2vk5

From Proteopedia

Jump to: navigation, search


2vk5, resolution 0.97Å ()
Sites: , , and
Ligands: ,
Activity: Exo-alpha-sialidase, with EC number 3.2.1.18
Related: 2bf6, 2vk7, 2vk6
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

Publication Abstract from PubMed

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.

The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates., Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL, J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

2vk5 is a 1 chain structure with sequence from Clostridium perfringens. Full crystallographic information is available from OCA.

Reference

  • Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL. The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates. J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621 doi:10.1074/jbc.M710247200

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools