PDBsum entry 2vk5

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Hydrolase PDB id
Protein chain
449 a.a.
GOL ×2
_CA ×2
Waters ×1030

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Key reference
Title The structure of clostridium perfringens nani sialidase and its catalytic intermediates.
Authors S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, G.L.Taylor.
Ref. J Biol Chem, 2008, 283, 9080-9088. [DOI no: 10.1074/jbc.M710247200]
PubMed id 18218621
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.
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.
Figure 6.
FIGURE 6. Proposed mechanism for the hydration of Neu5Ac2en to Neu5Ac.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 9080-9088) copyright 2008.
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