4LK1

Crystal Structure Analysis of the E.coli holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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This is version 1.2 of the entry. See complete history


Literature

Phage T7 Gp2 inhibition of Escherichia coli RNA polymerase involves misappropriation of sigma 70 domain 1.1.

Bae, B.Davis, E.Brown, D.Campbell, E.A.Wigneshweraraj, S.Darst, S.A.

(2013) Proc Natl Acad Sci U S A 110: 19772-19777

  • DOI: 10.1073/pnas.1314576110
  • Primary Citation of Related Structures:  
    4LK0, 4LK1, 4LJZ, 4LLG

  • PubMed Abstract: 
  • Bacteriophage T7 encodes an essential inhibitor of the Escherichia coli host RNA polymerase (RNAP), the product of gene 2 (Gp2). We determined a series of X-ray crystal structures of E. coli RNAP holoenzyme with or without Gp2. The results define the ...

    Bacteriophage T7 encodes an essential inhibitor of the Escherichia coli host RNA polymerase (RNAP), the product of gene 2 (Gp2). We determined a series of X-ray crystal structures of E. coli RNAP holoenzyme with or without Gp2. The results define the structure and location of the RNAP σ(70) subunit domain 1.1(σ(1.1)(70)) inside the RNAP active site channel, where it must be displaced by the DNA upon formation of the open promoter complex. The structures and associated data, combined with previous results, allow for a complete delineation of the mechanism for Gp2 inhibition of E. coli RNAP. In the primary inhibition mechanism, Gp2 forms a protein-protein interaction with σ(1.1)(70), preventing the normal egress of σ(1.1)(70) from the RNAP active site channel. Gp2 thus misappropriates a domain of the RNAP holoenzyme, σ(1.1)(70), to inhibit the function of the enzyme.


    Organizational Affiliation

    Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABGH239Escherichia coli DH1Mutation(s): 0 
Gene Names: rpoAEcDH1_0418ECDH1ME8569_3173
EC: 2.7.7.6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCI1342Escherichia coli DH1Mutation(s): 0 
Gene Names: rpoBEcDH1_4008ECDH1ME8569_3846
EC: 2.7.7.6
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'DJ1407Escherichia coli BW2952Mutation(s): 0 
Gene Names: rpoCBWG_3647
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaEK91Escherichia coli DH1Mutation(s): 0 
Gene Names: rpoZEcDH1_0056ECDH1ME8569_3534
EC: 2.7.7.6
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDFL613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
Go to UniProtKB:  P00579
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.675α = 90
b = 206.392β = 90
c = 308.836γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-07-05 
  • Released Date: 2013-11-13 
  • Deposition Author(s): Bae, B., Darst, S.A.

Revision History 

  • Version 1.0: 2013-11-13
    Type: Initial release
  • Version 1.1: 2013-12-04
    Changes: Database references
  • Version 1.2: 2013-12-18
    Changes: Database references