ArticleBiochimica et biophysica acta2013
The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.
Article in Biochimica et biophysica acta, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 39 citations in OpenAlex.
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- Pleomorphic effects of three small-molecule inhibitors on transcription elongation bybioRxiv : the preprint server for biology · 2025Article
- Transient-State Kinetic Analysis of the RNA Polymerase II Nucleotide Incorporation Mechanism.Biochemistry · 2023Article
- Article
- High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors.Nucleic acids research · 2020Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Active site closure stabilizes the backtracked state of RNA polymerase.Nucleic acids research · 2018Article
- RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.Nucleic acids research · 2018Article
- Hinge action versus grip in translocation by RNA polymerase.Transcription · 2018Article
- Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits.Nucleic acids research · 2017Article
- Regulation of transcription elongation and termination.Biomolecules · 2015Review
- RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications.Critical reviews in biochemistry and molecular biology · 2015Review
- Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.Nucleic acids research · 2014Article
- A genetic assay for transcription errors reveals multilayer control of RNA polymerase II fidelity.PLoS genetics · 2014Article
- Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis.DNA repair · 2014Review
- Coliphage HK022 Nun protein inhibits RNA polymerase translocation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Millisecond dynamics of RNA polymerase II translocation at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Article
- CBR antimicrobials alter coupling between the bridge helix and the β subunit in RNA polymerase.Nature communications · 2014Article
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9 authors at 6 institutions in 1 country.
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Abstract
The bridge α-helix in the β' subunit of RNA polymerase (RNAP) borders the active site and may have roles in catalysis and translocation. In Escherichia coli RNAP, a bulky hydrophobic segment near the N-terminal end of the bridge helix is identified (β' 772-YFI-774; the YFI motif). YFI is located at a distance from the active center and adjacent to a glycine hinge (β' 778-GARKG-782) involved in dynamic bending of the bridge helix. Remarkably, amino acid substitutions in YFI significantly alter intrinsic termination, pausing, fidelity and translocation of RNAP. F773V RNAP largely ignores the λ tR2 terminator at 200μM NTPs and is strongly reduced in λ tR2 recognition at 1μM NTPs. F773V alters RNAP pausing and backtracking and favors misincorporation. By contrast, the adjacent Y772A substitution increases fidelity and exhibits other transcriptional defects generally opposite to those of F773V. All atom molecular dynamics simulation revealed two separate functional connections emanating from YFI explaining the distinct effects of substitutions: Y772 communicates with the active site through the link domain in the β subunit, whereas F773 communicates through the fork domain in the β subunit. I774 interacts with the F-loop, which also contacts the glycine hinge of the bridge helix. These results identified negative and positive circuits coupled at YFI and employed for regulation of catalysis, elongation, termination and translocation.
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