ArticleThe Journal of biological chemistry2013
Watching the bacteriophage N4 RNA polymerase transcription by time-dependent soak-trigger-freeze X-ray crystallography.
Article in The Journal of biological chemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 36 citations in OpenAlex.
- Cryo-EM study of bacteriophage N4 virion RNA polymerase.Journal of bacteriology · 2026Article
- Structural basis for substrate binding and selection by human mitochondrial RNA polymerase.Nature communications · 2024Article
- From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons.Acta crystallographica. Section D, Structural biology · 2024Article
- New insights into DNA polymerase mechanisms provided by time-lapse crystallography.Current opinion in structural biology · 2022Review
- Insight into the mechanism of DNA synthesis by human terminal deoxynucleotidyltransferase.Life science alliance · 2022Article
- Structural and Molecular Kinetic Features of Activities of DNA Polymerases.International journal of molecular sciences · 2022Review
- Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography.The Enzymes · 2021Review
- Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.Nucleic acids research · 2020Article
- Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate.Nature catalysis · 2019Article
- Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II.The Journal of biological chemistry · 2018Article
- X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Dengue Virus Non-Structural Protein 5.Viruses · 2017Review
- Advances in Structural and Single-Molecule Methods for Investigating DNA Lesion Bypass and Repair Polymerases.Chemical research in toxicology · 2017Article
- Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes.PLoS computational biology · 2015Article
- Structural and biochemical investigation of bacteriophage N4-encoded RNA polymerases.Biomolecules · 2015Review
- Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.Journal of the American Chemical Society · 2015Article
- Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.The Journal of biological chemistry · 2014Article
- Fluorescence resonance energy transfer studies of DNA polymerase β: the critical role of fingers domain movements and a novel non-covalent step during nucleotide selection.The Journal of biological chemistry · 2014Article
- An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η.Biochemistry · 2014Review
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2 authors at 1 institution in 1 country.
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Abstract
The challenge for structural biology is to understand atomic-level macromolecular motions during enzymatic reaction. X-ray crystallography can reveal high resolution structures; however, one perceived limitation is that it reveals only static views. Here we use time-dependent soak-trigger-freeze X-ray crystallography, namely, soaking nucleotide and divalent metal into the bacteriophage RNA polymerase (RNAP)-promoter DNA complex crystals to trigger the nucleotidyl transfer reaction and freezing crystals at different time points, to capture real-time intermediates in the pathway of transcription. In each crystal structure, different intensities and shapes of electron density maps corresponding to the nucleotide and metal were revealed at the RNAP active site which allow watching the nucleotide and metal bindings and the phosphodiester bond formation in a time perspective. Our study provides the temporal order of substrate assembly and metal co-factor binding at the active site of enzyme which completes our understanding of the two-metal-ion mechanism and fidelity mechanism in single-subunit RNAPs. The nucleotide-binding metal (Me(B)) is coordinated at the active site prior to the catalytic metal (Me(A)). Me(A) coordination is only temporal, established just before and dissociated immediately after phosphodiester bond formation. We captured these elusive intermediates exploiting the slow enzymatic reaction in crystallo. These results demonstrate that the simple time-dependent soak-trigger-freeze X-ray crystallography offers a direct means for monitoring enzymatic reactions.
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