Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin

We report crystal structures of the antibacterial lasso peptides microcin J25 (MccJ25) and capistruin (Cap) bound to their natural enzymatic target, the bacterial RNA polymerase (RNAP). Both peptides bind within the RNAP secondary channel, through which NTP substrates enter the RNAP active site, and...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2019-01, Vol.116 (4), p.1273-1278
Main Authors: Braffman, Nathaniel R., Piscotta, Frank J., Hauver, Jesse, Campbell, Elizabeth A., Link, A. James, Darst, Seth A.
Format: Article
Language:English
Subjects:
Anti-Bacterial Agents - chemistry
Antiinfectives and antibacterials
Antimicrobial agents
Bacteria - drug effects
Bacteriocins - chemistry
BASIC BIOLOGICAL SCIENCES
Binding
Biological Sciences
biophysics and computational biology
capistruin
Catalysis
Catalytic Domain
Crystal structure
Crystallography
DNA-directed RNA polymerase
DNA-Directed RNA Polymerases - chemistry
Inhibition
lasso peptide
Microcin J25
Peptides
Peptides - chemistry
Protein Conformation
Ribonucleic acid
RNA
RNA polymerase
Substrates
Transcription
Transcription, Genetic - drug effects
x-ray crystallography
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Summary:We report crystal structures of the antibacterial lasso peptides microcin J25 (MccJ25) and capistruin (Cap) bound to their natural enzymatic target, the bacterial RNA polymerase (RNAP). Both peptides bind within the RNAP secondary channel, through which NTP substrates enter the RNAP active site, and sterically block trigger-loop folding, which is essential for efficient catalysis by the RNAP. MccJ25 binds deep within the secondary channel in a manner expected to interfere with NTP substrate binding, explaining the partial competitive mechanism of inhibition with respect to NTPs found previously [Mukhopadhyay J, Sineva E, Knight J, Levy RM, Ebright RH (2004) Mol Cell 14:739–751]. The Cap binding determinant on RNAP overlaps, but is not identical to, that of MccJ25. Cap binds further from the RNAP active site and does not sterically interfere with NTP binding, and we show that Cap inhibition is partially noncompetitive with respect to NTPs. This work lays the groundwork for structure determination of other lasso peptides that target the bacterial RNAP and provides a structural foundation to guide lasso peptide antimicrobial engineering approaches.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1817352116