4KN7

X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

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This is version 1.2 of the entry. See complete history


Literature

X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins.

Molodtsov, V.Nawarathne, I.N.Scharf, N.T.Kirchhoff, P.D.Showalter, H.D.Garcia, G.A.Murakami, K.S.

(2013) J Med Chem 56: 4758-4763

  • DOI: 10.1021/jm4004889
  • Primary Citation of Related Structures:  
    4KN4, 4KMU, 4KN7

  • PubMed Abstract: 
  • Rifampin, a semisynthetic rifamycin, is the cornerstone of current tuberculosis treatment. Among many semisynthetic rifamycins, benzoxazinorifamycins have great potential for TB treatment due to their superior affinity for wild-type and rifampin-resistant Mycobacterium tuberculosis RNA polymerases and their reduced hepatic Cyp450 induction activity ...

    Rifampin, a semisynthetic rifamycin, is the cornerstone of current tuberculosis treatment. Among many semisynthetic rifamycins, benzoxazinorifamycins have great potential for TB treatment due to their superior affinity for wild-type and rifampin-resistant Mycobacterium tuberculosis RNA polymerases and their reduced hepatic Cyp450 induction activity. In this study, we have determined the crystal structures of the Escherichia coli RNA polymerase complexes with two benzoxazinorifamycins. The ansa-naphthalene moieties of the benzoxazinorifamycins bind in a deep pocket of the β subunit, blocking the path of the RNA transcript. The C3'-tail of benzoxazinorifamycin fits a cavity between the β subunit and σ factor. We propose that in addition to blocking RNA exit, the benzoxazinorifamycin C3'-tail changes the σ region 3.2 loop position, which influences the template DNA at the active site, thereby reducing the efficiency of transcription initiation. This study supports expansion of structure-activity relationships of benzoxazinorifamycins inhibition of RNA polymerase toward uncovering superior analogues with development potential.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaABFG329Escherichia coliMutation(s): 0 
Gene Names: rpoA
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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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaCH1342Escherichia coliMutation(s): 0 
Gene Names: rpoB
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'DI1407Escherichia coliMutation(s): 0 
Gene Names: rpoC
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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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaEJ91Escherichia coliMutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDXY613Escherichia coliMutation(s): 0 
Gene Names: rpoD
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
Go to UniProtKB:  P00579
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1RMIC50 :  24   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.83α = 90
b = 204.579β = 90
c = 308.701γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-05-08 
  • Released Date: 2013-05-22 
  • Deposition Author(s): Murakami, K.S.

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-05-29
    Changes: Database references
  • Version 1.2: 2013-07-03
    Changes: Database references