3ey1: Difference between revisions

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[[Image:3ey1.png|left|200px]]


{{STRUCTURE_3ey1| PDB=3ey1 | SCENE= }}
==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==
<StructureSection load='3ey1' size='340' side='right'caption='[[3ey1]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3ey1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alkalihalobacillus_halodurans Alkalihalobacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EY1 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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=USM:2-S-METHYL-2-THIOURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>USM</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=3ey1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ey1 OCA], [https://pdbe.org/3ey1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ey1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ey1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ey1 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/3ey1_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ey1 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.


===A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution===
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.,Pallan PS, Prakash TP, Li F, Eoff RL, Manoharan M, Egli M Chem Commun (Camb). 2009 Apr 21;(15):2017-9. Epub 2009 Feb 26. PMID:19333476<ref>PMID:19333476</ref>


{{ABSTRACT_PUBMED_19333476}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 3ey1" style="background-color:#fffaf0;"></div>
[[3ey1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_halodurans Bacillus halodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EY1 OCA].


==See Also==
==See Also==
*[[Ribonuclease|Ribonuclease]]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:019333476</ref><references group="xtra"/>
__TOC__
[[Category: Bacillus halodurans]]
</StructureSection>
[[Category: Ribonuclease H]]
[[Category: Alkalihalobacillus halodurans]]
[[Category: Egli, M.]]
[[Category: Large Structures]]
[[Category: Pallan, P S.]]
[[Category: Egli M]]
[[Category: 2'-thiomethyl uridine ribonucleic acid]]
[[Category: Pallan PS]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Hydrolase-dna complex]]
[[Category: Magnesium]]
[[Category: Manganese]]
[[Category: Metal-binding]]
[[Category: Nuclease]]
[[Category: Protein-dna complex]]
[[Category: Rnase h-dna complex]]

Latest revision as of 06:37, 6 September 2023

A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution

3ey1, resolution 1.60Å

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