5dh8: Difference between revisions

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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5dh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dh8 OCA], [https://pdbe.org/5dh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dh8 RCSB], [https://www.ebi.ac.uk/pdbsum/5dh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dh8 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=5dh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dh8 OCA], [https://pdbe.org/5dh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dh8 RCSB], [https://www.ebi.ac.uk/pdbsum/5dh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dh8 ProSAT]</span></td></tr>
</table>
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<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn2+ specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH-rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction.
Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.,Mir A, Chen J, Robinson K, Lendy E, Goodman J, Neau D, Golden BL Biochemistry. 2015 Oct 2. PMID:26398724<ref>PMID:26398724</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 5dh8" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
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Latest revision as of 15:24, 6 March 2024

Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction- G12A mutant in Zn2+Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction- G12A mutant in Zn2+

Structural highlights

5dh8 is a 2 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.297Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

5dh8, resolution 3.30Å

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