5xeg
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='5xeg' size='340' side='right' caption='[[5xeg]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='5xeg' size='340' side='right' caption='[[5xeg]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5xeg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XEG FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LOC_Os03g60190, OsJ_13105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [http://pdbe.org/5xeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [http://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg ProSAT]</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=5xeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xeg OCA], [http://pdbe.org/5xeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xeg RCSB], [http://www.ebi.ac.uk/pdbsum/5xeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xeg ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | DNA N(6)-methyladenine (6mA) is a non-canonical DNA modification that is present at low levels in different eukaryotes(1-8), but its prevalence and genomic function in higher plants are unclear. Using mass spectrometry, immunoprecipitation and validation with analysis of single-molecule real-time sequencing, we observed that about 0.2% of all adenines are 6mA methylated in the rice genome. 6mA occurs most frequently at GAGG motifs and is mapped to about 20% of genes and 14% of transposable elements. In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylcytosine (5mC) at CG sites in gene bodies and is complementary to 5mC at CHH sites in transposable elements. We show that OsALKBH1 may be potentially involved in 6mA demethylation in rice. The results suggest that 6mA is complementary to 5mC as an epigenomic mark in rice and reinforce a distinct role for 6mA as a gene expression-associated epigenomic mark in eukaryotes. | ||
| + | |||
| + | Identification and analysis of adenine N(6)-methylation sites in the rice genome.,Zhou C, Wang C, Liu H, Zhou Q, Liu Q, Guo Y, Peng T, Song J, Zhang J, Chen L, Zhao Y, Zeng Z, Zhou DX Nat Plants. 2018 Aug;4(8):554-563. doi: 10.1038/s41477-018-0214-x. Epub 2018 Jul , 30. PMID:30061746<ref>PMID:30061746</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 5xeg" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Japanese rice]] | ||
[[Category: Guo, Y]] | [[Category: Guo, Y]] | ||
[[Category: Wang, C]] | [[Category: Wang, C]] | ||
[[Category: Zeng, Z]] | [[Category: Zeng, Z]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
Revision as of 08:44, 19 December 2018
The structure of OsALKBH1
| |||||||||||
