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PDBsum entry 2a6t
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RNA binding protein,hydrolase
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PDB id
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2a6t
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References listed in PDB file
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Key reference
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Title
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Crystal structure and functional analysis of dcp2p from schizosaccharomyces pombe.
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Authors
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M.She,
C.J.Decker,
N.Chen,
S.Tumati,
R.Parker,
H.Song.
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Ref.
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Nat Struct Mol Biol, 2006,
13,
63-70.
[DOI no: ]
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PubMed id
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Abstract
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Decapping is a key step in both general and nonsense-mediated 5' --> 3'
mRNA-decay pathways. Removal of the cap structure is catalyzed by the Dcp1-Dcp2
complex. The crystal structure of a C-terminally truncated Schizosaccharomyces
pombe Dcp2p reveals two distinct domains: an all-helical N-terminal domain and a
C-terminal domain that is a classic Nudix fold. The C-terminal domain of both
Saccharomyces cerevisiae and S. pombe Dcp2p proteins is sufficient for decapping
activity, although the N-terminal domain can affect the efficiency of Dcp2p
function. The binding of Dcp2p to Dcp1p is mediated by a conserved surface on
its N-terminal domain, and the N-terminal domain is required for Dcp1p to
stimulate Dcp2p activity. The flexible nature of the N-terminal domain relative
to the C-terminal domain suggests that Dcp1p binding to Dcp2p may regulate Dcp2p
activity through conformational changes of the two domains.
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Figure 1.
Figure 1. Crystal structure of spDcp2n and comparison with other
Nudix enzymes. (a) Schematic representation of the domain
organization of Dcp2p from S. pombe. (b) Ribbon diagram of
spDcp2n. Orange, the N-terminal helical domain; light green, the
C-terminal Nudix domain; red, the Nudix motif. Secondary
structure elements are labeled. (c) Structure of Ap4AP in
complex with a phosphate and AMP (PDB entry 1KTG). Sticks, AMP
and phosphates; purple, the Nudix motif. (d) Structure of ADPRP
in complex with ADP-ribose (PDB entry 1G9Q). Green, subunit A;
gray, subunit B; sticks, ADP-ribose; magenta, the Nudix motif.
The view of the Nudix domain for subunit A is the same as those
for spDcp2n and Ap4AP.
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Figure 3.
Figure 3. Surface views of spDcp2n. (a) Surface
representation of spDcp2n showing the regions of high to low
sequence conservation among the eukaryotic Dcp2 proteins.
Besides the highly conserved Nudix motif, a large conserved
patch in the N-terminal domain is revealed and corresponding
residues are labeled. (b) Back view of the molecular surface of
spDcp2n showing the sequence conservation. The molecule is
rotated 180° along a vertical axis relative to the view in a.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
63-70)
copyright 2006.
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