ID   TET3_XENTR              Reviewed;        1901 AA.
AC   A0JP82;
DT   22-NOV-2017, integrated into UniProtKB/Swiss-Prot.
DT   12-DEC-2006, sequence version 1.
DT   27-MAR-2024, entry version 89.
DE   RecName: Full=Methylcytosine dioxygenase tet3;
DE            EC=1.14.11.80 {ECO:0000269|PubMed:23217707};
GN   Name=tet3 {ECO:0000312|Xenbase:XB-GENE-877084};
OS   Xenopus tropicalis (Western clawed frog) (Silurana tropicalis).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC   Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana.
OX   NCBI_TaxID=8364 {ECO:0000312|EMBL:AAI27290.1};
RN   [1] {ECO:0000312|EMBL:AAI27290.1}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Testis {ECO:0000312|EMBL:AAI27290.1};
RG   NIH - Xenopus Gene Collection (XGC) project;
RL   Submitted (NOV-2006) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0007744|PDB:4HP1, ECO:0007744|PDB:4HP3}
RP   X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 58-111 IN COMPLEX WITH ZINC AND
RP   TARGET DNA, FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, DOMAIN,
RP   MUTAGENESIS OF HIS-90 AND 1206-HIS--ASP-1208, AND COFACTOR.
RX   PubMed=23217707; DOI=10.1016/j.cell.2012.11.014;
RA   Xu Y., Xu C., Kato A., Tempel W., Abreu J.G., Bian C., Hu Y., Hu D.,
RA   Zhao B., Cerovina T., Diao J., Wu F., He H.H., Cui Q., Clark E., Ma C.,
RA   Barbara A., Veenstra G.J.C., Xu G., Kaiser U.B., Liu X.S., Sugrue S.P.,
RA   He X., Min J., Kato Y., Shi Y.G.;
RT   "Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes
RT   for Xenopus eye and neural development.";
RL   Cell 151:1200-1213(2012).
RN   [3]
RP   MUTAGENESIS OF HIS-90.
RX   PubMed=29276034; DOI=10.1016/j.str.2017.11.022;
RA   Xu C., Liu K., Lei M., Yang A., Li Y., Hughes T.R., Min J.;
RT   "DNA Sequence Recognition of Human CXXC Domains and Their Structural
RT   Determinants.";
RL   Structure 26:85-95.e3(2018).
CC   -!- FUNCTION: Dioxygenase that catalyzes the conversion of the modified
CC       genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC)
CC       and plays a key role in epigenetic chromatin reprogramming during
CC       embryonic development. Conversion of 5mC into 5hmC probably constitutes
CC       the first step in cytosine demethylation. Selectively binds to the
CC       promoter region of target genes and contributes to regulate the
CC       expression of numerous developmental genes, including pax6, rax, sox9
CC       and six3. May also contribute to the regulation of target genes in ways
CC       that do not require its enzyme activity. {ECO:0000269|PubMed:23217707}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-oxoglutarate + a 5-methyl-2'-deoxycytidine in DNA + O2 = a
CC         5-hydroxymethyl-2'-deoxycytidine in DNA + CO2 + succinate;
CC         Xref=Rhea:RHEA:52636, Rhea:RHEA-COMP:11370, Rhea:RHEA-COMP:13315,
CC         ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC         ChEBI:CHEBI:30031, ChEBI:CHEBI:85454, ChEBI:CHEBI:136731;
CC         EC=1.14.11.80; Evidence={ECO:0000269|PubMed:23217707};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-oxoglutarate + a 5-hydroxymethyl-2'-deoxycytidine in DNA +
CC         O2 = a 5-formyl-2'-deoxycytidine in DNA + CO2 + H2O + succinate;
CC         Xref=Rhea:RHEA:53828, Rhea:RHEA-COMP:13315, Rhea:RHEA-COMP:13656,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:16810, ChEBI:CHEBI:30031, ChEBI:CHEBI:136731,
CC         ChEBI:CHEBI:137731; EC=1.14.11.80;
CC         Evidence={ECO:0000250|UniProtKB:Q6N021};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2-oxoglutarate + a 5-formyl-2'-deoxycytidine in DNA + O2 = a
CC         5-carboxyl-2'-deoxycytidine in DNA + CO2 + H(+) + succinate;
CC         Xref=Rhea:RHEA:53832, Rhea:RHEA-COMP:13656, Rhea:RHEA-COMP:13657,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC         ChEBI:CHEBI:16810, ChEBI:CHEBI:30031, ChEBI:CHEBI:137731,
CC         ChEBI:CHEBI:137732; EC=1.14.11.80;
CC         Evidence={ECO:0000250|UniProtKB:Q6N021};
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   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000250|UniProtKB:Q6N021};
CC       Note=The zinc ions have a structural role.
CC       {ECO:0000250|UniProtKB:Q6N021};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:23217707}. Chromosome
CC       {ECO:0000269|PubMed:23217707}. Note=Detected on chromatin, where it
CC       binds to target gene promoters. {ECO:0000269|PubMed:23217707}.
CC   -!- DOMAIN: Binds target DNA that contains at least one unmethylated
CC       cytosine via the CXXC-type zinc-finger domain.
CC       {ECO:0000269|PubMed:23217707}.
CC   -!- SIMILARITY: Belongs to the TET family. {ECO:0000305}.
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DR   EMBL; BC127289; AAI27290.1; -; mRNA.
DR   RefSeq; NP_001090656.1; NM_001097187.1.
DR   PDB; 4HP1; X-ray; 2.25 A; C=58-111.
DR   PDB; 4HP3; X-ray; 2.05 A; C=58-111.
DR   PDBsum; 4HP1; -.
DR   PDBsum; 4HP3; -.
DR   AlphaFoldDB; A0JP82; -.
DR   SMR; A0JP82; -.
DR   STRING; 8364.ENSXETP00000013965; -.
DR   PaxDb; 8364-ENSXETP00000054061; -.
DR   GeneID; 100036628; -.
DR   KEGG; xtr:100036628; -.
DR   AGR; Xenbase:XB-GENE-877084; -.
DR   CTD; 200424; -.
DR   Xenbase; XB-GENE-877084; tet3.
DR   eggNOG; ENOG502QURD; Eukaryota.
DR   InParanoid; A0JP82; -.
DR   OrthoDB; 5406604at2759; -.
DR   Proteomes; UP000008143; Chromosome 3.
DR   GO; GO:0005694; C:chromosome; IEA:UniProtKB-SubCell.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0008327; F:methyl-CpG binding; ISS:UniProtKB.
DR   GO; GO:0070579; F:methylcytosine dioxygenase activity; IEA:InterPro.
DR   GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR   GO; GO:0006211; P:5-methylcytosine catabolic process; IEA:InterPro.
DR   GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR   GO; GO:0080111; P:DNA demethylation; IEA:InterPro.
DR   GO; GO:0010468; P:regulation of gene expression; IEA:UniProt.
DR   CDD; cd18897; TET3; 1.
DR   InterPro; IPR024779; 2OGFeDO_JBP1/TET_oxygenase_dom.
DR   InterPro; IPR040175; TET1/2/3.
DR   InterPro; IPR046942; TET_oxygenase.
DR   InterPro; IPR002857; Znf_CXXC.
DR   PANTHER; PTHR23358:SF2; METHYLCYTOSINE DIOXYGENASE TET1; 1.
DR   PANTHER; PTHR23358; UNCHARACTERIZED; 1.
DR   Pfam; PF12851; Tet_JBP; 1.
DR   Pfam; PF02008; zf-CXXC; 1.
DR   SMART; SM01333; Tet_JBP; 1.
DR   PROSITE; PS51058; ZF_CXXC; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Chromatin regulator; Chromosome; Developmental protein;
KW   Dioxygenase; DNA-binding; Iron; Metal-binding; Nucleus; Oxidoreductase;
KW   Reference proteome; Zinc; Zinc-finger.
FT   CHAIN           1..1901
FT                   /note="Methylcytosine dioxygenase tet3"
FT                   /id="PRO_0000442317"
FT   ZN_FING         58..99
FT                   /note="CXXC-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   REGION          434..455
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          602..658
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          751..787
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          808..867
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1282..1338
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1457..1501
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1591..1624
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1680..1745
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        616..651
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        751..784
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        813..827
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        843..867
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1282..1322
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1323..1338
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1680..1723
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1724..1742
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         65
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         68
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         71
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         77
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         80
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         83
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         93
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         98
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00509"
FT   BINDING         957
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         959
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1017
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1043
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1045
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1085
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1095
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1097
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="4"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1113
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1122
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1182
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="3"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1198
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1204
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1206
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000305|PubMed:23217707"
FT   BINDING         1208
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000305|PubMed:23217707"
FT   BINDING         1240
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1780
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   BINDING         1795..1797
FT                   /ligand="2-oxoglutarate"
FT                   /ligand_id="ChEBI:CHEBI:16810"
FT                   /evidence="ECO:0000250|UniProtKB:Q6N021"
FT   MUTAGEN         90
FT                   /note="H->A: Abolishes binding to target DNA. No effect on
FT                   nuclear location and on enzyme activity."
FT                   /evidence="ECO:0000269|PubMed:23217707"
FT   MUTAGEN         90
FT                   /note="H->R: Increased binding affinity for CpT dsDNA."
FT                   /evidence="ECO:0000269|PubMed:29276034"
FT   MUTAGEN         1206..1208
FT                   /note="Missing: Abolishes enzyme activity."
FT                   /evidence="ECO:0000269|PubMed:23217707"
FT   STRAND          66..68
FT                   /evidence="ECO:0007829|PDB:4HP3"
FT   HELIX           69..72
FT                   /evidence="ECO:0007829|PDB:4HP3"
FT   STRAND          78..80
FT                   /evidence="ECO:0007829|PDB:4HP3"
FT   HELIX           81..84
FT                   /evidence="ECO:0007829|PDB:4HP3"
FT   HELIX           86..89
FT                   /evidence="ECO:0007829|PDB:4HP3"
FT   TURN            94..96
FT                   /evidence="ECO:0007829|PDB:4HP3"
FT   TURN            99..102
FT                   /evidence="ECO:0007829|PDB:4HP3"
SQ   SEQUENCE   1901 AA;  210426 MW;  C74D3B847C920212 CRC64;
     MDTQPAPVPH VLPQDVYEFP DDQESLGRLR VSEMPAELNG GGGGGSAAAF AMELPEQSNK
     KRKRCGVCVP CLRKEPCGAC YNCVNRSTSH QICKMRKCEQ LKKKRVVPMK GVENCSESIL
     VDGPKTDQME AGPVNHVQEG RLKQECDSTL PSKGCEDLAN QLLMEANSWL SNTAAPQDPC
     NKLNWDKPTI PNHAANNNSN LEDAKNLVAF SAVAEAMSTY GMPASGTPSS VSLQLYEKFN
     YETNRDNSGH LEGNAPSCPE DLNTLKAALA LAKHGVKPPN CNCDGPECPD YLEWLENKIK
     STVKGSQESP FPNLGQVSKE LVQKQYPKEQ VLNLENKNST CPSGNLPFSQ NALSLAKEKN
     ISLQTAIAIE ALTQLSSALP QTNNECPNAP SQPLINPHDQ LTHFPSAKGN QLPMLPVARN
     ELFQNQQSQL YTGKNALPVP QSPRQTSWEQ NKKSSYQEGQ YIPENLSHSS SVLPSDASTP
     QKPEFLQQWV QNADLLKSPS DPMTGLKQLL GNTDEYIKSV FKGPEALPNK KNVKPKHTIK
     SIKKESTEFL KMSPDQQLSQ LLQTNEFHRN TQAALQQHLH HKRNLFVDPN AMEACTQEQQ
     NWWVPSSQQA PVSKTTEKPV KERKKRRQSP SQKQVEPKPK PQRKQVQIKK PKVKEGSAVF
     MPVSQISLDT FRRVEKEENQ GKEMDAENSL PNNVQTELLE SQSLQLTGSQ ANPDDRKTVN
     TQEMCNENQS NIGKANNFAL CVNRANSFVA KDQCPTPSTH DTSSSSGQGD SANQHTNVSD
     VPGQNDLSCL DDKLEDLIRQ FEAEFGEDFS LPGSAVPSQN GEGPPKQTPS GDPQFKLPFP
     SQLLPPENST KPATHSNPAL SNNPVSREVS NNLDSLFSSK SPKQIKIESS GAITVVSTTC
     FYSEENQHLD GTPTKSDLPF NPTLSGFLDS PLKYLTSPTK SLIDTPAKKA QAEFPTCDCV
     EQINEKDEGP YYTHLGSGPT VASIRELMEE RFGQKGDAIR IEKVIYTGKE GKSSRGCPIA
     KWVIRRQSED EKLMCLVRQR AGHHCENAVI IILIMAWEGI PRSLGDSLYN DITETITKYG
     NPTSRRCGLN DDRTCACQGK DPNTCGASFS FGCSWSMYFN GCKYARSKTP RKFRLIGENP
     KEEDGLKDNF QNLATKVAPV YKMLAPQAYQ NQVNNEDIAI DCRLGLKEGR PFSGVTACMD
     FCAHAHKDQH NLYNGCTVVC TLTKEDNRMI GRVAEDEQLH VLPLYKVSTT DEFGSEEGQL
     EKIKKGGIHV LSSFPREVRK LSEPAKSCRQ RQLEAKKAAA EKKKLQKEKL VSPDKTKQEP
     SDKKTCQQNP GVPQQQTKPC IKVEPSNHYN NFKYNGNGVV ESYSVLGSCR PSDPYSMNSV
     YSYHSFYAQP NLPSVNGFHS KYALPPFGFY GFPNNPVVPN QFMNYGTSDA RNSGWMNNCF
     EKKPELQSLA DGMNQSYGSE LSEQSFRRSS EVPHHYSLQN PSSQKSVNVP HRTTPAPVET
     TPYSNLPCYN KVIKKEPGSD PLVDSFQRAN SVHSHSPGVN HSLQASDLPI SYKANGALSS
     SGRTNAESPC SMFMPNDKNG LEKKDYFGVH SNAPGLKDKQ WPPYGTDVSV RQHDSLDSQS
     PGKVWSSCKL SDSSAALPSS ASTQDKNWNG RQVSLNQGMK ESALFQEKLW NSVAASDRCS
     ATPSDRSSIT PCSELQDKNW GSFPNPTVNS LKTDSSQNHW DPYSLDDNMD DGQSKSVKEE
     DDEEIWSDSE HNFLDENIGG VAVAPGHGSI LIECARRELH ATTPLKKPNR CHPTRISLVF
     YQHKNLNQPN HGLALWEAKM KQLAERARAR EEEAAKLGIK QEVKSLGKKR KWGGAATTET
     PPVEKKDYTP TRQAATILTD SATTSFSYAY TKVTGPYSRF I
//