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PDBsum entry 2bzd

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Hydrolase PDB id
2bzd
Jmol
Contents
Protein chains
601 a.a.
Ligands
GAL ×3
GOL ×3
Metals
_NA ×3
Waters ×1496

References listed in PDB file
Key reference
Title Galactose recognition by the carbohydrate-Binding module of a bacterial sialidase.
Authors S.L.Newstead, J.N.Watson, A.J.Bennet, G.Taylor.
Ref. Acta Crystallogr D Biol Crystallogr, 2005, 61, 1483-1491. [DOI no: 10.1107/S0907444905026132]
PubMed id 16239725
Abstract
Glycoside hydrolases often possess carbohydrate-binding modules (CBMs) in addition to their catalytic domains, which help target the enzymes to appropriate substrates and thereby increase their catalytic efficiency. Sialidases hydrolyse the release of sialic acid from a variety of glycoconjugates and play significant roles in the pathogenesis of a number of important diseases. The sialidase from Micromonospora viridifaciens has a CBM which recognizes galactose. The CBM is linked to the catalytic domain by an immunoglobulin-like domain, resulting in the galactose binding site sitting above the catalytic site, suggesting an interplay between the two sites. By studying nine crystallographically independent structures of the M. viridifaciens sialidase, the relative flexibility of the three domains was analysed. A detailed study is also presented of the recognition of galactose and lactose by the M. viridifaciens CBM. The striking structure of this sialidase suggests a role for the CBM in binding to galactose residues unmasked by the adjacent catalytic site.
Figure 1.
Figure 1 (a) and (b) Orthogonal views of the M. viridifaciens sialidase. The catalytic domain (47-403) is in light brown with Neu5Ac2en bound in the active site, the immunoglobulin-like domain (403-505) is in green and the CBM (505-647) is in cyan with lactose bound. The metal ion is shown as a magenta ball. The disulfide between 351-405 linking the first two domains is also shown. (c) Molecular surface coloured according to electrostatic potential; same view as in (a).
Figure 2.
Figure 2 The galactose-binding site of the CBM. (a) and (b) show 2F[obs] - F[calc] electron-density maps for the galactose and lactose, respectively, contoured at 0.6 e -3 (approximately 2 [142][sigma] ). (c) and (d) show stereoviews of the binding site with galactose and lactose bound, respectively. Hydrogen bonds are drawn in green and waters are shown as magenta spheres.
The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1483-1491) copyright 2005.
PROCHECK
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