3gs5: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3gs5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GS5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3gs5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GS5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.75&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gs1|3gs1]], [[3gs8|3gs8]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=S9L:2-[2-(2-HYDROXYETHOXY)ETHOXY]ETHYL+DIHYDROGEN+PHOSPHATE'>S9L</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3gs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gs5 OCA], [https://pdbe.org/3gs5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gs5 RCSB], [https://www.ebi.ac.uk/pdbsum/3gs5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gs5 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=3gs5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gs5 OCA], [https://pdbe.org/3gs5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gs5 RCSB], [https://www.ebi.ac.uk/pdbsum/3gs5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gs5 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.
Identification of an Imino Group Indispensable for Cleavage by a Small Ribozyme.,Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE J Am Chem Soc. 2009 Apr 8. PMID:19354216<ref>PMID:19354216</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gs5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Cristalli, G]]
[[Category: Cristalli G]]
[[Category: Heller, M G]]
[[Category: Heller MG]]
[[Category: Krucinska, J]]
[[Category: Krucinska J]]
[[Category: Spitale, R C]]
[[Category: Spitale RC]]
[[Category: Volpini, R]]
[[Category: Volpini R]]
[[Category: Wedekind, J E]]
[[Category: Wedekind JE]]
[[Category: Hairpin ribozyme]]
[[Category: N1-deazaadenosine]]
[[Category: Rna]]
[[Category: Rna ribozyme]]

Latest revision as of 12:56, 21 February 2024

An all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strandAn all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strand

Structural highlights

3gs5 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 2.75Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3gs5, resolution 2.75Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=3gs5&oldid=4065078"