091, ECO:0000269|PubMed:24838246};
DE AltName: Full=TTUDGB {ECO:0000303|PubMed:12000829};
DE AltName: Full=Uracil/hypoxanthine/xanthine DNA glycosylase {ECO:0000305};
GN Name=udgb {ECO:0000303|PubMed:24838246};
GN OrderedLocusNames=TTHA1149 {ECO:0000312|EMBL:BAD70972.1};
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
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 [2]
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).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF ASP-75; ASN-120; HIS-190
RP AND ASN-195.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=24838246; DOI=10.1074/jbc.m114.567354;
RA Xia B., Liu Y., Li W., Brice A.R., Dominy B.N., Cao W.;
RT "Specificity and catalytic mechanism in family 5 uracil DNA glycosylase.";
RL J. Biol. Chem. 289:18413-18426(2014).
RN [4] {ECO:0007744|PDB:2DP6}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
RP (4FE-4S).
RA Kosaka H., Nakagawa N., Masui R., Kuramitsu S.;
RT "Structure of family 5 uracil-DNA glycosylase bound to DNA reveals insights
RT into the mechanism for substrate recognition and catalysis.";
RL Submitted (MAY-2006) to the PDB data bank.
RN [5] {ECO:0007744|PDB:2D3Y, ECO:0007744|PDB:2DDG, ECO:0007744|PDB:2DEM}
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR (4FE-4S)
RP AND DNA, FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF LEU-58 AND
RP ASP-75.
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RX PubMed=17870091; DOI=10.1016/j.jmb.2007.08.022;
RA Kosaka H., Hoseki J., Nakagawa N., Kuramitsu S., Masui R.;
RT "Crystal structure of family 5 uracil-DNA glycosylase bound to DNA.";
RL J. Mol. Biol. 373:839-850(2007).
CC -!- FUNCTION: DNA glycosylase with broad substrate specificity. Can remove
CC uracil from double-stranded DNA containing either a U/G, U/A, U/C or
CC U/T base pair (PubMed:12000829, PubMed:17870091, PubMed:24838246). Can
CC also excise hypoxanthine from double-stranded DNA containing G/I, T/I,
CC and A/I base pairs, xanthine from both double-stranded and single
CC stranded DNA, thymine from G/T mismatched DNA, 5'-hydroxymethyluracil
CC and 5'-fluorouracil (PubMed:17870091, PubMed:24838246).
CC {ECO:0000269|PubMed:12000829, ECO:0000269|PubMed:17870091,
CC ECO:0000269|PubMed:24838246}.
CC -!- SIMILARITY: Belongs to the uracil-DNA glycosylase (UDG) superfamily.
CC Type 5 (UDGb) family. {ECO:0000305}.
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DR EMBL; AP008226; BAD70972.1; -; Genomic_DNA.
DR RefSeq; WP_011173217.1; NC_006461.1.
DR RefSeq; YP_144415.1; NC_006461.1.
DR PDB; 2D3Y; X-ray; 1.55 A; A=1-219.
DR PDB; 2DDG; X-ray; 2.10 A; A=1-219.
DR PDB; 2DEM; X-ray; 1.95 A; A=1-219.
DR PDB; 2DP6; X-ray; 1.80 A; A=1-219.
DR PDBsum; 2D3Y; -.
DR PDBsum; 2DDG; -.
DR PDBsum; 2DEM; -.
DR PDBsum; 2DP6; -.
DR AlphaFoldDB; Q5SJ65; -.
DR SMR; Q5SJ65; -.
DR STRING; 300852.55772531; -.
DR EnsemblBacteria; BAD70972; BAD70972; BAD70972.
DR GeneID; 3169333; -.
DR KEGG; ttj:TTHA1149; -.
DR PATRIC; fig|300852.9.peg.1128; -.
DR eggNOG; COG1573; Bacteria.
DR HOGENOM; CLU_083279_0_0_0; -.
DR OMA; CVPPQNK; -.
DR PhylomeDB; Q5SJ65; -.
DR BRENDA; 3.2.2.15; 2305.
DR BRENDA; 3.2.2.28; 2305.
DR EvolutionaryTrace; Q5SJ65; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0097506; F:deaminated base DNA N-glycosylase activity; IDA:UniProtKB.
DR GO; GO:0033958; F:DNA-deoxyinosine glycosylase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004844; F:uracil DNA N-glycosylase activity; IEA:InterPro.
DR GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR GO; GO:0006281; P:DNA repair; IDA:UniProtKB.
DR CDD; cd10031; UDG-F5_TTUDGB_like; 1.
DR Gene3D; 3.40.470.10; -; 1.
DR InterPro; IPR044147; UdgB-like.
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.
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..219
FT /note="Type-5 uracil-DNA glycosylase"
FT /id="PRO_0000439187"
FT BINDING 13
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:2D3Y,
FT ECO:0007744|PDB:2DDG, ECO:0007744|PDB:2DEM"
FT BINDING 16
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:2D3Y,
FT ECO:0007744|PDB:2DDG, ECO:0007744|PDB:2DEM"
FT BINDING 115
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:2D3Y,
FT ECO:0007744|PDB:2DDG, ECO:0007744|PDB:2DEM"
FT BINDING 130
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:2D3Y,
FT ECO:0007744|PDB:2DDG, ECO:0007744|PDB:2DEM"
FT MUTAGEN 58
FT /note="L->D: 4-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:17870091"
FT MUTAGEN 75
FT /note="D->A: Loss of xanthine DNA glycosylase (XDG)
FT activity. Decrease in uracil DNA glycosylase (UDG) and
FT hypoxanthine DNA glycosylase (HDG) activities. Shows low
FT activity for the removal of uracil from U/G or thymine from
FT T/G."
FT /evidence="ECO:0000269|PubMed:17870091,
FT ECO:0000269|PubMed:24838246"
FT MUTAGEN 75
FT /note="D->E: Retains much of its activity."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 75
FT /note="D->N,Q: Loss of XDG activity, but retains much of
FT its UDG and HDG activities."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 120
FT /note="N->A: Loss of XDG activity. Decrease in UDG and HDG
FT activities."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 120
FT /note="N->D: Minimal effect on UDG and XDG activities.
FT Strong reduction on HDG activity on A/I and T/I base
FT pairs."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 120
FT /note="N->E: Strong decrease in UDG, HDG and XDG
FT activities."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 120
FT /note="N->Q: Loss of XDG activity. Strong decrease in UDG
FT and HDG activities."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 190
FT /note="H->A: Loss of UDG, HDG and XDG activities."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 190
FT /note="H->N,S: Strong decrease in UDG, HDG and XDG
FT activities."
FT /evidence="ECO:0000269|PubMed:24838246"
FT MUTAGEN 195
FT /note="N->A,D,E,Q: Retains much of its activity."
FT /evidence="ECO:0000269|PubMed:24838246"
FT HELIX 3..10
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 17..25
FT /evidence="ECO:0007829|PDB:2D3Y"
FT TURN 26..29
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:2D3Y"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:2D3Y"
FT TURN 62..64
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 65..68
FT /evidence="ECO:0007829|PDB:2D3Y"
FT TURN 71..74
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 76..87
FT /evidence="ECO:0007829|PDB:2D3Y"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:2DP6"
FT STRAND 104..112
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 118..120
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 124..139
FT /evidence="ECO:0007829|PDB:2D3Y"
FT STRAND 146..151
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 152..162
FT /evidence="ECO:0007829|PDB:2D3Y"
FT TURN 166..168
FT /evidence="ECO:0007829|PDB:2D3Y"
FT STRAND 176..179
FT /evidence="ECO:0007829|PDB:2D3Y"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:2D3Y"
FT STRAND 183..188
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 193..198
FT /evidence="ECO:0007829|PDB:2D3Y"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:2D3Y"
FT HELIX 203..216
FT /evidence="ECO:0007829|PDB:2D3Y"
SQ SEQUENCE 219 AA; 24286 MW; 10EE764537318207 CRC64;
MDREAFVQTL TACRLCPRLV AWREEVVGRK RAFRGEPYWA RPVPGFGDPE ARILLFGLAP
GAHGSNRTGR PFTGDASGAF LYPLLHEAGL SSKPESLPGD DLRLYGVYLT AAVRCAPPKN
KPTPEELRAC ARWTEVELGL LPEVRVYVAL GRIALEALLA HFGLRKSAHP FRHGAHYPLP
GGRHLLASYH VSRQNTQTGR LTREMFLEVL MEAKRLAGL
