National Institutes of Health/National Cancer Institute (NIH/NCI)
GM041376
United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel. Authors: Zhou Yin / Jeremy G Bird / Jason T Kaelber / Bryce E Nickels / Richard H Ebright / Abstract: Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP ...Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
History
Deposition
Mar 15, 2022
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Sep 28, 2022
Provider: repository / Type: Initial release
Revision 1.1
May 22, 2024
Group: Data collection / Category: chem_comp_atom / chem_comp_bond
A: Antitermination protein Q B: DNA (5'-D(P*CP*AP*CP*CP*CP*AP*AP*TP*TP*TP*TP*AP*TP*TP*CP*AP*AP*TP*G)-3') C: DNA (5'-D(P*CP*AP*TP*TP*GP*AP*AP*TP*AP*AP*AP*AP*TP*TP*GP*GP*GP*TP*G)-3') hetero molecules
Method to determine structure: SAD / Resolution: 2.177→46.352 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.72 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2285
3429
8.89 %
Rwork
0.1877
35154
-
obs
0.1914
23174
89.21 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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