SNAP output for PDB entry 5w51 [SNAP web server]

PDB-id

5w51; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-RNA-DNA

Method

X-ray (3.404 Å)

Summary

Pol ii elongation complex with an n6-methyladenine-containing template and a matched umpnpp

Reference

Wang W, Xu L, Hu L, Chong J, He C, Wang D (2017): "Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing." J.Am.Chem.Soc., 139, 14436-14442. doi: 10.1021/jacs.7b06381.

Abstract

N₆-Methyladenine (N₆-mA or 6 mA) is an epigenetic DNA modification in eukaryotic genomes. In contrast to the well-established roles of 5-methylcytosine for epigenetic regulation of gene expression, the functional roles of N₆-mA remain elusive. In particular, the impact of N₆-mA modification of the DNA template on RNA polymerase II (pol II) transcription elongation is not known. In this work, using the Saccharomyces cerevisiae pol II transcriptional elongation system as a model, we investigated the molecular mechanism of pol II recognition and processing of N₆-mA sites via both biochemical and structural approaches. We found that N₆-mA causes site-specific pol II pausing/stalling. Structural analysis revealed that while N₆-mA can reach the +1 template position, the stability of the N₆-mA and UTP base pairing is compromised. Taken together, we reveal that the presence of the 6-methyl group on adenine reduces incorporation efficiency and promotes backtracking translocation. Our studies with yeast pol II provide molecular insights into understanding the impacts of N₆-mA on pol II transcription dynamics in different organisms.