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PDBsum entry 1rc5
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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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Noncatalytic assembly of ribonuclease III with double-Stranded RNA.
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Authors
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J.Blaszczyk,
J.Gan,
J.E.Tropea,
D.L.Court,
D.S.Waugh,
X.Ji.
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Ref.
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Structure, 2004,
12,
457-466.
[DOI no: ]
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PubMed id
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Abstract
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Ribonuclease III (RNase III) represents a family of double-stranded RNA (dsRNA)
endonucleases. The simplest bacterial enzyme contains an endonuclease domain
(endoND) and a dsRNA binding domain (dsRBD). RNase III can affect RNA structure
and gene expression in either of two ways: as a dsRNA-processing enzyme that
cleaves dsRNA, or as a dsRNA binding protein that binds but does not cleave
dsRNA. We previously determined the endoND structure of Aquifex aeolicus RNase
III (Aa-RNase III) and modeled a catalytic complex of full-length Aa-RNase III
with dsRNA. Here, we present the crystal structure of Aa-RNase III in complex
with dsRNA, revealing a noncatalytic assembly. The major differences between the
two functional forms of RNase III.dsRNA are the conformation of the protein and
the orientation and location of dsRNA. The flexibility of a 7 residue linker
between the endoND and dsRBD enables the transition between these two forms.
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Figure 3.
Figure 3. Overall Structure of Aa-E110KˇdsRNA(A)
Illustration of a biological dimer of the Aa-E110KˇdsRNA
complex. The crystallographically independent molecule and its
symmetry mate are indicated by N-C, and N'-C', respectively.
Secondary structural elements are labeled for those in dsRBD and
a3 in the endoND. The endoND, dsRBD, dsRNA, endoND^sym,
dsRBD^sym, and dsRNA^sym are colored yellow, green, green, cyan,
blue, and blue, respectively. The RNase III signature motif at
the N terminus of a3 is highlighted in red. Helices, b strands
and loops are drawn as spirals, arrows, and pipes,
respectively.(B) A different view of dimeric Aa-E110KˇdsRNA
related to the view in (A) by a 90° rotation around the vertical
axis.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2004,
12,
457-466)
copyright 2004.
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Secondary reference #1
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Title
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Crystallographic and modeling studies of rnase III suggest a mechanism for double-Stranded rna cleavage.
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Authors
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J.Blaszczyk,
J.E.Tropea,
M.Bubunenko,
K.M.Routzahn,
D.S.Waugh,
D.L.Court,
X.Ji.
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Ref.
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Structure, 2001,
9,
1225-1236.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Structure of the Ligand-free Dimer of Aa-RNase
III Endonuclease Domain(a) Dimer interface of Aa-RNase III.
Molecule A is illustrated as a surface representation with
positive and negative potentials indicated by blue and red,
respectively. Molecule B is represented as a backbone "worm"
with a stick model for the "ball-and-socket" side chains. The
secondary structure elements involved in dimerization are
identified with green labels. In the upper portion of the
illustration, the shape of the "socket" is shown with the stick
model of F41 from Molecule B, whereas, in the lower potion, the
shape of the "ball" is outlined in the middle of five side
chains that form the socket (see text).(b) A ribbon diagram of
molecules A (in green) and B (in blue). The secondary structure
assignment is shown in molecule A only. Two sets of six active
site residues are labeled, including E37, E40, D44, D107, and
E110 from one molecule and E64 from the other. Each set forms a
compound active center.(c) A surface representation with red and
blue indicating negative and positive potentials, respectively.
Notice that the valley on the surface of the dimer has one
compound active center on each end of the valley. The
representations were prepared using MOLSCRIPT [61], GRASP [62],
and Raster3D [63].
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The above figure is
reproduced from the cited reference
with permission from Cell Press
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