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HoloenzymesDNA-Directed RNA PolymerasesSigma FactorDNA-Directed DNA PolymeraseRNA Polymerase Sigma 54Escherichia coliTranscription, GeneticPromoter Regions, GeneticMolecular Sequence DataBase SequenceBacteriophage T4Potassium PermanganateBacterial ProteinsTemplates, GeneticDNA Polymerase IIIRNA Polymerase IIT-PhagesCyclic AMP Receptor ProteinGene Expression Regulation, BacterialPolymerase Chain ReactionDNA, BacterialMacromolecular SubstancesDNA ReplicationViral ProteinsBacillus subtilisOperonProtein BindingEscherichia coli ProteinsTranscription FactorsKineticsDNA, ViralBinding SitesDNA-Binding ProteinsAmino Acid SequenceDNA Polymerase IIGenes, BacterialDNA Polymerase IDNA FootprintingModels, MolecularMutationRNA, BacterialDNANucleic Acid ConformationPlasmidsProtein ConformationTrans-ActivatorsAdenosine TriphosphateRNA Polymerase IRNA Polymerase IIIApoenzymesDNA Polymerase betaTranscriptional ActivationMediator ComplexProtein SubunitsCoenzymesCloning, MolecularRNA ReplicaseDNA PrimersRNA-Directed DNA PolymeraseCatalytic DomainProtein Phosphatase 2Saccharomyces cerevisiaeRNARecombinant ProteinsSubstrate SpecificityReverse Transcriptase Polymerase Chain ReactionPoly(ADP-ribose) PolymerasesElectrophoresis, Polyacrylamide GelProtein Structure, TertiarySaccharomyces cerevisiae ProteinsRNA NucleotidyltransferasesRNA, MessengerDNA, Single-StrandedMolecular WeightRibonuclease PDNA PrimaseBacteriophage phi X 174CatalysisExonucleasesHeLa CellsCyclin-Dependent Kinase 8Transcription Factors, TFIICell LineCasein Kinase IIExodeoxyribonucleasesDeoxyribonucleotidesCyclic AMP-Dependent Protein Kinase RIIalpha SubunitPolynucleotide AdenylyltransferaseMutagenesisMutagenesis, Site-DirectedDeoxyadenine NucleotidesRNA, ViralChromatography, GelPhosphoprotein PhosphatasesSequence AlignmentExodeoxyribonuclease VEnzyme ActivationThymine NucleotidesTranscriptional Elongation FactorsAspartate Carbamoyltransferase
RNAPBacterial RNA polymerase holoenzymeSubunitsEscherichia coli DNASubunitReplicative DNA polymeraseColiReplicationTranscriptionalEnzymeComplexesInhibitionExonucleaseProteinsSynthesisProcessivityKlenowClampSigmaElongationActivityPCNALigaseNucleotidesEnzymesFragmentComplexCatalyzesBoundStructureDistinctChainAssembly
RNAP7
  • All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
  • Sigma factors are a class of proteins constituting essential dissociable subunits that confer sequence-specific DNA binding properties to RNA polymerase (RNAP). (hindawi.com)
  • Within the RNAP holoenzyme, sigma factors provide promoter recognition specificity to the polymerase and contribute to DNA strand separation, then they dissociate from RNAP core enzyme and transcription initiation follows [ 1 ]. (hindawi.com)
  • AsiA simultaneously occupies the surface of region 4 that ordinarily contacts core RNA polymerase (RNAP), suggesting that an AsiA-bound sigma70 may also undergo conformational changes in the context of the RNAP holoenzyme. (rcsb.org)
  • Here we show that all three sites are required for NorR-dependent catalysis of open complex formation by 54-RNAP holoenzyme (E54). (strath.ac.uk)
  • Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). (proteopedia.org)
  • Given the physiological importance of gltBDF , and the potential opportunity to learn about integration of global regulatory signals, a combination of in vivo and in vitro approaches was used to investigate the involvement of additional regulatory proteins, and to determine their relative binding positions and potential interactions with one another and with RNA polymerase (RNAP). (biomedcentral.com)
Bacterial RNA polymerase holoenzyme1
  • A series of hybrid compounds that incorporated anthranilic acid with activated 1H-indoles through a glyoxylamide linker were designed to target bacterial RNA polymerase holoenzyme formation using computational docking. (edu.au)
Subunits3
  • Escherichia coli DNA polymerase III holoenzyme contains 10 different subunits which assort into three functional components: a core catalytic unit containing DNA polymerase activity, the beta sliding clamp that encircles DNA for processive replication, and a multisubunit clamp loader apparatus called gamma complex that uses ATP to assemble the beta clamp onto DNA. (neb.com)
  • A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. (umu.se)
  • The herpes simplex virus DNA polymerase is composed of two subunits, a large catalytic subunit (Pol) and a smaller subunit (UL42) that increases the processivity of the holoenzyme. (ed.ac.uk)
Escherichia coli DNA2
Subunit4
  • the α subunit (encoded by the dnaE gene) has the polymerase activity. (wikipedia.org)
  • Reference: Devoted to the lagging strand-the subunit of DNA polymerase III holoenzyme contacts SSB to promote processive elongation and sliding clamp assembly. (neb.com)
  • These results establish a role for the psi subunit in contacting SSB, thus enhancing the clamp loading and processivity of synthesis of the holoenzyme, presumably by helping to localize the holoenzyme to sites of SSB-coated ssDNA. (neb.com)
  • The catalytic subunit (p125) harbours the polymerase and exonuclease activities, and a metal-binding C-terminal domain (CTD). (nature.com)
Replicative DNA polymerase3
  • The Escherichia coli dnaN159 allele encodes a mutant form of the β-sliding clamp (β159) that is impaired for interaction with the replicative DNA polymerase (Pol), Pol III. (asm.org)
  • These phenotypes appear to result, at least in part, from impaired interactions of the mutant β159 clamp protein with the replicative DNA polymerase, Pol III ( 38 ). (asm.org)
  • PolD is an archaeal replicative DNA polymerase, which is widely distributed among Archaea and has been shown to be essential for cell viability. (pasteur.fr)
Coli8
  • The factors did not inhibit the activity of RNA polymerase of Escherichia coli. (elsevierpure.com)
  • E. coli strains bearing the dnaN159 allele display temperature-sensitive growth ( 14 , 35 , 38 ) and altered DNA polymerase (Pol) usage ( 29 , 38 - 40 ). (asm.org)
  • As a result of the impaired β159-Pol III interaction, E. coli strains bearing the dnaN159 allele display increased utilization of the three SOS-regulated DNA polymerases, Pol II ( polB ), Pol IV ( dinB ), and Pol V ( umuDC ) ( 29 , 38 - 40 ). (asm.org)
  • The 5'→3' exonuclease activity of E. coli DNA polymerase I makes it unsuitable for some applications. (qiagen.com)
  • The Klenow Fragment of E. coli DNA polymerase I lacks this 5'-exonuclease activity but retains the 5'→3' polymerase activity and the 3'→5' exonuclease activity for removal of precoding nucleotides and proofreading. (qiagen.com)
  • Just as the 5'→3' exonuclease activity of E. coli DNA polymerase I can be undesirable, the 3'→5' exonuclease proofreading activity of Klenow Fragment can also be undesirable in some circumstances. (qiagen.com)
  • The primers are synthesized by a DNA dependent RNA polymerase enzyme called primase-the product of the dna G gene in E. coli . (blogspot.com)
  • Unique to the norVW promoter in Escherichia coli is the presence of three enhancer sites associated with a binding site for 54-RNA polymerase. (strath.ac.uk)
Replication5
  • DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. (wikipedia.org)
  • DNA polymerase I & III, along with many other enzymes are all required for the high fidelity, high-processivity of DNA replication. (wikipedia.org)
  • Beta clamp DNA polymerase DNA replication Reyes-Lamothe R, Sherratt D, Leake M (2010). (wikipedia.org)
  • In contrast to these three Pols, which under certain conditions impede growth of the dnaN159 strain ( 29 , 39 , 40 ), presumably by impairing DNA replication, the catalytic DNA polymerase activity of Pol I ( polA ) is essential for viability of the dnaN159 strain ( 38 ). (asm.org)
  • DNA polymerases (DNAPs) are the key enzymes of DNA replication and diverse DNA repair processes. (pasteur.fr)
Transcriptional1
  • Hu Y, Morichaud Z, Chen S, Leonetti JP, Brodolin K. Mycobacterium tuberculosis RbpA protein is a new type of transcriptional activator that stabilizes the sigma A-containing RNA polymerase holoenzyme. (proteopedia.org)
Enzyme5
  • The PEP enzyme recognizes the -10 and -35 cis -elements, similar to those found in bacterial promoters whereas the NEP enzyme recognizes the YRTA-motif, which can also be found upstream of several genes with PEP promoters indicating that these genes can be transcribed by both polymerases ( Pfannschmidt and Liere, 2005 ). (frontiersin.org)
  • This problem is overcome by introducing mutations that result in the Klenow Fragment (3'→5' exo-) enzyme that retains 5'→3' polymerase activity but lacks any exonuclease activity. (qiagen.com)
  • The three-dimensional crystal structure of the DnaG catalytic domain revealed its folding and active site are distinct from the well studied polymerases, suggesting that it may employ a novel enzyme mechanism. (blogspot.com)
  • In vitro synthesis of RNA requires a purified DNA plasmid, purified RNA polymerase, metal-ion enzyme cofactors, and raw-material nucleotides. (bioprocessintl.com)
  • Among the complexes, cellular holoenzyme and minimal recombinant enzyme monomeric for TERT had catalytic activity. (elifesciences.org)
Complexes1
  • Deoxyribonucleic Acid (DNA) Recall that the replisome contains a DNA polymerase III holoenzyme dimer with two core complexes that can catalyze polymerization. (blogspot.com)
Inhibition1
  • Hartkoorn RC, Sala C, Magnet SJ, Chen JM, Pojer F, Cole ST. Sigma factor F does not prevent rifampin inhibition of RNA polymerase or cause rifampin tolerance in Mycobacterium tuberculosis. (proteopedia.org)
Exonuclease3
  • The holoenzyme possesses three activities: 5'→3' DNA-dependent DNA polymerase, 3'→5' proofreading and 3'→5' exonuclease (also known as flap endonuclease). (qiagen.com)
  • The main duty of the 5'→3' exonuclease activity is to remove the RNA primers at the 5' ends of newly synthesized DNA so that the polymerase activity can fill in the resulting gaps. (qiagen.com)
  • DNA polymerases lacking a 3'→5' exonuclease may add a single nontemplate-dependent nucleotide to the 3'-end of a sequence (tailing) with a preference for dATP depending on the reaction conditions and sequence context. (qiagen.com)
Proteins1
  • Across every domain of life, polymerase holoenzyme accessory proteins play an integral role in achieving the extraordinary efficacy and accuracy of the replicative polymerase complex. (pasteur.fr)
Synthesis6
  • Klenow Fragment (3'→5' exo-) is a mesophilic DNA polymerase that displays a moderate strand displacement activity during DNA synthesis. (qiagen.com)
  • The replisome contains activities that separate the strands and hold them apart for synthesis by the replisome version of DNA polymerase, called DNA polymerase III in bacteria. (blogspot.com)
  • The use of short RNA primers gets around the limitation imposed by the mechanism of DNA polymerase, namely, that it cannot initiate DNA synthesis de novo . (blogspot.com)
  • DNA polymerase III catalyzes synthesis of DNA in the 5′ → 3′ direction by extending each short RNA primer. (blogspot.com)
  • We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. (elifesciences.org)
  • Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. (nature.com)
Processivity2
  • DNA polymerase III has a high processivity and therefore, synthesizes DNA very quickly. (wikipedia.org)
  • Replicative DNA polymerases have evolved the ability to copy the genome with high processivity and fidelity. (pasteur.fr)
Klenow2
  • The inhibitory effects were less potent for the activities of the large (Klenow) fragment of DNA polymerase I and T4 DNA polymerase than for DNA polymerase HI holoenzyme. (elsevierpure.com)
  • Klenow Fragment (3'→5' exo-) is the large fragment of DNA polymerase I (Klenow Fragment) that has been rendered deficient in both proofreading (3'→5') and nick-translation (3'→5') nuclease activities. (qiagen.com)
Clamp1
  • Omission of psi from the holoenzyme prevents contact with single-stranded DNA-binding protein (SSB) and lowers the efficiency of clamp loading and chain elongation under conditions of elevated salt. (neb.com)
Sigma1
  • HAMAP-Rule:MF_01321] [ SIGA_MYCTU ] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. (proteopedia.org)
Elongation1
  • DNA polymerases catalyze chain elongation exclusively in the 5′ → 3′ direction. (blogspot.com)
Activity2
  • Similar to other replicative DNA polymerases, the activity of PolD is strongly stimulated through its interaction with PCNA. (pasteur.fr)
  • The functional importance of the interaction was confirmed by the finding that a pol mutant defective for UL42 binding retained polymerase activity, but did not synthesize longer DNA products in the presence of UL42. (ed.ac.uk)
PCNA3
  • By using an integrative approach which combines cryo-electron microscopy and X-ray crystallography, the Unit of Structural Dynamics of Macromolecules deciphered the recruitment and cooperativity mechanisms between DNA polymerase D and PCNA. (pasteur.fr)
  • This structure unveils the molecular basis for the interaction and cooperativity between the whole replicative polymerase and PCNA with an unprecedented level of detail. (pasteur.fr)
  • In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. (nature.com)
Ligase1
Nucleotides1
Enzymes1
  • Purity among commercially available polymerase enzymes is variable, and some enzymes are stabilized with bovine serum albumin (BSA). (bioprocessintl.com)
Fragment1
Complex1
  • Inhibitors of bacterial RNA polymerase transcription complex" by Daniel S. Wenholz, Michael Miller et al. (edu.au)
Catalyzes1
  • [1] [ RPOA_MYCTU ] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (proteopedia.org)
Bound1
  • 2 β units (dnaN) which act as sliding DNA clamps, they keep the polymerase bound to the DNA. (wikipedia.org)
Structure5
  • We present the strategy for the production of the VACV DNA polymerase holoenzyme composed of the E9 polymerase associated with its co-factor, the A20-D4 heterodimer, which led to the 3.8 Å cryo-electron microscopy (cryo-EM) structure of the DNA-free form of the holoenzyme. (biorxiv.org)
  • The structure of E9 does not change in context of the holoenzyme compared to the crystal structure. (biorxiv.org)
  • The holoenzyme structure is quite compact and surprisingly similar to the MPXV holoenzyme in presence of a DNA template, with the exception of a movement of the finger domain and the thumb domain, which becomes ordered in presence of DNA. (biorxiv.org)
  • Even in absence of DNA, the VACV holoenzyme structure is too compact for an agreement with SAXS data. (biorxiv.org)
  • Here we present the first structure of the vaccinia virus polymerase holoenzyme E9-A20-D4 at 3.8 Å obtained by cryo-electron microscopy. (biorxiv.org)
Distinct1
  • a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. (frontiersin.org)
Chain1
  • DNA polymerase I is a single polypeptide chain consisting of ∼930 residues. (qiagen.com)
Assembly1