1d9h: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d9h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9H FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d9h]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D9H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9H FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=U31:2-O-3-AMINOPROPYL+2-DEOXYURIDINE-5-MONOPHOSPHATE'>U31</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]] 1.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U31:2-O-3-AMINOPROPYL+2-DEOXYURIDINE-5-MONOPHOSPHATE'>U31</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=1d9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9h OCA], [https://pdbe.org/1d9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9h RCSB], [https://www.ebi.ac.uk/pdbsum/1d9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9h ProSAT]</span></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=1d9h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9h OCA], [https://pdbe.org/1d9h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9h RCSB], [https://www.ebi.ac.uk/pdbsum/1d9h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9h ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2'-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1 degrees C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3' ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3'-5' exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-A resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 A and compared with the structure of the complex between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest that interference of the positively charged 2'-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.
Structural origins of the exonuclease resistance of a zwitterionic RNA.,Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14240-5. PMID:10588690<ref>PMID:10588690</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d9h" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cook, P D]]
[[Category: Cook PD]]
[[Category: Egli, M]]
[[Category: Egli M]]
[[Category: Manoharan, M]]
[[Category: Manoharan M]]
[[Category: Minasov, G]]
[[Category: Minasov G]]
[[Category: Simons, A M]]
[[Category: Simons AM]]
[[Category: Teplova, M]]
[[Category: Teplova M]]
[[Category: Tereshko, V]]
[[Category: Tereshko V]]
[[Category: Wallace, S T]]
[[Category: Wallace ST]]
[[Category: A-dna]]
[[Category: Dna]]
[[Category: Exonuclease resistance]]
[[Category: Rna]]

Latest revision as of 09:51, 7 February 2024

Structural origins of the exonuclease resistance of a zwitterionic RNAStructural origins of the exonuclease resistance of a zwitterionic RNA

Structural highlights

1d9h is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d9h, resolution 1.60Å

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