2021
Structural visualization of transcription activated by a multidrug-sensing MerR family regulator
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B. Structural visualization of transcription activated by a multidrug-sensing MerR family regulator. Nature Communications 2021, 12: 2702. PMID: 33976201, PMCID: PMC8113463, DOI: 10.1038/s41467-021-22990-8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsBacterial ProteinsBase SequenceBinding SitesCloning, MolecularCryoelectron MicroscopyCrystallography, X-RayDNA, BacterialDNA-Binding ProteinsDNA-Directed RNA PolymerasesEscherichia coliGene ExpressionGene Expression Regulation, BacterialGenetic VectorsModels, MolecularNucleic Acid ConformationPromoter Regions, GeneticProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsRecombinant ProteinsTranscription Elongation, GeneticTranscription Initiation, GeneticConceptsMerR family regulatorsFamily regulatorCryo-electron microscopy structureBacterial RNA polymerase holoenzymeRegulation of transcriptionRNA polymerase holoenzymePromoter openingTranscription regulationMicroscopy structureTranscription initiationPolymerase holoenzymeRNA elongationTranscriptional regulatorsMerR familyDNA remodelingSpacer DNAPromoter recognitionPromoter elementsCellular signalsSpacer promoterInitial transcriptionTranscription processTranscriptionPromoterRegulator
2007
The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination
Drejer-Teel AH, Fugmann SD, Schatz DG. The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination. Molecular And Cellular Biology 2007, 27: 6288-6299. PMID: 17636023, PMCID: PMC2099602, DOI: 10.1128/mcb.00835-07.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA cleavageGene segmentsDNA cleavage stepRecombination-activating gene 1Dbeta gene segmentVariable region exonsJbeta gene segmentsRAG proteinsDNA elementsSignal sequenceDirect VbetaRegion exonsGene 1Oligonucleotide substratesLocus sequenceDistinct combinationsProteinRecombinationCleavageNickingCleavage stepSequenceDifferent stepsExons
2006
Mobilization of RAG-Generated Signal Ends by Transposition and Insertion In Vivo
Chatterji M, Tsai CL, Schatz DG. Mobilization of RAG-Generated Signal Ends by Transposition and Insertion In Vivo. Molecular And Cellular Biology 2006, 26: 1558-1568. PMID: 16449665, PMCID: PMC1367191, DOI: 10.1128/mcb.26.4.1558-1568.2006.Peer-Reviewed Original ResearchConceptsRAG proteinsVertebrate cellsTransposition eventsEnd fragmentsFull-length RAG2Embryonic kidney cell lineHuman embryonic kidney cell lineTarget site duplicationsGenome instabilityHuman genomeSignal endsKidney cell lineGenomic instabilityTranslocation eventsSite duplicationsChromosomal translocationsDNA cleavageComplex rearrangementsChromosome deletionsEssential roleProteinCell linesEpisomesDeletionAssays
2002
RAG1-DNA Binding in V(D)J Recombination SPECIFICITY AND DNA-INDUCED CONFORMATIONAL CHANGES REVEALED BY FLUORESCENCE AND CD SPECTROSCOPY*
Ciubotaru M, Ptaszek LM, Baker GA, Baker SN, Bright FV, Schatz DG. RAG1-DNA Binding in V(D)J Recombination SPECIFICITY AND DNA-INDUCED CONFORMATIONAL CHANGES REVEALED BY FLUORESCENCE AND CD SPECTROSCOPY*. Journal Of Biological Chemistry 2002, 278: 5584-5596. PMID: 12488446, DOI: 10.1074/jbc.m209758200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesCircular DichroismCloning, MolecularDNADNA NucleotidyltransferasesDNA-Binding ProteinsEscherichia coliGenes, RAG-1Homeodomain ProteinsKineticsMiceOligodeoxyribonucleotidesProtein ConformationRecombinant ProteinsRecombination, GeneticSubstrate SpecificityTransfectionTransposasesVDJ RecombinasesConceptsRecombination signal sequencesConformational changesSynaptic complex formationAbsence of DNAAssembly of immunoglobulinMajor conformational changesIntrinsic protein fluorophoresProtein intrinsic fluorescenceSolvent-exposed environmentRAG2 proteinsRAG1/2 complexSingle DNA moleculesRAG1 proteinSignal sequenceAcrylamide quenching studiesT-cell receptor genesStrep-tagRecombination specificityDNA moleculesProtein fluorophoresRAG1Receptor geneProteinIntrinsic fluorescenceCircular dichroism
2001
Identification of Basic Residues in RAG2 Critical for DNA Binding by the RAG1-RAG2 Complex
Fugmann S, Schatz D. Identification of Basic Residues in RAG2 Critical for DNA Binding by the RAG1-RAG2 Complex. Molecular Cell 2001, 8: 899-910. PMID: 11684024, DOI: 10.1016/s1097-2765(01)00352-5.Peer-Reviewed Original ResearchConceptsDNA bindingRAG2 proteinsCognate DNA target sequenceDNA target sequencesResidue mutantsMolecular roleBasic residuesDNA cleavageTarget sequenceRAG1Biochemical analysisRAG2BindingCentral roleProteinRecombinationResiduesDirect involvementEssential componentComplexesMutantsCleavage reactionIdentificationRoleSequence
2000
Identification of Two Catalytic Residues in RAG1 that Define a Single Active Site within the RAG1/RAG2 Protein Complex
Fugmann S, Villey I, Ptaszek L, Schatz D. Identification of Two Catalytic Residues in RAG1 that Define a Single Active Site within the RAG1/RAG2 Protein Complex. Molecular Cell 2000, 5: 97-107. PMID: 10678172, DOI: 10.1016/s1097-2765(00)80406-2.Peer-Reviewed Original ResearchConceptsActive siteDivalent metal ionsSingle active siteMetal ionsTransfer reactionsActive site regionProtein complexesBond breakageCatalysisCatalytic functionRegion of RAG1Strand transfer reactionSecondary structure prediction algorithmsAspartic acid residuesCatalytic residuesRAG2 proteinsComplexesStructure prediction algorithmsPossible structural similaritySite regionAcid residuesRetroviral integrasesRAG1Structural similarityIons
1996
RAG1 Mediates Signal Sequence Recognition and Recruitment of RAG2 in V(D)J Recombination
Difilippantonio M, McMahan C, Eastman Q, Spanopoulou E, Schatz D. RAG1 Mediates Signal Sequence Recognition and Recruitment of RAG2 in V(D)J Recombination. Cell 1996, 87: 253-262. PMID: 8861909, DOI: 10.1016/s0092-8674(00)81343-4.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCell LineDNA NucleotidyltransferasesDNA-Binding ProteinsGenes, ImmunoglobulinHomeodomain ProteinsHumansMacromolecular SubstancesMolecular Sequence DataNuclear ProteinsProtein BindingProteinsRecombinant ProteinsRecombination, GeneticSalmonellaSequence AlignmentStructure-Activity RelationshipTranscriptional ActivationTransfectionConceptsDNA bindingAbsence of RAG2Signal sequence recognitionRegion of RAG1RAG2 proteinsBacterial invertasesSequence similarityRecombination signalsSpecific binding interactionsRAG1Sequence recognitionDNA cleavageRAG2Binding interactionsProteinBindingRecombinationRecent studiesSignal recognitionInvertaseHeptamerRecruitmentCleavageLocalizationVivorag-1 and rag-2: Biochemistry and Protein Interactions
Schatz D, Leu T. rag-1 and rag-2: Biochemistry and Protein Interactions. Current Topics In Microbiology And Immunology 1996, 217: 11-29. PMID: 8787615, DOI: 10.1007/978-3-642-50140-1_2.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsAnimalsDNA-Binding ProteinsHomeodomain ProteinsLymphocytesMiceNuclear ProteinsProtein ConformationProteinsRecombinant ProteinsRecombination, GeneticConceptsRAG-1Protein-protein interactionsRAG-2 proteinT-cell receptor proteinsSite-specific recombination reactionLymphocyte-specific factorsProtein interactionsEnzymatic machineryGene productsRAG-2Lymphocyte developmentReceptor proteinBiochemical propertiesProteinCoordinated activityGenesTerminal deoxynucleotidyl transferaseRecombinationDiversityDeoxynucleotidyl transferaseMost componentsMachineryNucleotidesSpeciesTransferase