TY - JOUR
T1 - Structural basis of transcription inhibition by antibiotic streptolydigin
AU - Temiakov, Dmitry
AU - Zenkin, Nikolay
AU - Vassylyeva, Marina N.
AU - Perederina, Anna
AU - Tahirov, Tahir H.
AU - Kashkina, Ekaterina
AU - Savkina, Maria
AU - Zorov, Savva
AU - Nikiforov, Vadim
AU - Igarashi, Noriyuki
AU - Matsugaki, Naohiro
AU - Wakatsuki, Soichi
AU - Severinov, Konstantin
AU - Vassylyev, Dmitry G.
N1 - Funding Information:
We thank Dr. I. Artsimovitch for providing us with the plasmids encoding mutant RNAPs, fruitful discussions, and critically reading the manuscript. Dr. M. Anikin is acknowledged for his contribution to the experiments and for critically reading the manuscript. We are grateful to Drs. S. Yokoyama and William T. McAllister for their interest and support. Drs. A. Kulbachinskiy and I. Bass are acknowledged for the Stl sample. This work was supported in part by National Institutes of Health grants GM30717 to A. Goldfarb, GM38147 to W.T.M., GM74252 to D.G.V., National Institute of Genetics grant RO1 64530 to K.S., and by RIKEN to D.G.V.
PY - 2005/9/2
Y1 - 2005/9/2
N2 - Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 Å 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 Å 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.
AB - Streptolydigin (Stl) is a potent inhibitor of bacterial RNA polymerases (RNAPs). The 2.4 Å 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 Å 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.
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U2 - 10.1016/j.molcel.2005.07.020
DO - 10.1016/j.molcel.2005.07.020
M3 - Article
C2 - 16167380
AN - SCOPUS:24044497229
SN - 1097-2765
VL - 19
SP - 655
EP - 666
JO - Molecular cell
JF - Molecular cell
IS - 5
ER -