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==1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM==
==1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM==
<StructureSection load='1i2y' size='340' side='right' caption='[[1i2y]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
<StructureSection load='1i2y' size='340' side='right'caption='[[1i2y]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1i2y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1I2Y FirstGlance]. <br>
<table><tr><td colspan='2'>[[1i2y]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I2Y FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.66&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1i2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i2y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1i2y RCSB], [http://www.ebi.ac.uk/pdbsum/1i2y PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPM:SPERMINE'>SPM</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=1i2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i2y OCA], [https://pdbe.org/1i2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i2y RCSB], [https://www.ebi.ac.uk/pdbsum/1i2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i2y ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Egli, M]]
[[Category: Large Structures]]
[[Category: Tereshko, V]]
[[Category: Egli M]]
[[Category: Usman, N]]
[[Category: Tereshko V]]
[[Category: Wallace, S]]
[[Category: Usman N]]
[[Category: Wincott, F]]
[[Category: Wallace S]]
[[Category: A-type na]]
[[Category: Wincott F]]
[[Category: Adenine bulge]]
[[Category: Dna-rna hybrid]]
[[Category: Dna/rna hybrid]]

Latest revision as of 10:32, 7 February 2024

1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM1.66 A STRUCTURE OF A-DUPLEX WITH BULGED ADENOSINE, SPERMINE FORM

Structural highlights

1i2y is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.66Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1i2y, resolution 1.66Å

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