RNA Polymerase of Thermus thermophilus
David Marcey and Nathan Silva
© 2021

I. Introduction
II. Structure
III. References


Directions

Please leave comments/suggestions or please acknowledge use of this site by visiting our feedback page

[Back to OMM Exhibits]

This exhibit displays molecules in the left part of the screen, and text that addresses structure-function relationships of the molecules in the right part (below). Use the scrollbar to the right to scroll through the text. If you are using browser other than Firefox (the recommended browser for this site), be sure to allow popups. In Chrome, you can click on the popup blocker icon in the right part of the address bar..

To evoke renderings of the molecule that illustrate particular points, click the radio buttons:

Please click the load PDB buttons, , when present.

To reset the molecule, use the reset buttons:

If you are a practiced user, you can create the illusion of 3D if you turn on stereo mode. In this mode, when you train one eye on one image and the other eye on the other image, you will elicit a centered image that appears truly 3-dimensional. To turn on stereo mode when viewing a scene, return here and use this button . To turn off stereo mode, return here and use this button .



I. Introduction

The large molecule at left is the RNA Polymerase Holoenzyme from Thermus thermophilus. DNA-dependent RNA polymerases are responsible for building RNA transcripts (mRNA, tRNA, rRNA) complementary to template strands of double stranded DNA. Regulation of their activity is often the final step in cellular pathways that control the expression of genes.

return to beginning



II. Structure

The massive holoenzyme contains 6 subunits: sigma (σ), beta prime '), beta (β), omega (ω), and two alpha (α) subunits.

The σ subunit binds to the core polymerase (the remaining subunits) to initiate transcription at the promoter of a gene. The σ subunit is composed of alpha helices connected by turns and loops.

These σ subunit secondary structure elements are organized into four domains: N-terminal domain 1, N-terminal domain 2, Linker domain, and C-terminal domain. A fifth domain (N-terminal) is disordered and is not shown in the crystal structure. After synthesis of a 9-12 nucleotide RNA, the σ subunit loosens its grip on the core polymerase, and the core begins the elongation of the RNA transcript.

The two largest subunits of the polymerase, β and β', combine to form a deep cleft between "crab claw pincers." The cleft is the channel into which DNA template is bound.

Deep at the base of this cleft is the active site of RNA polymerization, defined by three, evolutionarily conserved aspartate residues of the β' subunit. These residues, together with active site water molecules (not shown), chelate two magnesium ions. The metal ions play a key role in catalyzing the polymerization of ribonucleotides (as for all nucleic acid polymerases).

The σ subunit binds to the core primarily through extensive interactions with the β' subunit. The N-terminal domain 2 of s is observed to bridge the β and β' "pincers," forming a wall that blocks one side of the DNA binding channel.

Numerous magnesium ions are observed to coat the polymerase surface (allow time for surface view to load). They may play a role in the binding and bending of DNA, which is thought to be wrapped around the polymerase as transcription proceeds.


 

return to beginning



III. References

Vassylyev, D. G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M. N., Borukhov, S., Yokoyama, S.: Crystal Structure of a Bacterial RNA Polymerase Holoenzyme at 2.6A Resolution. Nature 417: 712-719 (2002).