6asd: Difference between revisions

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'''Unreleased structure'''


The entry 6asd is ON HOLD
==Zinc finger region of human TET1 in complex with CpG DNA==
 
<StructureSection load='6asd' size='340' side='right' caption='[[6asd]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
Authors: Liu, K., Xu, C., Tempel, W., Walker, J.R., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)
== Structural highlights ==
 
<table><tr><td colspan='2'>[[6asd]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ASD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ASD FirstGlance]. <br>
Description: Zinc finger region of human TET1 in complex with CpG DNA
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
[[Category: Unreleased Structures]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6asd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6asd OCA], [http://pdbe.org/6asd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6asd RCSB], [http://www.ebi.ac.uk/pdbsum/6asd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6asd ProSAT]</span></td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/TET1_HUMAN TET1_HUMAN]] A chromosomal aberration involving TET1 may be a cause of acute leukemias (PubMed:12646957). Translocation t(10;11)(q22;q23) with KMT2A/MLL1. This is a rare chromosomal translocation 5' KMT2A/MLL1-TET1 3' (PubMed:12124344, PubMed:12646957).<ref>PMID:12124344</ref> <ref>PMID:12646957</ref> 
== Function ==
[[http://www.uniprot.org/uniprot/TET1_HUMAN TET1_HUMAN]] Dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and plays a key role in active DNA demethylation. Also mediates subsequent conversion of 5hmC into 5-formylcytosine (5fC), and conversion of 5fC to 5-carboxylcytosine (5caC). Conversion of 5mC into 5hmC, 5fC and 5caC probably constitutes the first step in cytosine demethylation. Methylation at the C5 position of cytosine bases is an epigenetic modification of the mammalian genome which plays an important role in transcriptional regulation. In addition to its role in DNA demethylation, plays a more general role in chromatin regulation. Preferentially binds to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Involved in the recruitment of the O-GlcNAc transferase OGT to CpG-rich transcription start sites of active genes, thereby promoting histone H2B GlcNAcylation by OGT. Also involved in transcription repression of a subset of genes through recruitment of transcriptional repressors to promoters. Involved in the balance between pluripotency and lineage commitment of cells it plays a role in embryonic stem cells maintenance and inner cell mass cell specification. Plays an important role in the tumorigenicity of glioblastoma cells. TET1-mediated production of 5hmC acts as a recruitment signal for the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789).<ref>PMID:12124344</ref> <ref>PMID:19372391</ref> <ref>PMID:19372393</ref> <ref>PMID:21496894</ref> <ref>PMID:21778364</ref> <ref>PMID:25284789</ref> 
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arrowsmith, C H]]
[[Category: Bountra, C]]
[[Category: Edwards, A M]]
[[Category: Liu, K]]
[[Category: Min, J]]
[[Category: Min, J]]
[[Category: Walker, J.R]]
[[Category: Structural genomic]]
[[Category: Bountra, C]]
[[Category: Tempel, W]]
[[Category: Tempel, W]]
[[Category: Arrowsmith, C.H]]
[[Category: Walker, J R]]
[[Category: Xu, C]]
[[Category: Xu, C]]
[[Category: Liu, K]]
[[Category: Dna binding protein-dna complex]]
[[Category: Edwards, A.M]]
[[Category: Dna-binding]]
[[Category: Structural Genomics Consortium (Sgc)]]
[[Category: Sgc]]
[[Category: Zinc finger]]

Revision as of 10:21, 18 October 2017

Zinc finger region of human TET1 in complex with CpG DNAZinc finger region of human TET1 in complex with CpG DNA

Structural highlights

6asd is a 3 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[TET1_HUMAN] A chromosomal aberration involving TET1 may be a cause of acute leukemias (PubMed:12646957). Translocation t(10;11)(q22;q23) with KMT2A/MLL1. This is a rare chromosomal translocation 5' KMT2A/MLL1-TET1 3' (PubMed:12124344, PubMed:12646957).[1] [2]

Function

[TET1_HUMAN] Dioxygenase that catalyzes the conversion of the modified genomic base 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and plays a key role in active DNA demethylation. Also mediates subsequent conversion of 5hmC into 5-formylcytosine (5fC), and conversion of 5fC to 5-carboxylcytosine (5caC). Conversion of 5mC into 5hmC, 5fC and 5caC probably constitutes the first step in cytosine demethylation. Methylation at the C5 position of cytosine bases is an epigenetic modification of the mammalian genome which plays an important role in transcriptional regulation. In addition to its role in DNA demethylation, plays a more general role in chromatin regulation. Preferentially binds to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Involved in the recruitment of the O-GlcNAc transferase OGT to CpG-rich transcription start sites of active genes, thereby promoting histone H2B GlcNAcylation by OGT. Also involved in transcription repression of a subset of genes through recruitment of transcriptional repressors to promoters. Involved in the balance between pluripotency and lineage commitment of cells it plays a role in embryonic stem cells maintenance and inner cell mass cell specification. Plays an important role in the tumorigenicity of glioblastoma cells. TET1-mediated production of 5hmC acts as a recruitment signal for the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789).[3] [4] [5] [6] [7] [8]

References

  1. ↑ Ono R, Taki T, Taketani T, Taniwaki M, Kobayashi H, Hayashi Y. LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). Cancer Res. 2002 Jul 15;62(14):4075-80. PMID:12124344
  2. ↑ Lorsbach RB, Moore J, Mathew S, Raimondi SC, Mukatira ST, Downing JR. TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23). Leukemia. 2003 Mar;17(3):637-41. PMID:12646957 doi:http://dx.doi.org/10.1038/sj.leu.2402834
  3. ↑ Ono R, Taki T, Taketani T, Taniwaki M, Kobayashi H, Hayashi Y. LCX, leukemia-associated protein with a CXXC domain, is fused to MLL in acute myeloid leukemia with trilineage dysplasia having t(10;11)(q22;q23). Cancer Res. 2002 Jul 15;62(14):4075-80. PMID:12124344
  4. ↑ Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009 May 15;324(5929):930-5. doi: 10.1126/science.1170116. Epub 2009 Apr, 16. PMID:19372391 doi:http://dx.doi.org/10.1126/science.1170116
  5. ↑ Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. 2009 May 15;324(5929):929-30. doi: 10.1126/science.1169786. Epub 2009, Apr 16. PMID:19372393 doi:http://dx.doi.org/10.1126/science.1169786
  6. ↑ Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011 Apr 29;145(3):423-34. doi: 10.1016/j.cell.2011.03.022. Epub 2011 Apr, 14. PMID:21496894 doi:10.1016/j.cell.2011.03.022
  7. ↑ Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011 Sep 2;333(6047):1300-3. doi: 10.1126/science.1210597. Epub 2011 Jul, 21. PMID:21778364 doi:http://dx.doi.org/10.1126/science.1210597
  8. ↑ Takai H, Masuda K, Sato T, Sakaguchi Y, Suzuki T, Suzuki T, Koyama-Nasu R, Nasu-Nishimura Y, Katou Y, Ogawa H, Morishita Y, Kozuka-Hata H, Oyama M, Todo T, Ino Y, Mukasa A, Saito N, Toyoshima C, Shirahige K, Akiyama T. 5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex. Cell Rep. 2014 Oct 9;9(1):48-60. doi: 10.1016/j.celrep.2014.08.071. Epub 2014 Oct, 2. PMID:25284789 doi:http://dx.doi.org/10.1016/j.celrep.2014.08.071

6asd, resolution 1.85Å

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