6BQF

Pol II elongation complex with 'dT-AP' at i+1, i-1 position

Summary for 6BQF

• Entry DOI: 10.2210/pdb6bqf/pdb
• Descriptor: DNA-directed RNA polymerase II subunit RPB1, DNA-directed RNA polymerases I, II, and III subunit RPABC4, DNA (5'-D(P*CP*TP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3'), ... (14 entities in total)
• Functional Keywords: complex, dna binding protein, dna-rna hybrid, transcription, transferase-transcription complex, transferase/transcription
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 12
• Total formula weight: 481863.02

Authors

Wang, W.,Wang, D. (deposition date: 2017-11-27, release date: 2018-02-28, Last modification date: 2024-03-13)

Primary citation

Wang, W.,Walmacq, C.,Chong, J.,Kashlev, M.,Wang, D.
Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Proc. Natl. Acad. Sci. U.S.A., 115:E2538-E2545, 2018

PubMed Abstract: Abasic sites are among the most abundant DNA lesions and interfere with DNA replication and transcription, but the mechanism of their action on transcription remains unknown. Here we applied a combined structural and biochemical approach for a comprehensive investigation of how RNA polymerase II (Pol II) processes an abasic site, leading to slow bypass of lesion. Encounter of Pol II with an abasic site involves two consecutive slow steps: insertion of adenine opposite a noninstructive abasic site (the A-rule), followed by extension of the 3'-rAMP with the next cognate nucleotide. Further studies provided structural insights into the A-rule: ATP is slowly incorporated into RNA in the absence of template guidance. Our structure revealed that ATP is bound to the Pol II active site, whereas the abasic site is located at an intermediate state above the Bridge Helix, a conserved structural motif that is cirtical for Pol II activity. The next extension step occurs in a template-dependent manner where a cognate substrate is incorporated, despite at a much slower rate compared with nondamaged template. During the extension step, neither the cognate substrate nor the template base is located at the canonical position, providing a structural explanation as to why this step is as slow as the insertion step. Taken together, our studies provide a comprehensive understanding of Pol II stalling and bypass of the abasic site in the DNA template.

PubMed: 29487211
DOI: 10.1073/pnas.1722050115

Experimental method

X-RAY DIFFRACTION (3.35 Å)