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Protein

Methylcytosine dioxygenase tet3

Gene

tet3

Organism
Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and plays a key role in epigenetic chromatin reprogramming during embryonic development. Conversion of 5mC into 5hmC probably constitutes the first step in cytosine demethylation. Selectively binds to the promoter region of target genes and contributes to regulate the expression of numerous developmental genes, including pax6, rax, sox9 and six3. May also contribute to the regulation of target genes in ways that do not require its enzyme activity.1 Publication

Catalytic activityi

DNA 5-methylcytosine + 2-oxoglutarate + O2 = DNA 5-hydroxymethylcytosine + succinate + CO2.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity
  • Zn2+By similarityNote: The zinc ions have a structural role.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi957Zinc 1By similarity1
Metal bindingi959Zinc 1By similarity1
Metal bindingi1017Zinc 2By similarity1
Metal bindingi1043Zinc 1; via pros nitrogenBy similarity1
Metal bindingi1045Zinc 1By similarity1
Binding sitei10852-oxoglutarateBy similarity1
Metal bindingi1095Zinc 2By similarity1
Metal bindingi1097Zinc 2By similarity1
Metal bindingi1113Zinc 3By similarity1
Metal bindingi1122Zinc 3By similarity1
Metal bindingi1182Zinc 3By similarity1
Binding sitei11982-oxoglutarateBy similarity1
Metal bindingi1204Zinc 2; via tele nitrogenBy similarity1
Metal bindingi1206Iron; catalytic1 Publication1
Metal bindingi1208Iron; catalytic1 Publication1
Binding sitei12402-oxoglutarateBy similarity1
Metal bindingi1780Iron; catalyticBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri58 – 99CXXC-typePROSITE-ProRule annotationAdd BLAST42

GO - Molecular functioni

Keywordsi

Molecular functionChromatin regulator, Developmental protein, Dioxygenase, DNA-binding, Oxidoreductase
LigandIron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Methylcytosine dioxygenase tet3 (EC:1.14.11.n21 Publication)
Gene namesi
Name:tet3Imported
OrganismiXenopus tropicalis (Western clawed frog) (Silurana tropicalis)Imported
Taxonomic identifieri8364 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusSilurana
Proteomesi
  • UP000008143 Componenti: Unassembled WGS sequence

Organism-specific databases

XenbaseiXB-GENE-877084. tet3.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi90H → A: Abolishes binding to target DNA. No effect on nuclear location and on enzyme activity. 1 Publication1
Mutagenesisi1206 – 1208Missing : Abolishes enzyme activity. 1 Publication3

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004423171 – 1901Methylcytosine dioxygenase tet3Add BLAST1901

Proteomic databases

PaxDbiA0JP82.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4HP1X-ray2.25C58-111[»]
4HP3X-ray2.05C58-111[»]
ProteinModelPortaliA0JP82.
SMRiA0JP82.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1795 – 17972-oxoglutarate bindingBy similarity3

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi40 – 45Poly-GlySequence analysis6
Compositional biasi763 – 766Poly-SerSequence analysis4

Domaini

Binds target DNA that contains at least one unmethylated cytosine via the CXXC-type zinc-finger domain.1 Publication

Sequence similaritiesi

Belongs to the TET family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri58 – 99CXXC-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG410IE22. Eukaryota.
ENOG410XPWW. LUCA.
HOGENOMiHOG000154550.
HOVERGENiHBG079550.

Family and domain databases

InterProiView protein in InterPro
IPR024779. 2OGFeDO_noxygenase_dom.
IPR002857. Znf_CXXC.
PfamiView protein in Pfam
PF12851. Tet_JBP. 1 hit.
PF02008. zf-CXXC. 1 hit.
SMARTiView protein in SMART
SM01333. Tet_JBP. 1 hit.
PROSITEiView protein in PROSITE
PS51058. ZF_CXXC. 1 hit.

Sequencei

Sequence statusi: Complete.

A0JP82-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDTQPAPVPH VLPQDVYEFP DDQESLGRLR VSEMPAELNG GGGGGSAAAF
60 70 80 90 100
AMELPEQSNK KRKRCGVCVP CLRKEPCGAC YNCVNRSTSH QICKMRKCEQ
110 120 130 140 150
LKKKRVVPMK GVENCSESIL VDGPKTDQME AGPVNHVQEG RLKQECDSTL
160 170 180 190 200
PSKGCEDLAN QLLMEANSWL SNTAAPQDPC NKLNWDKPTI PNHAANNNSN
210 220 230 240 250
LEDAKNLVAF SAVAEAMSTY GMPASGTPSS VSLQLYEKFN YETNRDNSGH
260 270 280 290 300
LEGNAPSCPE DLNTLKAALA LAKHGVKPPN CNCDGPECPD YLEWLENKIK
310 320 330 340 350
STVKGSQESP FPNLGQVSKE LVQKQYPKEQ VLNLENKNST CPSGNLPFSQ
360 370 380 390 400
NALSLAKEKN ISLQTAIAIE ALTQLSSALP QTNNECPNAP SQPLINPHDQ
410 420 430 440 450
LTHFPSAKGN QLPMLPVARN ELFQNQQSQL YTGKNALPVP QSPRQTSWEQ
460 470 480 490 500
NKKSSYQEGQ YIPENLSHSS SVLPSDASTP QKPEFLQQWV QNADLLKSPS
510 520 530 540 550
DPMTGLKQLL GNTDEYIKSV FKGPEALPNK KNVKPKHTIK SIKKESTEFL
560 570 580 590 600
KMSPDQQLSQ LLQTNEFHRN TQAALQQHLH HKRNLFVDPN AMEACTQEQQ
610 620 630 640 650
NWWVPSSQQA PVSKTTEKPV KERKKRRQSP SQKQVEPKPK PQRKQVQIKK
660 670 680 690 700
PKVKEGSAVF MPVSQISLDT FRRVEKEENQ GKEMDAENSL PNNVQTELLE
710 720 730 740 750
SQSLQLTGSQ ANPDDRKTVN TQEMCNENQS NIGKANNFAL CVNRANSFVA
760 770 780 790 800
KDQCPTPSTH DTSSSSGQGD SANQHTNVSD VPGQNDLSCL DDKLEDLIRQ
810 820 830 840 850
FEAEFGEDFS LPGSAVPSQN GEGPPKQTPS GDPQFKLPFP SQLLPPENST
860 870 880 890 900
KPATHSNPAL SNNPVSREVS NNLDSLFSSK SPKQIKIESS GAITVVSTTC
910 920 930 940 950
FYSEENQHLD GTPTKSDLPF NPTLSGFLDS PLKYLTSPTK SLIDTPAKKA
960 970 980 990 1000
QAEFPTCDCV EQINEKDEGP YYTHLGSGPT VASIRELMEE RFGQKGDAIR
1010 1020 1030 1040 1050
IEKVIYTGKE GKSSRGCPIA KWVIRRQSED EKLMCLVRQR AGHHCENAVI
1060 1070 1080 1090 1100
IILIMAWEGI PRSLGDSLYN DITETITKYG NPTSRRCGLN DDRTCACQGK
1110 1120 1130 1140 1150
DPNTCGASFS FGCSWSMYFN GCKYARSKTP RKFRLIGENP KEEDGLKDNF
1160 1170 1180 1190 1200
QNLATKVAPV YKMLAPQAYQ NQVNNEDIAI DCRLGLKEGR PFSGVTACMD
1210 1220 1230 1240 1250
FCAHAHKDQH NLYNGCTVVC TLTKEDNRMI GRVAEDEQLH VLPLYKVSTT
1260 1270 1280 1290 1300
DEFGSEEGQL EKIKKGGIHV LSSFPREVRK LSEPAKSCRQ RQLEAKKAAA
1310 1320 1330 1340 1350
EKKKLQKEKL VSPDKTKQEP SDKKTCQQNP GVPQQQTKPC IKVEPSNHYN
1360 1370 1380 1390 1400
NFKYNGNGVV ESYSVLGSCR PSDPYSMNSV YSYHSFYAQP NLPSVNGFHS
1410 1420 1430 1440 1450
KYALPPFGFY GFPNNPVVPN QFMNYGTSDA RNSGWMNNCF EKKPELQSLA
1460 1470 1480 1490 1500
DGMNQSYGSE LSEQSFRRSS EVPHHYSLQN PSSQKSVNVP HRTTPAPVET
1510 1520 1530 1540 1550
TPYSNLPCYN KVIKKEPGSD PLVDSFQRAN SVHSHSPGVN HSLQASDLPI
1560 1570 1580 1590 1600
SYKANGALSS SGRTNAESPC SMFMPNDKNG LEKKDYFGVH SNAPGLKDKQ
1610 1620 1630 1640 1650
WPPYGTDVSV RQHDSLDSQS PGKVWSSCKL SDSSAALPSS ASTQDKNWNG
1660 1670 1680 1690 1700
RQVSLNQGMK ESALFQEKLW NSVAASDRCS ATPSDRSSIT PCSELQDKNW
1710 1720 1730 1740 1750
GSFPNPTVNS LKTDSSQNHW DPYSLDDNMD DGQSKSVKEE DDEEIWSDSE
1760 1770 1780 1790 1800
HNFLDENIGG VAVAPGHGSI LIECARRELH ATTPLKKPNR CHPTRISLVF
1810 1820 1830 1840 1850
YQHKNLNQPN HGLALWEAKM KQLAERARAR EEEAAKLGIK QEVKSLGKKR
1860 1870 1880 1890 1900
KWGGAATTET PPVEKKDYTP TRQAATILTD SATTSFSYAY TKVTGPYSRF

I
Length:1,901
Mass (Da):210,426
Last modified:December 12, 2006 - v1
Checksum:iC74D3B847C920212
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC127289 mRNA. Translation: AAI27290.1.
RefSeqiNP_001090656.1. NM_001097187.1.
UniGeneiStr.53063.

Genome annotation databases

GeneIDi100036628.

Similar proteinsi

Entry informationi

Entry nameiTET3_XENTR
AccessioniPrimary (citable) accession number: A0JP82
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2017
Last sequence update: December 12, 2006
Last modified: November 22, 2017
This is version 61 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families