5W51

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP

Summary for 5W51

• Entry DOI: 10.2210/pdb5w51/pdb
• Related: 5w4u
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC4, 29mer template DNA, ... (16 entities in total)
• Functional Keywords: complex, dna binding protein, dna binding protein-rna-dna complex, dna binding protein/rna/dna
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 13
• Total formula weight: 486808.44

Authors

Wang, W.,Wang, D. (deposition date: 2017-06-13, release date: 2018-06-20, Last modification date: 2023-10-04)

Primary citation

Wang, W.,Xu, L.,Hu, L.,Chong, J.,He, C.,Wang, D.
Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
J.Am.Chem.Soc., 139:14436-14442, 2017

PubMed Abstract: N-Methyladenine (N-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 N-mA remain elusive. In particular, the impact of N-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 N-mA sites via both biochemical and structural approaches. We found that N-mA causes site-specific pol II pausing/stalling. Structural analysis revealed that while N-mA can reach the +1 template position, the stability of the N-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 N-mA on pol II transcription dynamics in different organisms.

PubMed: 28933854
DOI: 10.1021/jacs.7b06381

Experimental method

X-RAY DIFFRACTION (3.404 Å)