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PDBsum entry 1qyp
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Transcription
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PDB id
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1qyp
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References listed in PDB file
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Key reference
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Title
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High-Resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.
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Authors
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B.Wang,
D.N.Jones,
B.P.Kaine,
M.A.Weiss.
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Ref.
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Structure, 1998,
6,
555-569.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
0%.
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Abstract
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BACKGROUND: Transcriptional initiation and elongation provide control points in
gene expression. Eukaryotic RNA polymerase II subunit 9 (RPB9) regulates
start-site selection and elongational arrest. RPB9 contains Cys4 Zn(2+)-binding
motifs which are conserved in archaea and homologous to those of the general
transcription factors TFIIB and TFIIS. RESULTS: The structure of an RPB9 domain
from the hyperthermophilic archaeon Thermococcus celer was determined at high
resolution by NMR spectroscopy. The structure consists of an apical tetrahedral
Zn(2+)-binding site, central beta sheet and disordered loop. Although the
structure lacks a globular hydrophobic core, the two surfaces of the beta sheet
each contain well ordered aromatic rings engaged in serial edge-to-face
interactions. Basic sidechains are clustered near the Zn(2+)-binding site. The
disordered loop contains sidechains conserved in TFIIS, including acidic
residues essential for the stimulation of transcriptional elongation.
CONCLUSIONS: The planar architecture of the RPB9 zinc ribbon-distinct from that
of a conventional globular domain-can accommodate significant differences in the
alignment of polar, non-polar and charged sidechains. Such divergence is
associated with local and non-local changes in structure. The RPB9 structure is
distinguished by a fourth beta strand (extending the central beta sheet) in a
well ordered N-terminal segment and also differs from TFIIS (but not TFIIB) in
the orientation of its apical Zn(2+)-binding site. Cys4 Zn(2+)-binding sites
with distinct patterns of polar, non-polar and charged residues are conserved
among unrelated RNAP subunits and predicted to form variant zinc ribbons.
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Figure 5.
Figure 5. Structures of Zn2+-binding `knuckles'. (a) Stereo
view of the RPB9 Zn2+-binding region (knuckles). Structures of
the RPB9 ensemble were superimposed with respect to the
mainchain atoms of residues 13-31 and 41-55. Sulfur atoms are
shown as yellow balls, and Zn2+ as a white sphere. Predicted
amide-sulfur hydrogen bonds are shown in yellow dashed lines:
K20 NH-C18 Sg, C21 NH-C18 Sg, K48 NH-C46 Sg, and C49 NH-C46 Sg;
N23 NH-C21 Sg is not shown. The protein is otherwise depicted in
red. (b) Superposition of the Zn2+-binding region of RPB9 (red)
and TFIIS (green) aligned with respect to the mainchain atoms of
residues 13-31 and 41-55.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1998,
6,
555-569)
copyright 1998.
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Secondary reference #1
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Title
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Erratum. Structure of a new nucleic-Acid-Binding motif in eukaryotic transcriptional elongation factor tfiis
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Authors
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X.Qian,
C.Jeon,
H.Yoon,
K.Agarwal,
M.A.Weiss.
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Ref.
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nature, 1995,
376,
279.
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Secondary reference #2
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Title
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Structure of a new nucleic-Acid-Binding motif in eukaryotic transcriptional elongation factor tfiis.
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Authors
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X.Qian,
C.Jeon,
H.Yoon,
K.Agarwal,
M.A.Weiss.
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Ref.
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Nature, 1993,
365,
277-279.
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PubMed id
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