4U0W: Crystal structure of YvoA from Bacillus ... - RCSB PDB

Method: X-RAY DIFFRACTION; Resolution: 2.00 Å; R-Value Free: 0.254; R-Value Work: 0.205; R-Value Observed: 0.208. WarningYouareusingawebbrowserthatwedonotsupport.Ourwebsitewillnotworkproperly.Pleaseupdatetoanewerversionordownloadanewwebbrowser,suchasChromeorFirefox.TogglenavigationRCSBPDBDeposit PrepareDataPDBx/mmCIFfilepdb_extractSF-ToolLigandExpoMAXITValidateDataValidationServerInformationforJournalsValidationTaskForcesDepositDatawwPDBOneDepSystemPDB-DevDepositionHelp&ResourcesDepositFAQTutorialsAnnotationPoliciesProcessingProceduresPDBx/mmCIFDictionaryChemicalComponentDictionaryPDBFormatGuideBioSyncBeamlines/FacilitiesRelatedToolsSearch BasicSearchAdvancedSearchSequenceSearchChemicalSketchToolUnreleased&NewEntriesBrowseAnnotationsPDBDataDistributionsPDBStatisticsLigandsDrugs&DrugTargetsVisualize Mol*3DViewerProteinFeatureViewGenomeViewAnalyze PairwiseStructureAlignmentProteinSymmetryStructureQualityMapGenomicPositiontoProteinPDBStatisticsEPPICBiologicalAssembliesPDBCitationMeSHNetworkExplorerIntegratedResourcesAdditionalResourcesDownload Coordinates&ExperimentalDataSequencesLigandsFileDownloadServicesWebServicesLearn AboutMoleculeoftheMonthBrowseallResourcesEducationalResourcesCurriculaGuidetoPDBDataNewsandEventsMore ContactUsCitingUsPoliciesAboutRCSBPDBPDBHistoryPDB50TeamMembersAdvisoryCommitteeNewsPublicationsServiceStatusDocumentation GeneralHelpSearchandBrowseBasicSearchAdvancedSearchMol*SequenceViewersToolsProgrammaticAccessAdditionalResourcesSoftwareSupportersDepositionResourcesFAQsGlossaryCareers193183BiologicalMacromolecularStructuresEnablingBreakthroughsinResearchandEducationNavigationTabsStructureSummary3DViewAnnotationsExperimentSequenceGenomeLigandsVersionsAsymmetricUnit&nbsp3DView:&nbspStructure|1D-3DView|ElectronDensity|ValidationReport|LigandInteractionBiologicalAssembly1&nbsp&nbsp3DView:&nbspStructure|1D-3DView|ElectronDensity|ValidationReport|LigandInteractionGlobalSymmetry:Cyclic-C2  (3DView)GlobalStoichiometry:Homo2-mer- A2 LessFindSimilarAssembliesBiologicalassembly1 assignedbyauthorsandgeneratedbyPISA(software)PreviousNextMacromoleculeContentTotalStructureWeight:57.24kDa&nbspAtomCount:4246&nbspModelledResidueCount:486&nbspDepositedResidueCount:492&nbspUniqueproteinchains:1 DisplayFiles FASTASequencePDBFormatPDBFormat(Header)mmCIFFormatmmCIFFormat(Header) DownloadFiles FASTASequencePDBFormatPDBFormat(gz)PDBx/mmCIFFormatPDBx/mmCIFFormat(gz)PDBML/XMLFormat(gz)StructureFactors(CIF)StructureFactors(CIF-gz)ValidationFullPDFValidationXMLBiologicalAssembly1(CIF-gz) BiologicalAssembly1(PDB-gz)fo-fcMap(DSN6)2fo-fcMap(DSN6)MapCoefficients(MTZformat)4U0WCrystalstructureofYvoAfromBacillussubtilisincomplexwithN-acetylglucosamine-6-phosphatePDBDOI:&nbsp10.2210/pdb4U0W/pdbClassification:&nbspTRANSCRIPTIONOrganism(s):&nbspBacillussubtilissubsp.subtilisstr.168ExpressionSystem:&nbspEscherichiacoliMutation(s):&nbspNo&nbspDeposited:&nbsp2014-07-14&nbspReleased:&nbsp2015-01-14&nbspDepositionAuthor(s):&nbspFillenberg,S.B.,Muller,Y.A.FundingOrganization(s):&nbspGermanResearchFoundationExperimentalDataSnapshotMethod:&nbspX-RAYDIFFRACTIONResolution:&nbsp2.00ÅR-ValueFree:&nbsp0.254&nbspR-ValueWork:&nbsp0.205&nbspR-ValueObserved:&nbsp0.208&nbspwwPDBValidation&nbsp&nbsp3DReport&nbspFullReportLigandStructureQualityAssessment&nbspThisisversion2.0oftheentry.Seecomplete&nbsphistory.&nbspLiteratureDownloadPrimaryCitation&nbsp&nbspDownloadMendeleyStructuralinsightintooperatordre-sitesrecognitionandeffectorbindingintheGntR/HutCtranscriptionregulatorNagR.Fillenberg,S.B.,&nbspGrau,F.C.,&nbspSeidel,G.,&nbspMuller,Y.A.(2015)NucleicAcidsRes&nbsp43:1283-1296PubMed:&nbsp25564531&nbspSearchonPubMedSearchonPubMedCentralDOI:&nbsp10.1093/nar/gku1374PrimaryCitationofRelatedStructures:&nbsp4U0V,4U0W,4U0Y,4WWCPubMedAbstract:&nbspTheuptakeandmetabolismofN-acetylglucosamine(GlcNAc)inBacillussubtilisiscontrolledbyNagR(formerlynamedYvoA),amemberofthewidely-occurringGntR/HutCfamilyoftranscriptionregulators.UponbindingtospecificDNAoperatorsites(dre-sites)NagRblocksthetranscriptionofgenesforGlcNAcutilizationandinteractionofNagRwitheffectorsabrogatesgenerepression...TheuptakeandmetabolismofN-acetylglucosamine(GlcNAc)inBacillussubtilisiscontrolledbyNagR(formerlynamedYvoA),amemberofthewidely-occurringGntR/HutCfamilyoftranscriptionregulators.UponbindingtospecificDNAoperatorsites(dre-sites)NagRblocksthetranscriptionofgenesforGlcNAcutilizationandinteractionofNagRwitheffectorsabrogatesgenerepression.HerewereportcrystalstructuresofNagRincomplexwithoperatorDNAandincomplexwiththeputativeeffectormoleculesglucosamine-6-phosphate(GlcN-6-P)andN-acetylglucosamine-6-phosphate(GlcNAc-6-P).AcomparisonofthedistinctconformationalstatessuggeststhateffectorsareabletodisplacetheNagR-DNA-bindingdomains(NagR-DBDs)byalmost70Åuponbinding.Inaddition,ahigh-resolutioncrystalstructureofisolatedNagR-DBDsincomplexwithpalindromicdouble-strandedDNA(dsDNA)disclosesboththedeterminantsforhighlysequence-specificoperatordre-siterecognitionandfortheunspecificbindingofNagRtodsDNA.Extensivebiochemicalbindingstudiesinvestigatingtheaffinitiesoffull-lengthNagRandisolatedNagR-DBDsforeitherrandomDNA,dre-site-derivedpalindromicornaturallyoccurringnon-palindromicdre-sitesequencessuggestthatproperNagRfunctionreliesonaneffector-inducedfine-tuningoftheDNA-bindingaffinitiesofNagRandnotonacompleteabrogationofitsDNAbinding.OrganizationalAffiliation:&nbspLehrstuhlfürBiotechnik,DepartmentofBiology,Friedrich-AlexanderUniversityErlangen-Nuremberg,Henkestrasse91,D-91052Erlangen,Germanyyves.muller@fau.de.HideFullAbstractMacromoleculesFindsimilarproteinsby: Sequence 100%95%90%80%70%60%50%40%30%(byidentitycutoff) | 3DStructureEntityID:1MoleculeChainsSequenceLengthOrganismDetailsImageHTH-typetranscriptionalrepressorYvoAA,B246Bacillussubtilissubsp.subtilisstr.168Mutation(s):0&nbspGeneNames:&nbspyvoA,&nbspBSU35030,&nbspnagRUniProtFindproteinsfor&nbspO34817&nbsp(Bacillussubtilis(strain168))Explore&nbspO34817&nbspGotoUniProtKB:&nbspO34817EntityGroups &nbspSequenceClusters30%Identity50%Identity70%Identity90%Identity95%Identity100%IdentityUniProtGroupO34817ProteinFeatureViewExpandReferenceSequenceSmallMoleculesLigands&nbsp3UniqueIDChainsName/Formula/InChIKey2DDiagram3DInteractions16GQueryon16GDownloadIdealCoordinatesCCDFile&nbspDownloadInstanceCoordinates SDFformat,chainC[authA]SDFformat,chainK[authB]MOL2format,chainC[authA]MOL2format,chainK[authB]C[authA],K[authB]2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranoseC8H16NO9PBRGMHAYQAZFZDJ-PVFLNQBWSA-N LigandInteractionGOLQueryonGOLDownloadIdealCoordinatesCCDFile&nbspDownloadInstanceCoordinates SDFformat,chainD[authA]SDFformat,chainL[authB]MOL2format,chainD[authA]MOL2format,chainL[authB]D[authA],L[authB]GLYCEROLC3H8O3PEDCQBHIVMGVHV-UHFFFAOYSA-N LigandInteractionEDOQueryonEDODownloadIdealCoordinatesCCDFile&nbspDownloadInstanceCoordinates SDFformat,chainE[authA]SDFformat,chainF[authA]SDFformat,chainG[authA]SDFformat,chainH[authA]SDFformat,chainI[authA]SDFformat,chainJ[authA]SDFformat,chainM[authB]SDFformat,chainN[authB]SDFformat,chainO[authB]SDFformat,chainP[authB]SDFformat,chainQ[authB]SDFformat,chainR[authB]SDFformat,chainS[authB]MOL2format,chainE[authA]MOL2format,chainF[authA]MOL2format,chainG[authA]MOL2format,chainH[authA]MOL2format,chainI[authA]MOL2format,chainJ[authA]MOL2format,chainM[authB]MOL2format,chainN[authB]MOL2format,chainO[authB]MOL2format,chainP[authB]MOL2format,chainQ[authB]MOL2format,chainR[authB]MOL2format,chainS[authB]E[authA],F[authA],G[authA],H[authA],I[authA],E[authA],F[authA],G[authA],H[authA],I[authA],J[authA],M[authB],N[authB],O[authB],P[authB],Q[authB],R[authB],S[authB]Less1,2-ETHANEDIOLC2H6O2LYCAIKOWRPUZTN-UHFFFAOYSA-N LigandInteractionBindingAffinityAnnotations&nbspIDSourceBindingAffinity16GBindingMOAD:&nbsp4U0WKd:&nbsp1.00e+6&nbsp(nM)from1assay(s)ExperimentalData&ValidationExperimentalDataMethod:&nbspX-RAYDIFFRACTIONResolution:&nbsp2.00ÅR-ValueFree:&nbsp0.254&nbspR-ValueWork:&nbsp0.205&nbspR-ValueObserved:&nbsp0.208&nbspSpaceGroup:&nbspH32UnitCell:Length(Å)Angle(˚)a=99.142α=90b=99.142β=90c=353.978γ=120SoftwarePackage:SoftwareNamePurposeXSCALEdatascalingPHASERphasingPHENIXrefinementXDSdatareductionStructureValidationView&nbspFullValidationReportLigandStructureQualityAssessment&nbspViewmorein-depthexperimentaldataEntryHistory&nbsp&FundingInformationDepositionDataDepositedDate:&nbsp2014-07-14&nbspReleasedDate:&nbsp2015-01-14&nbspDepositionAuthor(s):&nbspFillenberg,S.B.,Muller,Y.A.FundingOrganizationLocationGrantNumberGermanResearchFoundationGermany--RevisionHistory (Fulldetailsanddatafiles)Version1.0:2015-01-14Type:InitialreleaseVersion1.1:2015-01-21Changes:DatabasereferencesVersion1.2:2015-02-04Changes:DatabasereferencesVersion2.0:2020-07-29Type:RemediationReason:CarbohydrateremediationChanges:Advisory,Atomicmodel,Authorsupportingevidence,Datacollection,Derivedcalculations,StructuresummaryAboutAboutUsCitingUsPublicationsTeamCareersUsage&PrivacyHelpContactUsDocumentationWebsiteFAQGlossaryServiceStatusRCSBPartnersNucleicAcidDatabasewwPDBPartnersRCSBPDBPDBePDBjBMRBEMDBRCSBPDB(citation)ishostedbyRCSBPDBisamemberoftheRCSBPDBisfundedby theNationalScienceFoundation(DBI-1832184), theUSDepartmentofEnergy(DE-SC0019749), andtheNationalCancerInstitute, NationalInstituteofAllergyandInfectiousDiseases, andNationalInstituteofGeneralMedicalSciencesoftheNationalInstitutesofHealthundergrantR01GM133198.