7lnf
From Proteopedia
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==3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G== | ==3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G== | ||
| - | <StructureSection load='7lnf' size='340' side='right'caption='[[7lnf]]' scene=''> | + | <StructureSection load='7lnf' size='340' side='right'caption='[[7lnf]], [[Resolution|resolution]] 1.65Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7lnf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LNF FirstGlance]. <br> |
| - | </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=7lnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnf OCA], [https://pdbe.org/7lnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnf RCSB], [https://www.ebi.ac.uk/pdbsum/7lnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnf ProSAT]</span></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]] 1.652Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GDO:3-DEOXY-GUANOSINE+5-MONOPHOSPHATE'>GDO</scene>, <scene name='pdbligand=GP3:DIGUANOSINE-5-TRIPHOSPHATE'>GP3</scene>, <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=LKC:4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE'>LKC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7lnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lnf OCA], [https://pdbe.org/7lnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lnf RCSB], [https://www.ebi.ac.uk/pdbsum/7lnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lnf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a 3 E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states. | ||
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| + | Structure-activity relationships in nonenzymatic template-directed RNA synthesis.,Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW Angew Chem Int Ed Engl. 2021 Aug 24. doi: 10.1002/anie.202109714. PMID:34428345<ref>PMID:34428345</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7lnf" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Synthetic construct]] | ||
[[Category: Fang Z]] | [[Category: Fang Z]] | ||
[[Category: Giurgiu C]] | [[Category: Giurgiu C]] | ||
[[Category: Szostak JW]] | [[Category: Szostak JW]] | ||
Current revision
3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G
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