1r2p: Difference between revisions
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< | ==Solution structure of domain 5 from the ai5(gamma) group II intron== | ||
<StructureSection load='1r2p' size='340' side='right'caption='[[1r2p]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1r2p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R2P FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1r2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r2p OCA], [https://pdbe.org/1r2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r2p RCSB], [https://www.ebi.ac.uk/pdbsum/1r2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r2p ProSAT]</span></td></tr> | ||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site. | |||
Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.,Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM Nat Struct Mol Biol. 2004 Feb;11(2):187-92. Epub 2004 Jan 25. PMID:14745440<ref>PMID:14745440</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1r2p" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Saccharomyces cerevisiae]] | |||
[[Category: Abramovitz DL]] | |||
== | [[Category: Butcher SE]] | ||
[[Category: Palmer III AG]] | |||
[[Category: Pyle AM]] | |||
[[Category: Sashital DG]] | |||
[[Category: Sigel RKO]] | |||
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Latest revision as of 12:20, 6 December 2023
Solution structure of domain 5 from the ai5(gamma) group II intronSolution structure of domain 5 from the ai5(gamma) group II intron
Structural highlights
Publication Abstract from PubMedDomain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif.,Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM Nat Struct Mol Biol. 2004 Feb;11(2):187-92. Epub 2004 Jan 25. PMID:14745440[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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