6N61

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.274 

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:  
    6N61, 6N60, 6N62

  • 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

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065; darst@rockefeller.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaAB239Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A7Z4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coliMutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8V2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1409Escherichia coliMutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A8T7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE90Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF613Escherichia coliMutation(s): 0 
Gene Names: rpoDGHR40_08205NCTC12650_00972
Find proteins for Q0P6L9 (Escherichia coli)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CapistruinI19Burkholderia thailandensis E264Mutation(s): 0 
Gene Names: DR63_3338
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Entity ID: 6
MoleculeChainsLengthOrganismImage
non-template strand DNAN29Escherichia coli
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Entity ID: 7
MoleculeChainsLengthOrganismImage
template strand DNAT24Escherichia coli
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
D
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.274 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.888α = 90
b = 172.888β = 90
c = 385.015γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118130

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence