6u89: Difference between revisions

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<StructureSection load='6u89' size='340' side='right'caption='[[6u89]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
<StructureSection load='6u89' size='340' side='right'caption='[[6u89]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6u89]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U89 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6U89 FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6U89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6U89 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TG:(2S,4R)-1-(3-AMINO-2-METHYLBENZOYL)-4-HYDROXY-N-(4-(4-METHYLTHIAZOL-5-YL)BENZYL)PYRROLIDINE-2-CARBOXAMIDE'>TG</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]] 2.36&#8491;</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>, <scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene>, <scene name='pdbligand=TLN:[(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>TLN</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>, <scene name='pdbligand=LCG:[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCG</scene>, <scene name='pdbligand=TG:(2S,4R)-1-(3-AMINO-2-METHYLBENZOYL)-4-HYDROXY-N-(4-(4-METHYLTHIAZOL-5-YL)BENZYL)PYRROLIDINE-2-CARBOXAMIDE'>TG</scene>, <scene name='pdbligand=TLN:[(1R,3R,4R,7S)-7-HYDROXY-3-(THYMIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>TLN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6u89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u89 OCA], [http://pdbe.org/6u89 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6u89 RCSB], [http://www.ebi.ac.uk/pdbsum/6u89 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6u89 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=6u89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6u89 OCA], [https://pdbe.org/6u89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6u89 RCSB], [https://www.ebi.ac.uk/pdbsum/6u89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6u89 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3'-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.
Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.,Zhang W, Kim SC, Tam CP, Lelyveld VS, Bala S, Chaput JC, Szostak JW Nucleic Acids Res. 2020 Dec 21. pii: 6042960. doi: 10.1093/nar/gkaa1215. PMID:33347562<ref>PMID:33347562</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6u89" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Szostak, J W]]
[[Category: Szostak JW]]
[[Category: Zhang, W]]
[[Category: Zhang W]]
[[Category: Rna]]
Retrieved from "https://proteopedia.org/6u89"