7S01

X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter

Summary for 7S01

• Entry DOI: 10.2210/pdb7s01/pdb
• Descriptor: DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase beta' subunit, DNA-directed RNA polymerase beta subunit, ... (8 entities in total)
• Functional Keywords: dna-dependent multisubunit rna polymerase, sigma factor, deoxyuridine, template strand promoter, rnap, transcription, transcription-dna complex, transcription/dna
• Biological source: Bacillus phage AR9; More
• Total number of polymer chains: 9
• Total formula weight: 340707.81

Authors

Leiman, P.G.,Sokolova, M.L.,Gordeeva, J.,Fraser, A.,Severinov, K.V. (deposition date: 2021-08-28, release date: 2022-07-06, Last modification date: 2025-02-12)

Primary citation

Fraser, A.,Sokolova, M.L.,Drobysheva, A.V.,Gordeeva, J.V.,Borukhov, S.,Jumper, J.,Severinov, K.V.,Leiman, P.G.
Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.
Nat Commun, 13:3526-3526, 2022

PubMed Abstract: Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host.

PubMed: 35725571
DOI: 10.1038/s41467-022-31214-6

Experimental method

X-RAY DIFFRACTION (3.4 Å)