PDBsum entry 2a69

Transferase

PDB id: 2a69

Contents

Protein chains

229 a.a.

1119 a.a.

1392 a.a.

95 a.a.

345 a.a.

Ligands

RPT ×2

Metals

_MG ×487

_ZN ×4

Waters ×6399

References listed in PDB file

Key reference

Title

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

Authors

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

Ref.

Cell, 2005, 122, 351-363. [DOI no: 10.1016/j.cell.2005.07.014]

PubMed id

16096056

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.

Figure 3.
Figure 3. RNAP/Rifs Binding

Figure 5.
Figure 5. Increased Levels of Mg^2+ Ion Protect RNAP against Inhibition by Rifs

The above figures are reprinted by permission from Cell Press: Cell (2005, 122, 351-363) copyright 2005.