3WOD

RNA polymerase-gp39 complex

Summary for 3WOD

• Entry DOI: 10.2210/pdb3wod/pdb
• Related: 3WOE 3WOF
• Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... (7 entities in total)
• Functional Keywords: rna polymerase, transcription, transferase-transcription complex, transferase/transcription
• Biological source: Thermus phage P23-45; More
• Cellular location: Cytoplasm : Q5SKW1
• Total number of polymer chains: 8
• Total formula weight: 459198.06

Authors

Tagami, S.,Sekine, S.,Minakhin, L.,Esyunina, D.,Akasaka, R.,Shirouzu, M.,Kulbachinskiy, A.,Severinov, K.,Yokoyama, S. (deposition date: 2013-12-26, release date: 2014-03-12, Last modification date: 2024-10-30)

Primary citation

Tagami, S.,Sekine, S.,Minakhin, L.,Esyunina, D.,Akasaka, R.,Shirouzu, M.,Kulbachinskiy, A.,Severinov, K.,Yokoyama, S.
Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Genes Dev., 28:521-531, 2014

PubMed Abstract: Transcription of DNA to RNA by DNA-dependent RNA polymerase (RNAP) is the first step of gene expression and a major regulation point. Bacteriophages hijack their host's transcription machinery and direct it to serve their needs. The gp39 protein encoded by Thermus thermophilus phage P23-45 binds the host's RNAP and inhibits transcription initiation from its major "-10/-35" class promoters. Phage promoters belonging to the minor "extended -10" class are minimally inhibited. We report the crystal structure of the T. thermophilus RNAP holoenzyme complexed with gp39, which explains the mechanism for RNAP promoter specificity switching. gp39 simultaneously binds to the RNAP β-flap domain and the C-terminal domain of the σ subunit (region 4 of the σ subunit [σ4]), thus relocating the β-flap tip and σ4. The ~45 Å displacement of σ4 is incompatible with its binding to the -35 promoter consensus element, thus accounting for the inhibition of transcription from -10/-35 class promoters. In contrast, this conformational change is compatible with the recognition of extended -10 class promoters. These results provide the structural bases for the conformational modulation of the host's RNAP promoter specificity to switch gene expression toward supporting phage development for gp39 and, potentially, other phage proteins, such as T4 AsiA.

PubMed: 24589779
DOI: 10.1101/gad.233916.113

Experimental method

X-RAY DIFFRACTION (3.6 Å)