4Q4Z

Thermus thermophilus RNA polymerase de novo transcription initiation complex

Summary for 4Q4Z

• Entry DOI: 10.2210/pdb4q4z/pdb
• Related: 4Q5A 4Q5S
• Descriptor: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, ... (12 entities in total)
• Functional Keywords: transcription, dna and ntp, transcription-dna complex, transcription/dna
• Biological source: Thermus thermophilus; More
• Cellular location: Cytoplasm (By similarity): Q5SKW1
• Total number of polymer chains: 8
• Total formula weight: 443004.47

Authors

Murakami, K.S. (deposition date: 2014-04-15, release date: 2014-07-30, Last modification date: 2024-02-28)

Primary citation

Basu, R.S.,Warner, B.A.,Molodtsov, V.,Pupov, D.,Esyunina, D.,Fernandez-Tornero, C.,Kulbachinskiy, A.,Murakami, K.S.
Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.
J.Biol.Chem., 289:24549-24559, 2014

PubMed Abstract: The bacterial RNA polymerase (RNAP) holoenzyme containing σ factor initiates transcription at specific promoter sites by de novo RNA priming, the first step of RNA synthesis where RNAP accepts two initiating ribonucleoside triphosphates (iNTPs) and performs the first phosphodiester bond formation. We present the structure of de novo transcription initiation complex that reveals unique contacts of the iNTPs bound at the transcription start site with the template DNA and also with RNAP and demonstrate the importance of these contacts for transcription initiation. To get further insight into the mechanism of RNA priming, we determined the structure of initially transcribing complex of RNAP holoenzyme with 6-mer RNA, obtained by in crystallo transcription approach. The structure highlights RNAP-RNA contacts that stabilize the short RNA transcript in the active site and demonstrates that the RNA 5'-end displaces σ region 3.2 from its position near the active site, which likely plays a key role in σ ejection during the initiation-to-elongation transition. Given the structural conservation of the RNAP active site, the mechanism of de novo RNA priming appears to be conserved in all cellular RNAPs.

PubMed: 24973216
DOI: 10.1074/jbc.M114.584037

Experimental method

X-RAY DIFFRACTION (2.9 Å)