JBP1_TRYB2
ID JBP1_TRYB2 Reviewed; 839 AA.
AC P86938; Q382H3; Q9U6M3;
DT 27-JUL-2011, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 1.
DT 03-AUG-2022, entry version 42.
DE RecName: Full=Thymine dioxygenase JBP1;
DE EC=1.14.11.6 {ECO:0000305|PubMed:15694344, ECO:0000305|PubMed:17389644};
DE AltName: Full=J-binding protein 1;
DE AltName: Full=Thymidine hydroxylase JBP1;
GN Name=JBP1; ORFNames=Tb11.01.5220;
OS Trypanosoma brucei brucei (strain 927/4 GUTat10.1).
OC Eukaryota; Discoba; Euglenozoa; Kinetoplastea; Metakinetoplastina;
OC Trypanosomatida; Trypanosomatidae; Trypanosoma.
OX NCBI_TaxID=185431;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=927/4 GUTat10.1 {ECO:0000312|Proteomes:UP000008524};
RX PubMed=16020726; DOI=10.1126/science.1112642;
RA Berriman M., Ghedin E., Hertz-Fowler C., Blandin G., Renauld H.,
RA Bartholomeu D.C., Lennard N.J., Caler E., Hamlin N.E., Haas B., Bohme U.,
RA Hannick L., Aslett M.A., Shallom J., Marcello L., Hou L., Wickstead B.,
RA Alsmark U.C.M., Arrowsmith C., Atkin R.J., Barron A.J., Bringaud F.,
RA Brooks K., Carrington M., Cherevach I., Chillingworth T.J., Churcher C.,
RA Clark L.N., Corton C.H., Cronin A., Davies R.M., Doggett J., Djikeng A.,
RA Feldblyum T., Field M.C., Fraser A., Goodhead I., Hance Z., Harper D.,
RA Harris B.R., Hauser H., Hostetler J., Ivens A., Jagels K., Johnson D.,
RA Johnson J., Jones K., Kerhornou A.X., Koo H., Larke N., Landfear S.,
RA Larkin C., Leech V., Line A., Lord A., Macleod A., Mooney P.J., Moule S.,
RA Martin D.M., Morgan G.W., Mungall K., Norbertczak H., Ormond D., Pai G.,
RA Peacock C.S., Peterson J., Quail M.A., Rabbinowitsch E., Rajandream M.A.,
RA Reitter C., Salzberg S.L., Sanders M., Schobel S., Sharp S., Simmonds M.,
RA Simpson A.J., Tallon L., Turner C.M., Tait A., Tivey A.R., Van Aken S.,
RA Walker D., Wanless D., Wang S., White B., White O., Whitehead S.,
RA Woodward J., Wortman J., Adams M.D., Embley T.M., Gull K., Ullu E.,
RA Barry J.D., Fairlamb A.H., Opperdoes F., Barrell B.G., Donelson J.E.,
RA Hall N., Fraser C.M., Melville S.E., El-Sayed N.M.A.;
RT "The genome of the African trypanosome Trypanosoma brucei.";
RL Science 309:416-422(2005).
RN [2]
RP DISRUPTION PHENOTYPE.
RX PubMed=12366829; DOI=10.1046/j.1365-2958.2002.03144.x;
RA Cross M., Kieft R., Sabatini R., Dirks-Mulder A., Chaves I., Borst P.;
RT "J-binding protein increases the level and retention of the unusual base J
RT in trypanosome DNA.";
RL Mol. Microbiol. 46:37-47(2002).
RN [3]
RP FUNCTION, SUBCELLULAR LOCATION, DOMAIN, AND DEVELOPMENTAL STAGE.
RC STRAIN=29-13, and 427;
RX PubMed=15694344; DOI=10.1016/j.molcel.2004.12.022;
RA DiPaolo C., Kieft R., Cross M., Sabatini R.;
RT "Regulation of trypanosome DNA glycosylation by a SWI2/SNF2-like protein.";
RL Mol. Cell 17:441-451(2005).
RN [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND MUTAGENESIS OF HIS-213 AND ASP-215.
RX PubMed=17389644; DOI=10.1093/nar/gkm049;
RA Yu Z., Genest P.-A., ter Riet B., Sweeney K., DiPaolo C., Kieft R.,
RA Christodoulou E., Perrakis A., Simmons J.M., Hausinger R.P.,
RA van Luenen H.G.A.M., Rigden D.J., Sabatini R., Borst P.;
RT "The protein that binds to DNA base J in trypanosomatids has features of a
RT thymidine hydroxylase.";
RL Nucleic Acids Res. 35:2107-2115(2007).
RN [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=29-13, and 427;
RX PubMed=19136460; DOI=10.1093/nar/gkn1067;
RA Cliffe L.J., Kieft R., Southern T., Birkeland S.R., Marshall M.,
RA Sweeney K., Sabatini R.;
RT "JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J
RT biosynthesis in genomic DNA of African trypanosomes.";
RL Nucleic Acids Res. 37:1452-1462(2009).
CC -!- FUNCTION: Dioxygenase that catalyzes the first step of DNA base J
CC (beta-d-glucosyl-HOMedU) biosynthesis by converting thymine to 5-
CC hydroxymethyluracil (HOMedU). DNA base J is a hypermodified thymidine
CC residue found in the genome of kinetoplastid parasites, which is
CC localized primarily to repetitive DNA, namely the telomeres, and is
CC implicated in the regulation of antigenic variation. Also specifically
CC binds to base J-containing DNA (J-DNA). Involved in propagation and
CC maintenance of DNA base J synthesis initiated by JBP2 by specifically
CC binding already synthesized DNA base J and propagating J synthesis.
CC Thymine dioxygenase activity and J-DNA-binding are independent
CC functions. {ECO:0000269|PubMed:15694344, ECO:0000269|PubMed:17389644}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + O2 + thymine = 5-hydroxymethyluracil + CO2 +
CC succinate; Xref=Rhea:RHEA:10316, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16964,
CC ChEBI:CHEBI:17821, ChEBI:CHEBI:30031; EC=1.14.11.6;
CC Evidence={ECO:0000305|PubMed:15694344, ECO:0000305|PubMed:17389644};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q6N021};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q6N021};
CC -!- SUBUNIT: Monomer. Binds to DNA as a monomer (By similarity).
CC {ECO:0000250|UniProtKB:Q9U6M1}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15694344,
CC ECO:0000269|PubMed:17389644}.
CC -!- DEVELOPMENTAL STAGE: Expressed in bloodstream form and significantly
CC less in procyclic form. {ECO:0000269|PubMed:15694344}.
CC -!- DOMAIN: The DNA-binding JBP1 domain (DB-JBP1) is necessary and
CC sufficient for binding to J-DNA. {ECO:0000250|UniProtKB:Q9U6M1}.
CC -!- DISRUPTION PHENOTYPE: Does not affect growth, gene expression or the
CC stability of some repetitive DNA sequences. The genome contains only
CC about 5% of the wild-type level of J in their DNA. Cells lacking both
CC JBP1 and JBP2 show a complete absence of base J.
CC {ECO:0000269|PubMed:12366829, ECO:0000269|PubMed:19136460}.
CC -!- SIMILARITY: Belongs to the TET family. JBP1 subfamily. {ECO:0000305}.
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DR EMBL; CH464491; EAN80308.1; -; Genomic_DNA.
DR RefSeq; XP_829420.1; XM_824327.1.
DR AlphaFoldDB; P86938; -.
DR SMR; P86938; -.
DR PaxDb; P86938; -.
DR GeneID; 3665128; -.
DR KEGG; tbr:Tb11.01.5220; -.
DR VEuPathDB; TriTrypDB:Tb927.11.13640; -.
DR eggNOG; ENOG502RTYX; Eukaryota.
DR InParanoid; P86938; -.
DR Proteomes; UP000008524; Chromosome 11 Scaffold 1.
DR GO; GO:0005634; C:nucleus; IDA:GeneDB.
DR GO; GO:0008094; F:ATP-dependent activity, acting on DNA; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IDA:GeneDB.
DR GO; GO:0008198; F:ferrous iron binding; IMP:GeneDB.
DR GO; GO:0050341; F:thymine dioxygenase activity; ISO:GeneDB.
DR GO; GO:0070580; P:base J metabolic process; IMP:GeneDB.
DR GO; GO:0006283; P:transcription-coupled nucleotide-excision repair; IBA:GO_Central.
DR Gene3D; 1.20.120.1440; -; 1.
DR InterPro; IPR024779; 2OGFeDO_noxygenase_dom.
DR InterPro; IPR041241; DB_JBP1.
DR InterPro; IPR043111; DB_JBP1_sf.
DR Pfam; PF18526; DB_JBP1; 1.
DR Pfam; PF12851; Tet_JBP; 1.
PE 1: Evidence at protein level;
KW Dioxygenase; DNA-binding; Iron; Metal-binding; Nucleus; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..839
FT /note="Thymine dioxygenase JBP1"
FT /id="PRO_0000377555"
FT REGION 86..288
FT /note="Thymine dioxygenase"
FT /evidence="ECO:0000250|UniProtKB:Q9U6M1"
FT REGION 415..583
FT /note="DNA-binding JBP1 domain"
FT /evidence="ECO:0000250|UniProtKB:Q9U6M1"
FT BINDING 213
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17389644"
FT BINDING 215
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:17389644"
FT BINDING 263
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q6N021"
FT BINDING 279
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q6N021"
FT SITE 548
FT /note="Involved in J base recognition, conferring
FT specificity towards J-DNA"
FT /evidence="ECO:0000250|UniProtKB:Q9U6M1"
FT MUTAGEN 213
FT /note="H->S: Impairs DNA base J biosynthesis."
FT /evidence="ECO:0000269|PubMed:17389644"
FT MUTAGEN 215
FT /note="D->S: Impairs DNA base J biosynthesis."
FT /evidence="ECO:0000269|PubMed:17389644"
SQ SEQUENCE 839 AA; 95251 MW; B3BEECD851CC0FE7 CRC64;
MRRQVKKVLR EKADDSMKPG WDVYQPSNDV VYAFNHYMQG SQIDAEAREK AEKAFQEAVK
KHPFHNNADH TVDFHGTTVF RNAKGKVCGV LIPKALPSFA TSMAADVLEC AVARTSLRSA
LFGGVSPNSG IAGYFDYRGT PVELKCRKTS FTYEHTKEWR SVFPMIDYTS AIYKAALPDH
WKAQDAAVPD VVRIHGSPFS TLTVNERFRT ASHTDNGDFD NGYGVLAVLK GEYSGLSLAL
DDYGVCFNMQ PTDVLLFDTH LFHSNTELEA KEANATWNRL SCVFYYRAAL GEQPCVEEYR
RRLKKAKEEK STSLSFNHIE QKDNGENTNK PAPVYPVSLT PFSCAASAWA LRGCAAAMLT
RLHGLVRENA SLMTELFGEP VEVADGLPRR APEEIIPVHK HTNVQMHYLG GFSEKGDILN
EAMNKRHYLD KENLQKMFGE EFVNIWTQSR THWLQLVKKE WEHQKETNPT RTRFSWNNTS
AMNFAFFDLC DVAKQLMCGA FGDREVNKKE EQSFWGMFAA HLDNACINEI GMLQGSMGMH
KLNVKLKDYN FGGTRYLKDM PPEEQERRRR RRLEIEQARR RAPICDSESG DWLRNEAFDY
QTEDVAVNYE REQWITPENN AKRFGFPERG VYGAEGAATG TISVLIVLPK PTNHRQKTCE
LPTSREADRI MKNPAAQRLL CAKPCNIGLS TSSNKSRTVL CGNIRIDKVF DGGSVGGKMY
DFVIMRHLLA ATTGEREPLE CLVRWTSLAR YCTFVVEVDL LDRHHYILKS EIGEEYSAVS
EICFSALYSA TYARDKVNLR TTPCLLSFID KSGNMLESRF KFNGSPLNTV AFVVRRREK
