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3ey1

From Proteopedia

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{{Seed}}
 
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[[Image:3ey1.jpg|left|200px]]
 
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==A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution==
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The line below this paragraph, containing "STRUCTURE_3ey1", creates the "Structure Box" on the page.
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<StructureSection load='3ey1' size='340' side='right'caption='[[3ey1]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_3ey1| PDB=3ey1 | SCENE= }}
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNH1_HALH5 RNH1_HALH5] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.<ref>PMID:15989951</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ey/3ey1_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ey1" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19333476}}, adds the Publication Abstract to the page
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19333476 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19333476}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Alkalihalobacillus halodurans]]
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3EY1 is a 2 chains structure of sequences 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].
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[[Category: Large Structures]]
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[[Category: Egli M]]
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==Reference==
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[[Category: Pallan PS]]
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<ref group="xtra">PMID:19333476</ref><references group="xtra"/>
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[[Category: Bacillus halodurans]]
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[[Category: Ribonuclease H]]
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[[Category: Egli, M.]]
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[[Category: Pallan, P S.]]
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[[Category: 2'-thiomethyl uridine ribonucleic acid]]
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[[Category: Cytoplasm]]
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[[Category: Endonuclease]]
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[[Category: Hydrolase]]
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[[Category: Hydrolase/dna complex]]
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[[Category: Magnesium]]
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[[Category: Manganese]]
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[[Category: Metal-binding]]
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[[Category: Nuclease]]
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[[Category: Protein-dna complex]]
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[[Category: Rnase h-dna complex]]
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[[Category: X-ray crystallography]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 30 10:08:18 2009''
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Current revision

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

PDB ID 3ey1

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