RNA polymerase active center: the molecular engine of transcription

E Nudler - Annual review of biochemistry, 2009 - annualreviews.org
RNA polymerase (RNAP) is a complex molecular machine that governs gene expression
and its regulation in all cellular organisms. To accomplish its function of accurately …

The mechanisms of substrate selection, catalysis, and translocation by the elongating RNA polymerase

GA Belogurov, I Artsimovitch - Journal of molecular biology, 2019 - Elsevier
Multi-subunit DNA-dependent RNA polymerases synthesize all classes of cellular RNAs,
ranging from short regulatory transcripts to gigantic messenger RNAs. RNA polymerase has …

Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage

H Kettenberger, KJ Armache, P Cramer - Cell, 2003 - cell.com
The transcription elongation factor TFIIS induces mRNA cleavage by enhancing the intrinsic
nuclease activity of RNA polymerase (Pol) II. We have diffused TFIIS into Pol II crystals and …

[HTML][HTML] A ratchet mechanism of transcription elongation and its control

G Bar-Nahum, V Epshtein, AE Ruckenstein, R Rafikov… - Cell, 2005 - cell.com
RNA chain elongation is a highly processive and accurate process that is finely regulated by
numerous intrinsic and extrinsic signals. Here we describe a general mechanism that …

The RNA polymerase II trigger loop functions in substrate selection and is directly targeted by α-amanitin

CD Kaplan, KM Larsson, RD Kornberg - Molecular cell, 2008 - cell.com
Structural, biochemical, and genetic studies have led to proposals that a mobile element of
multisubunit RNA polymerases, the Trigger Loop (TL), plays a critical role in catalysis and …

Nature of the nucleosomal barrier to RNA polymerase II

ML Kireeva, B Hancock, GH Cremona, W Walter… - Molecular cell, 2005 - cell.com
In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into
nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation …

[HTML][HTML] Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel

J Mukhopadhyay, E Sineva, J Knight, RM Levy… - Molecular cell, 2004 - cell.com
The antibacterial peptide microcin J25 (MccJ25) inhibits transcription by bacterial RNA
polymerase (RNAP). Biochemical results indicate that inhibition of transcription occurs at the …

A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing

I Toulokhonov, J Zhang, M Palangat, R Landick - Molecular cell, 2007 - cell.com
Transcriptional pausing by RNA polymerase is an underlying event in the regulation of
transcript elongation, yet the physical changes in the transcribing complex that create the …

Trigger loop dynamics mediate the balance between the transcriptional fidelity and speed of RNA polymerase II

MH Larson, J Zhou, CD Kaplan… - Proceedings of the …, 2012 - National Acad Sciences
During transcription, RNA polymerase II (RNAPII) must select the correct nucleotide,
catalyze its addition to the growing RNA transcript, and move stepwise along the DNA until a …

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism

M Dangkulwanich, T Ishibashi, S Liu, ML Kireeva… - Elife, 2013 - elifesciences.org
During transcription elongation, RNA polymerase has been assumed to attain equilibrium
between pre-and post-translocated states rapidly relative to the subsequent catalysis. Under …