2008
A relaxed active site after exon ligation by the group I intron
Lipchock SV, Strobel SA. A relaxed active site after exon ligation by the group I intron. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 5699-5704. PMID: 18408159, PMCID: PMC2311373, DOI: 10.1073/pnas.0712016105.Peer-Reviewed Original ResearchConceptsActive siteMetal ionsRelaxed active siteActive site metal ionScissile phosphateDirect metal coordinationHydrogen bonding contactsMetal coordinationBonding contactsTransition stateCrystal structureThermodynamic measurementsIonsGround stateStructureCoordinationStructural observationsTertiary interactionsIntron releaseExon ligationGroup I intronPhosphateComplexesReactionSecond step
2001
Biochemical Detection of Monovalent Metal Ion Binding Sites within RNA
Basu S, Strobel S. Biochemical Detection of Monovalent Metal Ion Binding Sites within RNA. Methods 2001, 23: 264-275. PMID: 11243839, DOI: 10.1006/meth.2000.1137.Peer-Reviewed Original ResearchConceptsX-ray crystal structureMonovalent cationsMetal ion binding siteMetal ion bindingHeavy metal cationsIon binding siteMetal sitesMetal cationsSoft LewisCrystal structureIon bindingCationsChemical propertiesNucleotide analog interference mappingP4-P6 domainAzoarcus group I intronMetal potassiumSimilar binding sitesNucleic acidsBinding sitesBiochemical detectionTetrahymena group I intronLarge RNAsGroup I intronDistinct biochemical signatures
1999
An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site
Szewczak A, Ortoleva-Donnelly L, Zivarts M, Oyelere A, Kazantsev A, Strobel S. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 11183-11188. PMID: 10500151, PMCID: PMC18008, DOI: 10.1073/pnas.96.20.11183.Peer-Reviewed Original ResearchConceptsHelix dockingBase triplesRecognition surfaceGroup I intronActive siteNetwork of interactionsTetrahymena group IP3 helixStructural biologySubstrate bindingI intronCatalytic RNAProduct bindingSuppression analysisFunctional importanceRNA foldingRNA constructsSubstrate helixBiochemical evidenceMutant ribozymesRibozyme active siteSubstantial rearrangementHelixCrystallographic modelRibozyme
1998
A minor groove RNA triple helix within the catalytic core of a group I intron
Szewczak A, Ortoleva-Donnelly L, Ryder S, Moncoeur E, Strobel S. A minor groove RNA triple helix within the catalytic core of a group I intron. Nature Structural & Molecular Biology 1998, 5: 1037-1042. PMID: 9846872, DOI: 10.1038/4146.Peer-Reviewed Original ResearchA specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
Basu S, P. Rambo R, Strauss-Soukup J, H.Cate J, R. Ferré-D´Amaré A, Strobel S, Doudna J. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nature Structural & Molecular Biology 1998, 5: 986-992. PMID: 9808044, DOI: 10.1038/2960.Peer-Reviewed Original ResearchConceptsP4-P6 domainTetraloop receptorCatalytic RNALarge catalytic RNAsGroup I intronRNA tertiary structure formationTertiary structure formationTertiary structural motifsI intronRNAWide diversityFoldingStructural motifsDivalent metal ionsPotassium ionsReceptorsIntronsAzoarcusDomainDiversityMotifSitesActivityMonovalent ions