3ltu: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (7 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
< | ==5-SeMe-dU containing DNA 8mer== | ||
<StructureSection load='3ltu' size='340' side='right'caption='[[3ltu]], [[Resolution|resolution]] 1.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ltu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LTU FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=T5S:2-deoxy-5-(methylselanyl)uridine+5-phosphate'>T5S</scene>, <scene name='pdbligand=UMS:2-METHYLSELENYL-2-DEOXYURIDINE-5-PHOSPHATE'>UMS</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ltu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ltu OCA], [https://pdbe.org/3ltu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ltu RCSB], [https://www.ebi.ac.uk/pdbsum/3ltu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ltu ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH(3)) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH(3) and its 5'-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH(3) is replaced with a larger atom (selenium or sulfur). The 5-O-CH(3) modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH(3) modification, which might potentially rigidify the local conformation and facilitates translation. | |||
Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone.,Sheng J, Zhang W, Hassan AE, Gan J, Soares AS, Geng S, Ren Y, Huang Z Nucleic Acids Res. 2012 May 28. PMID:22641848<ref>PMID:22641848</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ltu" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Gan J]] | |||
[[Category: Hassan AEA]] | |||
== | [[Category: Huang Z]] | ||
< | [[Category: Sheng J]] | ||
[[Category: Gan | [[Category: Zhang W]] | ||
[[Category: Hassan | |||
[[Category: Huang | |||
[[Category: Sheng | |||
[[Category: Zhang | |||
