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PDBsum entry 1nt9
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Transcription, transferase
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PDB id
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1nt9
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Contents |
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1383 a.a.*
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1089 a.a.*
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266 a.a.*
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97 a.a.*
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214 a.a.*
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84 a.a.*
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169 a.a.*
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133 a.a.*
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119 a.a.*
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65 a.a.*
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114 a.a.*
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46 a.a.*
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* C-alpha coords only
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References listed in PDB file
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Key reference
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Title
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Architecture of initiation-Competent 12-Subunit RNA polymerase ii.
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Authors
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K.J.Armache,
H.Kettenberger,
P.Cramer.
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Ref.
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Proc Natl Acad Sci U S A, 2003,
100,
6964-6968.
[DOI no: ]
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PubMed id
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Abstract
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RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core and the
two-subunit Rpb4/7 complex that is required for transcription initiation.
Previous structures of the Pol II core revealed a "clamp," which binds
the DNA template strand via three "switch regions," and a flexible
"linker" to the C-terminal repeat domain (CTD). Here we derived a
model of the complete Pol II by fitting structures of the core and Rpb4/7 to a
4.2-A crystallographic electron density map. Rpb4/7 protrudes from the
polymerase "upstream face," on which initiation factors assemble for
promoter DNA loading. Rpb7 forms a wedge between the clamp and the linker,
restricting the clamp to a closed position. The wedge allosterically prevents
entry of the promoter DNA duplex into the active center cleft and induces in two
switch regions a conformation poised for template-strand binding. Interaction of
Rpb4/7 with the linker explains Rpb4-mediated recruitment of the CTD phosphatase
to the CTD during Pol II recycling. The core-Rpb7 interaction and some functions
of Rpb4/7 are apparently conserved in all eukaryotic and archaeal RNA
polymerases but not in the bacterial enzyme.
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Figure 2.
Fig. 2. Architecture of the 12-subunit Pol II, coupling of
Rpb4/7 binding and clamp closure, and upstream interaction face.
(A) Ribbon model of Pol II. The view is as described for Fig. 1.
Cyan spheres and a pink sphere depict eight zinc ions and an
active-site magnesium ion, respectively. A black line circles
the clamp. The linker to the CTD is indicated as a dashed line.
In the lower-right corner, a schematic cut-away view is shown. A
dashed line indicates the open clamp position observed in form 2
of the Pol II core structure (7). (B) Pol II upstream
interaction face. Shown in a view of the model from the "top"
(6). The circle segment is centered at the active site and has a
radius that corresponds to the minimal distance between the TATA
box and the transcription start site (85 Å,  25 bp). The
saddle between the wall and the clamp and the assumed direction
of RNA exit are indicated. A blue asterisk indicates a potential
RNA-binding face of Rpb7 (15, 22). A key to subunit color is
shown in the upper right corner. The figure was prepared with
RIBBONS (54).
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Figure 3.
Fig. 3. Pocket-tip interaction. (A) Ribbon model of the
Rpb7 tip binding with its two outermost loops (15) to the five
protein regions (7) that line the pocket. The view is from the
"back," roughly the reverse of that shown in Figs. 1 and 2A.
Colors are as described for Fig. 2 except that switch region 5
is green. (B) Sequence alignments of protein regions are as
described for A. Hs, Homo sapiens; Dm, Drosophila melanogaster;
Sp, Schizosaccharomyces pombe; Sc, S. cerevisiae; Mj,
Methanococcus jannaschii; Ss, Sulfolobus solfataricus. Conserved
residues are highlighted. The stars below the alignments
indicate invariant residues. The figure was prepared with
RIBBONS (54).
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Headers
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