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PDBsum entry 2w5e
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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 and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 a resolution.
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Authors
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S.Speroni,
J.Rohayem,
S.Nenci,
D.Bonivento,
I.Robel,
J.Barthel,
V.B.Luzhkov,
B.Coutard,
B.Canard,
A.Mattevi.
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Ref.
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J Mol Biol, 2009,
387,
1137-1152.
[DOI no: ]
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PubMed id
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Abstract
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Astroviruses are single-stranded RNA viruses with a replication strategy based
on the proteolytic processing of a polyprotein precursor and subsequent release
of the viral enzymes of replication. So far, the catalytic properties of the
astrovirus protease as well as its structure have remained uncharacterized. In
this study, the three-dimensional crystal structure of the predicted protease of
human pathogenic astrovirus has been solved to 2.0 A resolution. The protein
displays the typical properties of trypsin-like enzymes but also several
characteristic features: (i) a catalytic Asp-His-Ser triad in which the
aspartate side chain is oriented away from the histidine, being replaced by a
water molecule; (ii) a non-common conformation and composition of the S1 pocket;
and (iii) the lack of the typical surface beta-ribbons together with a
"featureless" shape of the substrate-binding site. Hydrolytic activity assays
indicate that the S1 pocket recognises Glu and Asp side chains specifically,
which, therefore, are predicted to occupy the P1 position on the substrate
cleavage site. The positive electrostatic potential featured by the S1 region
underlies this specificity. The comparative structural analysis highlights the
peculiarity of the astrovirus protease, and differentiates it from the human and
viral serine proteases.
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Figure 4.
Fig. 4. Crystal structure of HAstV protease. (a) The monomer.
The N- and C-terminal domains are coloured cyan and light blue,
respectively. The active site residues are depicted as red
sticks and lie at the interface between the two domains. (b)
HAstV protease crystallises as a hexamer, which is composed of
three dimers labelled A-B, C-D, and E-F. Cadmium ions are shown
as orange balls. (c) The dimer. The two subunits interact along
the β-strand bII, forming six intermolecular hydrogen bonds
that generate an intermolecular β-sheet across the two
subunits. Moreover, a number of intermolecular interactions are
mediated by cadmium ions (green spheres) and His[6]-tag residues
(shown as ball-and-sticks). The depicted dimer corresponds to
subunit A and B in b, and it is viewed along its 2-fold axis.
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Figure 6.
Fig. 6. Catalytic triad conformations in: (a) HAstV; (b)
human pathogenic rhinovirus (PDB entry code 1cqq); and (c)
hepatitis A virus (PDB entry code 1qa7) proteases. In the HAstV
structure, Asp489 of the catalytic triad points away from His461
(Fig. 3) in a geometry similar to that observed in the
ligand-free structure of hepatitis A virus enzyme. The
conformation of Asp489 leaves room for a water molecule to
hydrogen bond His461 and Gln567 (broken lines). The canonical
catalytic triad architecture is present in the protease of
rhinovirus.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2009,
387,
1137-1152)
copyright 2009.
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