2A68

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

Summary for 2A68

• Entry DOI: 10.2210/pdb2a68/pdb
• Related: 1IW7 1SMY 2a69 2a6e 2a6h
• Descriptor: DNA-directed RNA polymerase alpha chain, DNA-directed RNA polymerase beta chain, DNA-directed RNA polymerase beta' chain, ... (9 entities in total)
• Functional Keywords: rna polymerase holoenzyme, rifabutin, antibiotic, transcription regulation, riken structural genomics/proteomics initiative, rsgi, structural genomics, transferase
• Biological source: Thermus thermophilus; More
• Total number of polymer chains: 12
• Total formula weight: 868886.03

Authors

Artsimovitch, I.,Vassylyeva, M.N.,Svetlov, D.,Svetlov, V.,Perederina, A.,Igarashi, N.,Matsugaki, N.,Wakatsuki, S.,Tahirov, T.H.,Vassylyev, D.G.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-07-01, release date: 2005-09-20, Last modification date: 2023-08-23)

Primary citation

Artsimovitch, I.,Vassylyeva, M.N.,Svetlov, D.,Svetlov, V.,Perederina, A.,Igarashi, N.,Matsugaki, N.,Wakatsuki, S.,Tahirov, T.H.,Vassylyev, D.G.
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
Cell(Cambridge,Mass.), 122:351-363, 2005

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 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.

PubMed: 16096056
DOI: 10.1016/j.cell.2005.07.014

Experimental method

X-RAY DIFFRACTION (2.5 Å)