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PDBsum entry 2bf6
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References listed in PDB file
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Key reference
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Title
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The structure of clostridium perfringens nani sialidase and its catalytic intermediates.
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Authors
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S.L.Newstead,
J.A.Potter,
J.C.Wilson,
G.Xu,
C.H.Chien,
A.G.Watts,
S.G.Withers,
G.L.Taylor.
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Ref.
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J Biol Chem, 2008,
283,
9080-9088.
[DOI no: ]
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PubMed id
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Abstract
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Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia,
gas gangrene, and occasionally food poisoning. Its genome encodes three
sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic
acids from a variety of glycoconjugates and that play a role in bacterial
nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases
have suggested that catalysis in all sialidases may proceed via a covalent
intermediate similar to that of other retaining glycosidases. Here we provide
further evidence to support this suggestion by reporting the 0.97A resolution
atomic structure of the catalytic domain of the C. perfringens NanI sialidase,
and complexes with its substrate sialic acid (N-acetylneuramic acid) also to
0.97A resolution, with a transition-state analogue
(2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a
covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A
resolution. Together, these structures provide high resolution snapshots along
the catalytic pathway. The crystal structures suggested that NanI is able to
hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid.
This was confirmed by NMR, and a mechanism for this activity is suggested.
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Figure 4.
FIGURE 4. Stereo views of the NanI active site. A, complex
with Neu5Ac showing the hydrogen-bonding interactions as green
dotted lines. B, superposition of the three ligand complexes and
ligand free structure: Neu5Ac with yellow carbons, Neu5Ac2en
with magenta carbons, and the covalent fluorinated ligand with
cyan carbons.
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Figure 6.
FIGURE 6. Proposed mechanism for the hydration of Neu5Ac2en
to Neu5Ac.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
9080-9088)
copyright 2008.
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