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PDBsum entry 1vlr
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RNA binding protein
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PDB id
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1vlr
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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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Crystal structure of an apo mRNA decapping enzyme (dcps) from mouse at 1.83 a resolution.
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Authors
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G.W.Han,
R.Schwarzenbacher,
D.Mcmullan,
P.Abdubek,
E.Ambing,
H.Axelrod,
T.Biorac,
J.M.Canaves,
H.J.Chiu,
X.Dai,
A.M.Deacon,
M.Didonato,
M.A.Elsliger,
A.Godzik,
C.Grittini,
S.K.Grzechnik,
J.Hale,
E.Hampton,
J.Haugen,
M.Hornsby,
L.Jaroszewski,
H.E.Klock,
E.Koesema,
A.Kreusch,
P.Kuhn,
S.A.Lesley,
T.M.Mcphillips,
M.D.Miller,
K.Moy,
E.Nigoghossian,
J.Paulsen,
K.Quijano,
R.Reyes,
G.Spraggon,
R.C.Stevens,
H.Van den bedem,
J.Velasquez,
J.Vincent,
A.White,
G.Wolf,
Q.Xu,
K.O.Hodgson,
J.Wooley,
I.A.Wilson.
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Ref.
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Proteins, 2005,
60,
797-802.
[DOI no: ]
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PubMed id
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Abstract
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No abstract given.
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Figure 1.
Figure 1. Crystal structure of mRNA decapping enzyme (DcpS)
from Mouse. (A) Stereo ribbon diagram of Mouse DcpS color-coded
from N-terminus (blue) to C-terminus (red) showing the domain
organization with helices H1-H13 and  -strands
1-
14,
as well as -sheets
A, B, C, and D. (B) Diagram showing the secondary structure
elements in Mouse DcpS (chain A) superimposed on its primary
sequence. The -sheet
strands are indicated by a red A, B, C, and D. -bulges
and  -turns
are indicated. -hairpins
are depicted as red loops. Disordered regions are depicted by a
dashed line with the corresponding sequence in brackets. The HIT
sequence motif is indicated by a black line above the three
histidines.
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Figure 2.
Figure 2. Comparison of Mouse and human DcpS. (A) Ribbon
diagram of the Mouse DcpS dimer. Chain A is in gray and chain B
is in pink. The dimer is symmetric with a C  -C
distance
between Asp110 and Trp174 of  28
Å. Residues 131 and 147 flanking the linker region are
labeled. (B) Ribbon diagram of the human DcpS/mGpppG complex.
Chain A is shown in gray and chain B in purple. The dimer has a
symmetric bottom and an asymmetric top and features an open side
and a closed side with a 36 Å and 6 Å C -C
gap
between Asp111 and Trp175, respectively. The mGpppG nucleotides
bound to the active sites are shown in ball-and-stick
configuration, with carbon atoms colored in yellow, phosphorous
in purple, oxygen in red, and nitrogen in blue. The movement of
the N-terminal domain is facilitated by a conformational change
in the linker region around helix  3.
Superposition of the DcpS active sites in the relaxed empty
state with the open (C) and closed (D) mGpppG bound state. The
mGpppG-interacting residues from human DcpS (gray, residues
labeled in brackets) and their counterparts in Mouse DcpS (blue)
are shown in ball-and-stick configuration.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2005,
60,
797-802)
copyright 2005.
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