5w1s

From Proteopedia

X-ray crystal structure of Escherichia coli RNA polymerase and TraR complex

PDB ID 5w1s

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Structural highlights

5w1s is a 14 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.805Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPOA_ECOLI DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059]

Publication Abstract from PubMed

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.

Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA.,Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS Mol Cell. 2018 Mar 1;69(5):828-839.e5. doi: 10.1016/j.molcel.2018.01.035. Epub, 2018 Feb 22. PMID:29478808^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Molodtsov V, Sineva E, Zhang L, Huang X, Cashel M, Ades SE, Murakami KS. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. Mol Cell. 2018 Mar 1;69(5):828-839.e5. doi: 10.1016/j.molcel.2018.01.035. Epub, 2018 Feb 22. PMID:29478808 doi:http://dx.doi.org/10.1016/j.molcel.2018.01.035