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PDBsum entry 1pv4
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Transcription/DNA
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PDB id
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1pv4
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of the rho transcription terminator: mechanism of mRNA recognition and helicase loading.
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Authors
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E.Skordalakes,
J.M.Berger.
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Ref.
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Cell, 2003,
114,
135-146.
[DOI no: ]
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PubMed id
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Abstract
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In bacteria, one of the major transcriptional termination mechanisms requires a
RNA/DNA helicase known as the Rho factor. We have determined two structures of
Rho complexed with nucleic acid recognition site mimics in both free and
nucleotide bound states to 3.0 A resolution. Both structures show that Rho forms
a hexameric ring in which two RNA binding sites--a primary one responsible for
target mRNA recognition and a secondary one required for mRNA translocation and
unwinding--point toward the center of the ring. Rather than forming a closed
ring, the Rho hexamer is split open, resembling a "lock washer" in its
global architecture. The distance between subunits at the opening is
sufficiently wide (12 A) to accommodate single-stranded RNA. This open
configuration most likely resembles a state poised to load onto mRNA and
suggests how related ring-shaped enzymes may be breached to bind nucleic acids.
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Figure 3.
Figure 3. Rho RNA Binding Sites(A) Molecular surface (GRASP
[Nicholls et al., 1991]) of the Rho hexamer. Primary RNA binding
sites in the OB-fold of the N-terminal domain are colored cyan.
Secondary (C-terminal) RNA binding sites in the ATPase domain
are colored magenta. Nucleic acid bound at the primary RNA
binding sites is shown as yellow rods. View is the same as in
Figure 2B.(B) Schematic of the primary (N-terminal) RNA binding
site configuration. The N- and C-terminal domains are colored
green and red, respectively. Solid black lines represent the
positions for the single-stranded nucleic acid, which binds
across the primary RNA binding site and orients the 3′ end
toward the hole of the ring. The broken black line shows the
path needed to be traversed by nucleic acid between adjacent
binding sites.(C) Rho's secondary RNA binding site. Stereo
diagram of the Rho hexamer showing the location of the P loops
(blue), the Q loops (magenta) and the R loops (green). View is
from the “bottom,” rotated 180° from the perspective of
Figure 2B.
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Figure 5.
Figure 5. Schematic Model for Rho FunctionNumbers
correspond to stages outlined in the text. Asterisks represent
catalytic sites thought to be competent for ATP hydrolysis.
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2003,
114,
135-146)
copyright 2003.
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