2p7d: Difference between revisions

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-[[Image:2p7d.gif|left|200px]]
+{{Seed}}
+[[Image:2p7d.png|left|200px]]
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 {{STRUCTURE_2p7d|  PDB=2p7d  |  SCENE=  }}
-'''A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution'''
+===A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution===
-==Overview==
+<!--
-The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.
+The line below this paragraph, {{ABSTRACT_PUBMED_17488874}}, adds the Publication Abstract to the page
+(as it appears on PubMed at http://www.pubmed.gov), where 17488874 is the PubMed ID number.
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+{{ABSTRACT_PUBMED_17488874}}
 ==About this Structure==
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 ==Reference==
 A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization., Torelli AT, Krucinska J, Wedekind JE, RNA. 2007 Jul;13(7):1052-70. Epub 2007 May 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17488874 17488874]
+Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer., Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE, Biochemistry. 2006 Jan 24;45(3):686-700. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16411744 16411744]
+Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn., Alam S, Grum-Tokars V, Krucinska J, Kundracik ML, Wedekind JE, Biochemistry. 2005 Nov 8;44(44):14396-408. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16262240 16262240]
 [[Category: Krucinska, J.]]
 [[Category: Torelli, A T.]]
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 [[Category: Product mimic]]
 [[Category: Transition-state stabilization]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 12:32:27 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 16:02:57 2008''