2A69

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.

Artsimovitch, I.Vassylyeva, M.N.Svetlov, D.Svetlov, V.Perederina, A.Igarashi, N.Matsugaki, N.Wakatsuki, S.Tahirov, T.H.Vassylyev, D.G.

(2005) Cell 122: 351-363

  • DOI: 10.1016/j.cell.2005.07.014
  • Primary Citation of Related Structures:  
    2A69, 2A68, 2A6E

  • PubMed Abstract: 
  • Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutation ...

    Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.


    Organizational Affiliation

    Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chainABKL315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SHR6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chainCM1119Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE9
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainDN1524Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE8
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase omega chainEO99Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q8RQE7
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor rpoDFP423Thermus thermophilusMutation(s): 0 
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SKW1
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RPT
Query on RPT

Download CCD File 
C, M
RIFAPENTINE
C47 H64 N4 O12
WDZCUPBHRAEYDL-GZAUEHORSA-N
 Ligand Interaction
ZN
Query on ZN

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

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A, B, C, D, E, F, K, L, M, N, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 239.5α = 90
b = 239.5β = 90
c = 253.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Revision History 

  • Version 1.0: 2005-09-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance