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PDBsum entry 2rf4
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References listed in PDB file
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Key reference
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Title
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Functional architecture of RNA polymerase i.
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Authors
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C.D.Kuhn,
S.R.Geiger,
S.Baumli,
M.Gartmann,
J.Gerber,
S.Jennebach,
T.Mielke,
H.Tschochner,
R.Beckmann,
P.Cramer.
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Ref.
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Cell, 2007,
131,
1260-1272.
[DOI no: ]
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PubMed id
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Abstract
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Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in
ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we
report the 12 A cryo-electron microscopic structure for the complete 14-subunit
yeast Pol I, a homology model for the core enzyme, and the crystal structure of
the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the
clamp, and the dock domain contribute to a unique surface interacting with
promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5
form a heterodimer near the enzyme funnel that acts as a built-in elongation
factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol
II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the
C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA
proofreading and 3'-end trimming.
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Figure 2.
Figure 2. Model and EM Features of the Pol I Core
(A)
Placement of the Pol II ten-subunit core structure (Armache et
al., 2005) (gray) into the EM density (blue). The foot was
deleted, and subunits Rpb5, Rpb8, and Rpb9 are highlighted in
magenta, green, and orange, respectively. The clamp has been
fitted as a separate rigid body.
(B) Fit of the common
subunits Rpb5 and Rpb8 to the EM map, and density for the core
subunit A12.2 (the Pol II homolog Rpb9 is shown as a ribbon
model).
(C) Pol II structure-guided sequence alignment of
the five Pol I subunits with homologs in Pol II (compare Table
1). The domain organization of Pol II subunits Rpb1, Rpb2, Rpb3,
Rpb11, and Rpb9 is shown as diagrams (Cramer et al., 2001).
Insertions and deletions exceeding five amino acid residues are
indicated. Conserved folds are indicated by orange highlighting
of the bar above the diagrams. For details see Figure S1.
(D) View of the core Pol II structure (Cramer et al., 2001) from
the side, with domains depicted in (E) highlighted.
(E) Pol
I-specific structural elements. Fitted Pol II elements are shown
as ribbon models. Insertions and deletions explaining the EM
density are named according to (C). The clamp head is in light
red and the clamp core in red. The dock and foot domains are in
beige and blue, respectively, and Rpb3, Rpb10, and Rpb11 are in
red, dark blue, and in yellow, respectively. Zinc ions are
depicted as marine spheres.
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Figure 5.
Figure 5. Intrinsic RNA Cleavage Activity and Functional
Architecture of Pol I
(A) DNA-RNA hybrid scaffold used in
cleavage assays.
(B) Comparison of RNA cleavage by Pol I
variants with Pol II and the Pol II-TFIIS complex. Pol I mainly
removed four nucleotides from the RNA, consistent with binding
of the terminal hybrid base pair to the nucleotide insertion
site (+1), extrusion of the RNA 3′ overhang into the
polymerase pore and cleavage of the phosphodiester bond between
nucleotides at positions −1 and +1 (Figure 5A). The Pol
II-TFIIS complex removed three or four nucleotides, indicating
that a mixture of complexes was present with the terminal hybrid
base pair occupying either position −1 or +1.
(C) pH
dependence of pol I cleavage activity.
(D) Elongation
activity of the Pol I variant A12.2ΔC.
(E) Hybrid
structure and functional architecture of Pol I. The EM envelope
is shown as a blue line, the Pol I core ribbon model in gray
with Rpb9 (A12.2) highlighted in orange, and the A14/43 crystal
structure in red/blue. The window shows a cut-away view of the
active center containing a modeled DNA-RNA hybrid. Red dashes
indicate the RNA 3′ end extruded into the pore.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2007,
131,
1260-1272)
copyright 2007.
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