9Q93
CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4
This is a non-PDB format compatible entry.
Summary for 9Q93
| Entry DOI | 10.2210/pdb9q93/pdb |
| EMDB information | 52916 |
| Descriptor | Psp operon transcriptional activator, ALUMINUM FLUORIDE, MAGNESIUM ION, ... (11 entities in total) |
| Functional Keywords | sigma factor, transcription, complex, aaa+, dna-binding protein |
| Biological source | Escherichia coli K-12 More |
| Total number of polymer chains | 14 |
| Total formula weight | 645518.31 |
| Authors | |
| Primary citation | Gao, F.,Ye, F.,Buck, M.,Zhang, X. Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling. Proc.Natl.Acad.Sci.USA, 122:e2425868122-e2425868122, 2025 Cited by PubMed Abstract: Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ. σ recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does not spontaneously isomerize to the open state where promoter DNA is melted out and competent for transcription. The σ-mediated open complex formation requires specific AAA+ proteins (TPases ssociated with diverse cellular ctivities) known as bacterial enhancer-binding proteins (bEBPs). We have now obtained structures of new intermediate states of bEBP-bound complexes during transcription initiation, which elucidate the mechanism of DNA melting driven by ATPase activity of bEBPs and suggest a mechanistic model that couples the Adenosine triphosphate (ATP) hydrolysis cycle within the bEBP hexamer with σ unfolding. Our data reveal that bEBP forms a nonplanar hexamer with the hydrolysis-ready subunit located at the furthest/highest point of the spiral hexamer relative to the RNAP. ATP hydrolysis induces conformational changes in bEBP that drives a vectoral transiting of the regulatory N terminus of σ into the bEBP hexamer central pore causing the partial unfolding of σ, while forming specific bEBP contacts with promoter DNA. Furthermore, our data suggest a mechanism of the bEBP AAA+ protein that is distinct from the hand-over-hand mechanism proposed for many other AAA+ proteins, highlighting the versatile mechanisms utilized by the large protein family. PubMed: 40273105DOI: 10.1073/pnas.2425868122 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (6.6 Å) |
Structure validation
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