7UM0

Structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with two DNA oligonucleotides containing the AR9 P077 promoter as determined by cryo-EM

Summary for 7UM0

• Entry DOI: 10.2210/pdb7um0/pdb
• Related: 7S00 7S01
• EMDB information: 24763
• Descriptor: DNA-directed RNA polymerase subunit, DNA-directed RNA polymerase beta' subunit, DNA-directed RNA polymerase beta subunit, ... (7 entities in total)
• Functional Keywords: rnap, deoxyuridine, template-strand promoter, sigma-like factor, gp226, transcription
• Biological source: Bacillus phage AR9; More
• Total number of polymer chains: 6
• Total formula weight: 315986.93

Authors

Leiman, P.G.,Fraser, A.,Sokolova, M.L. (deposition date: 2022-04-05, release date: 2022-07-06, Last modification date: 2024-05-29)

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

ELECTRON MICROSCOPY (3.8 Å)