UDGA_THEMA
ID UDGA_THEMA Reviewed; 192 AA.
AC Q9WYY1; G4FDW0;
DT 15-MAR-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Type-4 uracil-DNA glycosylase {ECO:0000305};
DE EC=3.2.2.27 {ECO:0000269|PubMed:10339434, ECO:0000269|PubMed:11267830};
DE AltName: Full=TMUDG {ECO:0000303|PubMed:10339434};
GN Name=tmung {ECO:0000303|PubMed:10339434};
GN OrderedLocusNames=TM_0511 {ECO:0000312|EMBL:AAD35596.1};
GN ORFNames=Tmari_0507 {ECO:0000312|EMBL:AGL49432.1};
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=23637642; DOI=10.1371/journal.pgen.1003485;
RA Latif H., Lerman J.A., Portnoy V.A., Tarasova Y., Nagarajan H.,
RA Schrimpe-Rutledge A.C., Smith R.D., Adkins J.N., Lee D.H., Qiu Y.,
RA Zengler K.;
RT "The genome organization of Thermotoga maritima reflects its lifestyle.";
RL PLoS Genet. 9:E1003485-E1003485(2013).
RN [3]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10339434; DOI=10.1016/s0960-9822(99)80237-1;
RA Sandigursky M., Franklin W.A.;
RT "Thermostable uracil-DNA glycosylase from Thermotoga maritima a member of a
RT novel class of DNA repair enzymes.";
RL Curr. Biol. 9:531-534(1999).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND DOMAIN.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=11267830; DOI=10.1016/s0921-8777(00)00083-5;
RA Sandigursky M., Faje A., Franklin W.A.;
RT "Characterization of the full length uracil-DNA glycosylase in the extreme
RT thermophile Thermotoga maritima.";
RL Mutat. Res. 485:187-195(2001).
RN [5] {ECO:0007744|PDB:1L9G}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
RP (4FE-4S).
RA Rajashankar K.R., Dodatko T., Thirumuruhan R.A., Sandigursky M.,
RA Bresnik A., Chance M.R., Franklin W.A., Almo S.C.;
RT "Crystal structure of uracil-DNA glycosylase from T. maritima.";
RL Submitted (MAR-2002) to the PDB data bank.
RN [6] {ECO:0007744|PDB:1VK2}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
RP (4FE-4S).
RG Joint center for structural genomics (JCSG);
RT "Crystal structure of uracil-DNA glycosylase (TM0511) from Thermotoga
RT maritima at 1.90 A resolution.";
RL Submitted (APR-2004) to the PDB data bank.
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 or U/A base pair as well as from single-stranded DNA.
CC {ECO:0000269|PubMed:10339434, ECO:0000269|PubMed:11267830}.
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:10339434, ECO:0000269|PubMed:11267830};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Temperature dependence:
CC Remains fully active after heating 15 minutes at 85 degrees Celsius.
CC Completely inactive after 15 minutes of pre-incubation at 95 degrees
CC Celsius. {ECO:0000269|PubMed:11267830};
CC -!- DOMAIN: The seven N-terminal amino acids are important for maintaining
CC proper protein folding and increase temperature stability of the
CC protein. {ECO:0000269|PubMed:11267830}.
CC -!- SIMILARITY: Belongs to the uracil-DNA glycosylase (UDG) superfamily.
CC Type 4 (UDGa) family. {ECO:0000305}.
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DR EMBL; AE000512; AAD35596.1; -; Genomic_DNA.
DR EMBL; CP004077; AGL49432.1; -; Genomic_DNA.
DR PIR; E72368; E72368.
DR RefSeq; NP_228321.1; NC_000853.1.
DR RefSeq; WP_004081422.1; NZ_CP011107.1.
DR PDB; 1L9G; X-ray; 2.50 A; A=1-192.
DR PDB; 1VK2; X-ray; 1.90 A; A=1-192.
DR PDBsum; 1L9G; -.
DR PDBsum; 1VK2; -.
DR AlphaFoldDB; Q9WYY1; -.
DR SMR; Q9WYY1; -.
DR STRING; 243274.THEMA_02120; -.
DR DNASU; 897555; -.
DR EnsemblBacteria; AAD35596; AAD35596; TM_0511.
DR EnsemblBacteria; AGL49432; AGL49432; Tmari_0507.
DR KEGG; tma:TM0511; -.
DR KEGG; tmm:Tmari_0507; -.
DR KEGG; tmw:THMA_0523; -.
DR PATRIC; fig|243274.17.peg.509; -.
DR eggNOG; COG1573; Bacteria.
DR InParanoid; Q9WYY1; -.
DR OMA; RPWLIAE; -.
DR OrthoDB; 1529383at2; -.
DR BRENDA; 3.2.2.27; 6331.
DR EvolutionaryTrace; Q9WYY1; -.
DR Proteomes; UP000008183; Chromosome.
DR Proteomes; UP000013901; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
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..192
FT /note="Type-4 uracil-DNA glycosylase"
FT /id="PRO_0000439181"
FT BINDING 18
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.5, ECO:0000269|Ref.6,
FT ECO:0007744|PDB:1L9G, ECO:0007744|PDB:1VK2"
FT BINDING 21
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.5, ECO:0000269|Ref.6,
FT ECO:0007744|PDB:1L9G, ECO:0007744|PDB:1VK2"
FT BINDING 45..47
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000250|UniProtKB:Q5SKC5"
FT BINDING 59
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000250|UniProtKB:Q5SKC5"
FT BINDING 85
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000250|UniProtKB:Q5SKC5"
FT BINDING 89
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.5, ECO:0000269|Ref.6,
FT ECO:0007744|PDB:1L9G, ECO:0007744|PDB:1VK2"
FT BINDING 105
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000269|Ref.5, ECO:0000269|Ref.6,
FT ECO:0007744|PDB:1L9G, ECO:0007744|PDB:1VK2"
FT BINDING 161
FT /ligand="uracil"
FT /ligand_id="ChEBI:CHEBI:17568"
FT /evidence="ECO:0000250|UniProtKB:Q5SKC5"
FT HELIX 4..17
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 22..25
FT /evidence="ECO:0007829|PDB:1VK2"
FT STRAND 40..46
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 50..55
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 62..73
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 78..80
FT /evidence="ECO:0007829|PDB:1VK2"
FT STRAND 81..86
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 99..116
FT /evidence="ECO:0007829|PDB:1VK2"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 126..131
FT /evidence="ECO:0007829|PDB:1VK2"
FT TURN 132..135
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:1VK2"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 162..167
FT /evidence="ECO:0007829|PDB:1VK2"
FT HELIX 171..185
FT /evidence="ECO:0007829|PDB:1VK2"
SQ SEQUENCE 192 AA; 21501 MW; 6978DE0721EF1BD1 CRC64;
MYTREELMEI VSERVKKCTA CPLHLNRTNV VVGEGNLDTR IVFVGEGPGE EEDKTGRPFV
GRAGMLLTEL LRESGIRRED VYICNVVKCR PPNNRTPTPE EQAACGHFLL AQIEIINPDV
IVALGATALS FFVDGKKVSI TKVRGNPIDW LGGKKVIPTF HPSYLLRNRS NELRRIVLED
IEKAKSFIKK EG
