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PDBsum entry 2eul
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Transcription
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PDB id
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2eul
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References listed in PDB file
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Key reference
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Title
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Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-Coil transcription factors.
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Authors
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J.Symersky,
A.Perederina,
M.N.Vassylyeva,
V.Svetlov,
I.Artsimovitch,
D.G.Vassylyev.
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Ref.
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J Biol Chem, 2006,
281,
1309-1312.
[DOI no: ]
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PubMed id
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Abstract
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Gre factors enhance the intrinsic endonucleolytic activity of RNA polymerase to
rescue arrested transcription complexes and are thought to confer the high
fidelity and processivity of RNA synthesis. The Gre factors insert the extended
alpha-helical coiled-coil domains into the RNA polymerase secondary channel to
position two invariant acidic residues at the coiled-coil tip near the active
site to stabilize the catalytic metal ion. Gfh1, a GreA homolog from Thermus
thermophilus, inhibits rather than activates RNA cleavage. Here we report the
structure of the T. thermophilus Gfh1 at 2.4 A resolution revealing a two-domain
architecture closely resembling that of GreA. However, the interdomain
orientation is strikingly distinct (approximately 162 degrees rotation) between
the two proteins. In contrast to GreA, which has two acidic residues on a well
fixed self-stabilized alpha-turn, the tip of the Gfh1 coiled-coil is flexible
and contains four acidic residues. This difference is likely the key to the Gre
functional diversity, while Gfh1 inhibits exo- and endonucleolytic cleavage, RNA
synthesis, and pyrophosphorolysis, GreA enhances only the endonucleolytic
cleavage. We propose that Gfh1 acidic residues stabilize the RNA polymerase
active center in a catalytically inactive configuration through Mg2+-mediated
interactions. The excess of the acidic residues and inherent flexibility of the
coiled-coil tip might allow Gfh1 to adjust its activity to structurally distinct
substrates, thereby inhibiting diverse catalytic reactions of RNA polymerase.
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Figure 1.
The Gfh1 structure and comparison with GreA and DksA. A,
alignment of the Gfh1 and GreA sequences. The residues with
conserved chemical properties among Gfh1 and GreA sequences that
might thus form the Gfh1-like (hydrophobic) and GreA-like
(”polar“) interface in both protein families are marked with
yellow and green boxes, respectively, whereas the unfavorable
substitutions in both Gfh1 and GreA are outlined by red boxes.
The potentially functionally crucial segments at the tip of the
CC-domains are highlighted with magenta. B, the structure of the
Gfh1 protein. The acidic side chains at the CC tip are shown in
red. C, the Gfh1 and GreA structures superimposed by the
G-domains. D, the CC tips of DksA (green), GreA (yellow), and
Gfh1 (cyan). DksA and GreA are superimposed by the CC-domains,
and the Gfh1 CC tip is shown in a similar orientation. The
hydrogen bonds stabilizing the α-turns in GreA, and DksA are
shown as white dashed lines.
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Figure 3.
Proposed mechanisms of the Gfh1 action. A and B, the
flexibility and the number of the acidic residues at the CC tip
of Gfh1 allow for the alternative binding (MG1 or MG2) of the
Mg^2+ ions. C, two hypothetical pathways (competitive and
noncompetitive) by which the Gfh1 protein may inhibit nucleotide
addition. cMg1 and cMg2 are the two catalytic metals, whereas
iMg is a putative inhibitory Mg^2+ ion.
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The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2006,
281,
1309-1312)
copyright 2006.
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