9FND

Transcriptional activator PafBC bound to mycobacterial RNA polymerase

Summary for 9FND

• Entry DOI: 10.2210/pdb9fnd/pdb
• EMDB information: 50590
• Descriptor: Transcriptional regulator-like protein, PafC (2 entities in total)
• Functional Keywords: pafbc, sigma adaptation, wyl domain, transcriptional activator, transcription
• Biological source: Mycolicibacterium smegmatis MC2 155; More
• Total number of polymer chains: 2
• Total formula weight: 70251.96

Authors

Zdanowicz, R.,Schilling, C.M.,Rabl, J.,Mueller, A.U.,Boehringer, D.,Glockshuber, R.,Weber-Ban, E. (deposition date: 2024-06-10, release date: 2025-02-12, Last modification date: 2025-02-19)

Primary citation

Schilling, C.M.,Zdanowicz, R.,Rabl, J.,Muller, A.U.,Boehringer, D.,Glockshuber, R.,Weber-Ban, E.
Single-stranded DNA binding to the transcription factor PafBC triggers the mycobacterial DNA damage response.
Sci Adv, 11:eadq9054-eadq9054, 2025

PubMed Abstract: The DNA damage response in mycobacteria is controlled by the heterodimeric transcription factor PafBC, a member of the WYL domain-containing protein family. It has been shown that PafBC induces transcription of its regulon by reprogramming the housekeeping RNA polymerase holoenzyme to recognize PafBC-dependent promoters through sigma adaptation. However, the mechanism by which DNA damage is sensed and translated into PafBC activation has remained unclear. Here, we demonstrate that the binding of single-stranded DNA (ssDNA) to the WYL domains of PafBC activates the transcription factor. Our cryo-electron microscopy structure of full-length PafBC in its active conformation, bound to the transcription initiation complex, reveals a previously unknown mode of interaction between the ssDNA and the WYL domains. Using biochemical experiments, we show that short ssDNA fragments bind to PafBC dynamically, resulting in deactivation as ssDNA levels decrease postrepair. Our findings shed light on the mechanism linking DNA damage to PafBC activation and expand our understanding of WYL domain-containing proteins.

PubMed: 39919186
DOI: 10.1126/sciadv.adq9054

Experimental method

ELECTRON MICROSCOPY (4 Å)