1i2x

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==2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM==
==2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM==
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<StructureSection load='1i2x' size='340' side='right' caption='[[1i2x]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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<StructureSection load='1i2x' size='340' side='right'caption='[[1i2x]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1i2x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I2X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1I2X FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1i2x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I2X FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene><br>
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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]] 2.4&#8491;</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=1i2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i2x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1i2x RCSB], [http://www.ebi.ac.uk/pdbsum/1i2x PDBsum]</span></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=SPD:SPERMIDINE'>SPD</scene></td></tr>
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<table>
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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=1i2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i2x OCA], [https://pdbe.org/1i2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i2x RCSB], [https://www.ebi.ac.uk/pdbsum/1i2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i2x ProSAT]</span></td></tr>
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<div style="background-color:#fffaf0;">
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</table>
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== Publication Abstract from PubMed ==
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The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Husken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup &amp; Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.
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X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.,Tereshko V, Wallace ST, Usman N, Wincott FE, Egli M RNA. 2001 Mar;7(3):405-20. PMID:11333021<ref>PMID:11333021</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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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Egli, M.]]
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[[Category: Large Structures]]
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[[Category: Tereshko, V.]]
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[[Category: Egli M]]
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[[Category: Usman, N.]]
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[[Category: Tereshko V]]
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[[Category: Wallace, S.]]
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[[Category: Usman N]]
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[[Category: Wincott, F.]]
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[[Category: Wallace S]]
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[[Category: Adenine bulge]]
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[[Category: Wincott F]]
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[[Category: A-type na]]
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[[Category: Dna-rna hybrid]]
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[[Category: Dna/rna hybrids']]
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Current revision

2.4 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMIDINE FORM

PDB ID 1i2x

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