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PDBsum entry 2a1r
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Hydrolase/RNA
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PDB id
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2a1r
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References listed in PDB file
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Key reference
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Title
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Structural insight into poly(a) binding and catalytic mechanism of human parn.
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Authors
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M.Wu,
M.Reuter,
H.Lilie,
Y.Liu,
E.Wahle,
H.Song.
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Ref.
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EMBO J, 2005,
24,
4082-4093.
[DOI no: ]
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PubMed id
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Abstract
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Poly(A)-specific ribonuclease (PARN) is a processive, poly(A)-specific 3'
exoribonuclease. The crystal structure of C-terminal truncated human PARN
determined in two states (free and RNA-bound forms) reveals that PARNn is folded
into two domains, an R3H domain and a nuclease domain similar to those of Pop2p
and epsilon186. The high similarity of the active site structures of PARNn and
epsilon186 suggests that they may have a similar catalytic mechanism. PARNn
forms a tight homodimer, with the R3H domain of one subunit partially enclosing
the active site of the other subunit and poly(A) bound in a deep cavity of its
nuclease domain in a sequence-nonspecific manner. The R3H domain and, possibly,
the cap-binding domain are involved in poly(A) binding but these domains alone
do not appear to contribute to poly(A) specificity. Mutations disrupting
dimerization abolish both the enzymatic and RNA-binding activities, suggesting
that the PARN dimer is a structural and functional unit. The cap-binding domain
may act in concert with the R3H domain to amplify the processivity of PARN.
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Figure 1.
Figure 1 Structures of PARNn in free and RNA-bound forms. (A)
Stereo diagram of 2.6 Å simulated annealing (SA) omit map
contoured at 2  covering
the bound poly(A) in the PARNn-RNA complex. The last three
nucleotides are shown in stick model. (B) A ribbon diagram of
the PARNn-RNA complex. The two molecules are shown in yellow and
green, respectively. Nucleotides are shown in stick model.  3,
4
and  5
are labeled in (B, C). (C) Superimposition of the PARNn-RNA
complex with native PARNn. The color coding for the PARNn-RNA
complex is as in (B). The two molecules (chain A and chain B) of
native PARNn are highlighted with dark green and orange,
respectively. Nucleotides are shown in stick model.
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Figure 2.
Figure 2 Comparison of PARNn with other members of the DEDD
family. (A) Structural comparison of the nuclease domain of
PARNn with those of  epsilon
186 and Pop2p. The DEDD core domains are colored yellow, cyan
and green for PARN, epsilon
186 and Pop2p, respectively, with the rest of the molecules
colored in pale gray. Bound nucleotides are shown in stick
model. (B) Structures of the active sites of PARNn, epsilon
186 of Pol III and the klenow fragment of Pol I. Bound
nucleotides are shown in stick model, catalytic residues in
ball-and-stick model and metal ions in CPK model colored with
magenta. (C) Solvent-accessible and electrostatic potential of
PARNn colored from blue (basic) to red (acidic). For simplicity,
only one subunit is shown. Left panel: the side view of the
electrostatic potential surface. Right panel: the top view of
the surface rotated about 90° around y axis relative to the view
in the left panel.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2005,
24,
4082-4093)
copyright 2005.
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