2A6H

Crystal structure of the T. thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of transcription inhibition by antibiotic streptolydigin.

Temiakov, D.Zenkin, N.Vassylyeva, M.N.Perederina, A.Tahirov, T.H.Kashkina, E.Savkina, M.Zorov, S.Nikiforov, V.Igarashi, N.Matsugaki, N.Wakatsuki, S.Severinov, K.Vassylyev, D.G.

(2005) Mol.Cell 19: 655-666


  • PubMed Abstract: 
  • Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is ...

    Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 A resolution structure of the Thermus thermophilus RNAP-Stl complex showed that, in full agreement with the available genetic data, the inhibitor binding site is located 20 A away from the RNAP active site and encompasses the bridge helix and the trigger loop, two elements that are considered to be crucial for RNAP catalytic center function. Structure-based biochemical experiments revealed additional determinants of Stl binding and demonstrated that Stl does not affect NTP substrate binding, DNA translocation, and phosphodiester bond formation. The RNAP-Stl complex structure, its comparison with the closely related substrate bound eukaryotic transcription elongation complexes, and biochemical analysis suggest an inhibitory mechanism in which Stl stabilizes catalytically inactive (preinsertion) substrate bound transcription intermediate, thereby blocking structural isomerization of RNAP to an active configuration. The results provide a basis for a design of new antibiotics utilizing the Stl-like mechanism.


    Organizational Affiliation

    Department of Cell Biology, School of Osteopathic Medicine, University of Medicine and Dentistry of New Jersey, Stratford, New Jersey 08084, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase alpha chain
A, B, K, L
315Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase beta chain
C, M
1119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase beta' chain
D, N
1524Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase omega chain
E, O
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor rpoD
F, P
423Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: sigA
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKW1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
D, N
STREPTOLYDIGIN
2-PYRROLIDINEACETAMIDE, 4-[6-(1,4-DIMETHYLSPIRO[2,9-DIOXABICYCLO[3.3.1]NON-6-ENE-8,2'-OXIRAN-3-YL)-1-HYDROXY-4-METHYL-2,4-HEPTADIENYLIDENE]-N,ALPHA-DIMETHYL-3,5-DIOXO-1-(TETRAHYDRO-5-HYDROXY-6-METHYL-2H-PYRAN-2-YL)-; PORTAMYCIN
C32 H44 N2 O9
KVTPRMVXYZKLIG-NCAOFHFGSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 239.500α = 90.00
b = 239.500β = 90.00
c = 253.100γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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