5VSW

X-ray crystal structure of Escherichia coli RNA polymerase and DksA/ppGpp complex

Summary for 5VSW

• Entry DOI: 10.2210/pdb5vsw/pdb
• Related: 4YG2
• Descriptor: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', ... (9 entities in total)
• Functional Keywords: rna polymerase, dksa, ppgpp, transferase-dna complex, transferase/dna
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 13
• Total formula weight: 939553.53

Authors

Murakami, K.S.,Molodtsov, V. (deposition date: 2017-05-12, release date: 2017-06-14, Last modification date: 2024-03-13)

Primary citation

Molodtsov, V.,Sineva, E.,Zhang, L.,Huang, X.,Cashel, M.,Ades, S.E.,Murakami, K.S.
Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.
Mol. Cell, 69:828-839.e5, 2018

PubMed Abstract: DksA and ppGpp are the central players in the stringent response and mediate a complete reprogramming of the transcriptome. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures of Escherichia coli RNAP in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP-DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes by DksA. This work establishes a structural basis for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.

PubMed: 29478808
DOI: 10.1016/j.molcel.2018.01.035

Experimental method

X-RAY DIFFRACTION (4.295 Å)