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

I. Introduction
II. Structure
III. References


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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.

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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 σ 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.


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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).