{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Torelli AT"],"funding":["NCRR NIH HHS","NIGMS NIH HHS"],"pagination":["1052-70"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC1894929"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["13(7)"],"pubmed_abstract":["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"],"journal":["RNA (New York, N.Y.)"],"pubmed_title":["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."],"pmcid":["PMC1894929"],"funding_grant_id":["R01 GM063162","R01 GM063162-05","R01 GM63162","P41 RR001209","P41 RR001209-298120"],"pubmed_authors":["Krucinska J","Wedekind JE","Torelli AT"],"additional_accession":[]},"is_claimable":false,"name":"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.","description":"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","dates":{"release":"2007-01-01T00:00:00Z","publication":"2007 Jul","modification":"2025-04-04T10:35:23.468Z","creation":"2019-03-27T02:04:09Z"},"accession":"S-EPMC1894929","cross_references":{"pubmed":["17488874"],"doi":["10.1261/rna.510807"]}}