6N60

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

Braffman, N.R.Piscotta, F.J.Hauver, J.Campbell, E.A.Link, A.J.Darst, S.A.

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 1273-1278

  • DOI: 10.1073/pnas.1817352116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 wh ...

    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.


    Organizational Affiliation

    Department of Chemistry, Princeton University, Princeton, NJ 08544.,Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544.,Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065; darst@rockefeller.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
239Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoA (pez, phs, sez)
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Z4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1342Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1409Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoC (tabB)
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8T7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A800
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F
612Escherichia coliMutation(s): 0 
Gene Names: rpoD
Find proteins for Q0P6L9 (Escherichia coli)
Go to UniProtKB:  Q0P6L9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Microcin J25
M
21Escherichia coliMutation(s): 0 
Gene Names: mcjA
Find proteins for Q9X2V7 (Escherichia coli)
Go to UniProtKB:  Q9X2V7
Entity ID: 7
MoleculeChainsLengthOrganism
non-template strand DNAN29Escherichia coli
Entity ID: 8
MoleculeChainsLengthOrganism
template strand DNAT24Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000184
Query on PRD_000184
MMicrocin J25Polypeptide / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.68 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.263 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 172.906α = 90.00
b = 172.906β = 90.00
c = 387.263γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM118130

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-23
    Type: Data collection, Database references
  • Version 1.2: 2019-02-06
    Type: Data collection, Database references
  • Version 1.3: 2019-02-27
    Type: Data collection, Structure summary