Summary: Oxygenase domain of the 2OGFeDO superfamily
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Oxygenase domain of the 2OGFeDO superfamily Provide feedback
A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in various eukaryotes, bacteria and bacteriophages . Members of this family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids  and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (hmC)  or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) . Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various myeloid cancers . Fungal and algal versions of this family are linked to a predicted transposase and show lineage-specific expansions .
Iyer LM, Tahiliani M, Rao A, Aravind L;, Cell Cycle. 2009;8:1698-1710.: Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. PUBMED:19411852 EPMC:19411852
Cliffe LJ, Siegel TN, Marshall M, Cross GA, Sabatini R;, Nucleic Acids Res. 2010;38:3923-3935.: Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei. PUBMED:20215442 EPMC:20215442
Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A;, Science. 2009;324:930-935.: Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. PUBMED:19372391 EPMC:19372391
He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, He C, Xu GL;, Science. 2011; [Epub ahead of print]: Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA. PUBMED:21817016 EPMC:21817016
Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS, An J, Lamperti ED, Koh KP, Ganetzky R, Liu XS, Aravind L, Agarwal S, Maciejewski JP, Rao A;, Nature. 2010;468:839-843.: Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. PUBMED:21057493 EPMC:21057493
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024779
This entry represents the catalytic domain from nucleic-acid modifying members of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily [PUBMED:19411852]. These proteins catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids [PUBMED:20215442], and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (hmC) [PUBMED:19372391], or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) [PUBMED:21817016]. Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various myeloid cancers [PUBMED:21057493]. Fungal and algal versions of this family are linked to a predicted transposase and show lineage-specific expansions [PUBMED:19411852].
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This clan represents the conserved barrel domain of the 'cupin' superfamily  ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.
The clan contains the following 57 members:2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DMSP_lyase dTDP_sugar_isom DUF1255 DUF1479 DUF1498 DUF1637 DUF1971 DUF386 DUF4437 DUF4867 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC KduI MannoseP_isomer Ofd1_CTDD Oxygenase-NA PhyH Pirin Pirin_C PMI_typeI Popeye Pox_C4_C10 TauD Tet_JBP Ureidogly_hydro VIT VIT_2
We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Author:||Bateman A, Zenonos ZA, Iyer LM, Aravind L|
|Number in seed:||16|
|Number in full:||426|
|Average length of the domain:||391.30 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||34.32 %|
|HMM build commands:||
build method: hmmbuild --amino -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||3|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Tet_JBP domain has been found. There are 1 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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