Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 3526, Year 2022
Publish date	Jun 20, 2022
Authors	Alec Fraser / Maria L Sokolova / Arina V Drobysheva / Julia V Gordeeva / Sergei Borukhov / John Jumper / Konstantin V Severinov / Petr G Leiman /
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 ...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.
External links	Nat Commun / PubMed:35725571 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.3 - 4.2 Å
Structure data	24763 7um0 EMDB-24763: Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme in complex with DNA containing the AR9 P077 promoter PDB-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 Method: EM (single particle) / Resolution: 3.8 Å 24765 7um1 EMDB-24765: Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme PDB-7um1: Structure of bacteriophage AR9 non-virion RNAP polymerase holoenzyme determined by cryo-EM Method: EM (single particle) / Resolution: 4.1 Å PDB-7s00: X-ray structure of the phage AR9 non-virion RNA polymerase core Method: X-RAY DIFFRACTION / Resolution: 3.3 Å PDB-7s01: X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter Method: X-RAY DIFFRACTION / Resolution: 3.4 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine monophosphate ChemComp-DG: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / dGMPYM / Deoxyguanosine monophosphate ChemComp-DT: THYMIDINE-5'-MONOPHOSPHATE / dTMPYM / Thymidine monophosphate ChemComp-DA: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / dAMPYM / Deoxyadenosine monophosphate ChemComp-DU*: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Deoxyuridine monophosphate
Source	bacillus phage ar9 (virus)
Keywords	TRANSCRIPTION / DNA-dependent multisubunit RNA polymerase / deoxyuridine / template strand promoter / RNAP / TRANSCRIPTION/DNA / sigma factor / TRANSCRIPTION-DNA complex / template-strand promoter / sigma-like factor / gp226