5uef: Difference between revisions
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The | ==RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand== | ||
<StructureSection load='5uef' size='340' side='right' caption='[[5uef]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5uef]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UEF FirstGlance]. <br> | |||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LCC:[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCC</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ued|5ued]], [[5uee|5uee]], [[5ueg|5ueg]]</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=5uef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uef OCA], [http://pdbe.org/5uef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uef RCSB], [http://www.ebi.ac.uk/pdbsum/5uef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uef ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The nonenzymatic copying of RNA templates with imidazole-activated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3'-hydroxyl oriented to attack the 5'-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazolium-bridged dinucleotide intermediate would be preorganized to react with the primer by in-line SN2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5'-5' linkage are important for optimal preorganization of the complex, whereas the position of the 5'-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension. | |||
Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.,Zhang W, Tam CP, Walton T, Fahrenbach AC, Birrane G, Szostak JW Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7659-7664. doi:, 10.1073/pnas.1704006114. Epub 2017 Jul 3. PMID:28673998<ref>PMID:28673998</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5uef" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Szostak, J W]] | |||
[[Category: Tam, C P]] | |||
[[Category: Zhang, W]] | [[Category: Zhang, W]] | ||
[[Category: | [[Category: Dinucleotide]] | ||
[[Category: Rna]] | |||
