RNA Polymerase

RNA polymerase
Prokaryotic RNA polymerase

• Also called DNA dependent RNA polymerase
• In bacteria a single RNA pol. Catalyzes the transcription of
all types of RNA.
• RNA pol. Provide easy accommodation to DNA due to
their groove having diameter & length of 25 Aᵒ (2.5 nm) &
55 Aᵒ (5.5 nm)
• RNA pol. Looks like crab claw shape & the two pincers of
RNA pol. make up by β & β’.
• Active centre cleft, a region of enzyme is present at the
base of pincers in which the active site of enzyme resides.
• For polymerization of nt. Two Mg2+ are required by the
enzyme which bind to active site; rate of polymerization is
45nt.per second
• There are 5 channels for exit & entry of RNA,DNA,
rNTP within RNA pol. such as
1. NTP-uptake channel
2. RNA exit channel
3. Non-template exit channel
4. Template strand channel (for exit of template)
5. Downstream DNA channel (for entry of non-
transcribed DNA strand)
• RNA pol. Exists in 2 forms i.e. Core RNA pol. Of
~400kDa has 5 subnits (ααββ’Ѡ subunits) or α2ββ’Ѡ
& RNA pol. Holoenzyme ~480kDa has 6 subunits
(α2ββ’Ѡσ)
α- subunit
• 2 sub units of α of 40kDa encoded by rpoA gene . Its
function is to mediate (1) assembly of core enzyme
(2) promoter recognition; if any modification occurs
at α-subunit then affinity of holoenzyme to
promoter is reduced. It helps for promoter
recognition. (3) it also binds with some regulatory
factors
Β-subunit:
• Its mol. Wt. is155kDa which is encoded by rpoB
gene.
• It has catalytic activity i.e. synthesis of RNA by
polymerization of rNTPs.
Β’-subunit
• Its mol.wt. is 160kDa which is encoded by rpoC
gene & it binds at several regions of coding strandin
the region of transcription bubble & stabilizes the
separated single strands & it is also responsible for
template binding.
σ-subunit:
• Its mol.wt. is 40000Da which is encoded by rpoD
gene.it recognizes origin site or initiation site for
transcription at -10 & -35 sequence
Ѡ-subunit:
• Its mol.wt. is 10kDa & it also mediates RNA pol.
assembly
• Β,β’,α & Ѡ form core enzyme; σ is weakly attached to
other chain & core enzyme catalyzes linkage of ribose
nucleotide by phosphodiester bond
• σ factor recognizes start sequence in the promoter
region of DNA where transcription begins. In the
presence of sigma factor, the holoenzyme binds to those
nucleotides in promoter region which initiates
transcription.
• α2ββ’Ѡ actually carries out the polymerization reaction.
• RNA pol. Has an overall shape of a crab claw whose two
pincers are formed by β&β’ subunits enclosing a space of
~27Å between them & this channel is occupied by
dsDNA
• 3’ end of RNA forms a 9bp hybrid helix with 5’ end
of the template DNA strand & then exits the
protein through channel between β & β’ subunits,
called RNA exit channel.
• DNA binds to σ subunit via its promoter element to
form so called closed complex
Table 10.1 : RNA polymerase subunits and other transcription
factors.
Eukaryotic RNA polymerases
• The eukaryotic RNA polymerases I, II and III consist
of 8 to 14 different subunits in each. They recognise
different promoters and recognise different classes
of genes.
• The two largest subunits of all three eukaryotic RNA
polymerases are related to the β and β’ subunits of
the E. coli polymerase. Five subunits of the
eukaryotic RNA polymerases are common to all the
three enzymes.
(a) RNA polymerase I (RNA Pol I):
• It is located in the nucleolus and synthesizes
precursors of most rRNAs. It is sensitive to α-
amanitin.
(b) RNA polymerase II (RNA Pol II):
It is located in the nucleoplasm and synthesizes
mRNA precursors and some small nuclear RNAs. It is
very sensitive to α-amanitin
(c) RNA polymerase III (RNA Pol III):
• It is located in the nucleoplasm. It synthesizes the
precursors of tRNA, 5S rRNA and other small
nuclear and cytoplasmic RNAs. It is moderately
sensitive to α-amanitin.
Fig. 10.4 : Functional map of RNA polymerase subunits
The End

RNA Polymerase

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RNA polymerase

Prokaryotic RNA polymerase

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