RNA Polymerase
David Marcey & Nathan Silva

I. Introduction
II. Structure
III. References

I. Introduction

The 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, and regulation of their activity is often the final step in cellular pathways that control the expression of genes.

II. Structure

The massive holoenzyme contains 6 subunits: the s subunit, b' subunit, b subunit, w subunit, and two a dimer subunits.

The s subunit binds to the core polymerase (the remaining subunits) to initiate transcription at the core promoter of a gene. The s subunit is composed of alpha helices connected by turns and loops. These 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 s subunit dissociates from the core polymerase, and the core begins the elongation of the RNA transcript.

The two largest subunits, b and b', 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 the cleft is the active site of RNA polymerization, defined by three, evolutionarily conserved aspartate residues of the b' 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 mechanism (as for all nucleic acid polymerases).

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

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

reset RNA Polymerase reset molecule

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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).

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