4lt5: Difference between revisions
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4lt5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Amoeba Amoeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LT5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LT5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4lt5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Amoeba Amoeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LT5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LT5 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=OGA:N-OXALYLGLYCINE'>OGA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAEGRDRAFT_55029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5762 Amoeba])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAEGRDRAFT_55029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5762 Amoeba])</td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4lt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lt5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lt5 RCSB], [http://www.ebi.ac.uk/pdbsum/4lt5 PDBsum]</span></td></tr> | <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=4lt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lt5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lt5 RCSB], [http://www.ebi.ac.uk/pdbsum/4lt5 PDBsum]</span></td></tr> | ||
<table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 14: | Line 14: | ||
Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA.,Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Correa IR, Zheng Y, Cheng X Nature. 2013 Dec 25. doi: 10.1038/nature12905. PMID:24390346<ref>PMID:24390346</ref> | Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA.,Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Correa IR, Zheng Y, Cheng X Nature. 2013 Dec 25. doi: 10.1038/nature12905. PMID:24390346<ref>PMID:24390346</ref> | ||
From | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
== References == | == References == | ||
| Line 21: | Line 21: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Amoeba]] | [[Category: Amoeba]] | ||
[[Category: Cheng, X | [[Category: Cheng, X]] | ||
[[Category: Correa, I R | [[Category: Correa, I R]] | ||
[[Category: Dai, N | [[Category: Dai, N]] | ||
[[Category: Fu, Z Q | [[Category: Fu, Z Q]] | ||
[[Category: Hashimoto, H | [[Category: Hashimoto, H]] | ||
[[Category: Pais, J E | [[Category: Pais, J E]] | ||
[[Category: Roberts, R J | [[Category: Roberts, R J]] | ||
[[Category: Saleh, L | [[Category: Saleh, L]] | ||
[[Category: Zhang, X | [[Category: Zhang, X]] | ||
[[Category: Zheng, Y | [[Category: Zheng, Y]] | ||
[[Category: 5-methylcytosine]] | [[Category: 5-methylcytosine]] | ||
[[Category: Dioxygenase-dna complex]] | [[Category: Dioxygenase-dna complex]] | ||
[[Category: Oxidoreductase-dna complex]] | [[Category: Oxidoreductase-dna complex]] | ||
Revision as of 12:36, 5 January 2015
Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNAStructure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA
Structural highlights
Publication Abstract from PubMedCytosine residues in mammalian DNA occur in five forms: cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The ten-eleven translocation (Tet) dioxygenases convert 5mC to 5hmC, 5fC and 5caC in three consecutive, Fe(ii)- and alpha-ketoglutarate-dependent oxidation reactions. The Tet family of dioxygenases is widely distributed across the tree of life, including in the heterolobosean amoeboflagellate Naegleria gruberi. The genome of Naegleria encodes homologues of mammalian DNA methyltransferase and Tet proteins. Here we study biochemically and structurally one of the Naegleria Tet-like proteins (NgTet1), which shares significant sequence conservation (approximately 14% identity or 39% similarity) with mammalian Tet1. Like mammalian Tet proteins, NgTet1 acts on 5mC and generates 5hmC, 5fC and 5caC. The crystal structure of NgTet1 in complex with DNA containing a 5mCpG site revealed that NgTet1 uses a base-flipping mechanism to access 5mC. The DNA is contacted from the minor groove and bent towards the major groove. The flipped 5mC is positioned in the active-site pocket with planar stacking contacts, Watson-Crick polar hydrogen bonds and van der Waals interactions specific for 5mC. The sequence conservation between NgTet1 and mammalian Tet1, including residues involved in structural integrity and functional significance, suggests structural conservation across phyla. Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA.,Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Correa IR, Zheng Y, Cheng X Nature. 2013 Dec 25. doi: 10.1038/nature12905. PMID:24390346[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||||