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2oiy

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[[Image:2oiy.png|left|200px]]
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==Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site==
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<StructureSection load='2oiy' size='340' side='right' caption='[[2oiy]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2oiy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OIY OCA]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oij|2oij]], [[462d|462d]], [[1y99|1y99]], [[2oj0|2oj0]]</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
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<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=2oiy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oiy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oiy RCSB], [http://www.ebi.ac.uk/pdbsum/2oiy PDBsum]</span></td></tr>
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<table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion.
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Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.,Ennifar E, Walter P, Dumas P Nucleic Acids Res. 2010 Sep 1;38(17):5807-16. Epub 2010 May 11. PMID:20460458<ref>PMID:20460458</ref>
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The line below this paragraph, containing "STRUCTURE_2oiy", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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{{STRUCTURE_2oiy| PDB=2oiy | SCENE= }}
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===Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site===
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_20460458}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 20460458 is the PubMed ID number.
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</StructureSection>
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{{ABSTRACT_PUBMED_20460458}}
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==About this Structure==
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[[2oiy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OIY OCA].
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==Reference==
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<ref group="xtra">PMID:020460458</ref><references group="xtra"/>
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[[Category: Dumas, P.]]
[[Category: Dumas, P.]]
[[Category: Ennifar, E.]]
[[Category: Ennifar, E.]]

Revision as of 08:38, 7 May 2014

Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site

2oiy, resolution 1.60Å

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