RNA
Polymerase of Thermus thermophilus
David Marcey
and Nathan Silva
© 2006
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
(s), beta
prime (ß'),
beta (ß),
omega
(w), and two alpha
(a)subunits.
The s
subunit binds to the core polymerase
(the remaining subunits) to initiate transcription at the 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
loosens its grip on the core polymerase, and the core begins the elongation
of the RNA transcript.
The two
largest subunits of the polymerase, ß
and ß',
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 ß'
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 s
subunit binds to the core primarily through
extensive interactions with the ß'
subunit. The N-terminal
domain 2 of s
is observed to bridge the ß
and ß'
"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).
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