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Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1207-16. doi: 10.1107/S090744491202495X. Epub 2012 Aug 18.

Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III.

Author information

1
Department of Applied Life Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan. mikami@kais.kyoto-u.ac.jp

Abstract

The structures of two mutants (H192A and Y246F) of a mannuronate-specific alginate lyase, A1-III, from Sphingomonas species A1 complexed with a tetrasaccharide substrate [4-deoxy-L-erythro-hex-4-ene-pyranosyluronate-(mannuronate)(2)-mannuronic acid] were determined by X-ray crystallography at around 2.2 Å resolution together with the apo form of the H192A mutant. The final models of the complex forms, which comprised two monomers (of 353 amino-acid residues each), 268-287 water molecules and two tetrasaccharide substrates, had R factors of around 0.17. A large conformational change occurred in the position of the lid loop (residues 64-85) in holo H192A and Y246F compared with that in apo H192A. The lid loop migrated about 14 Å from an open form to a closed form to interact with the bound tetrasaccharide and a catalytic residue. The tetrasaccharide was bound in the active cleft at subsites -3 to +1 as a substrate form in which the glycosidic linkage to be cleaved existed between subsites -1 and +1. In particular, the O(η) atom of Tyr68 in the closed lid loop forms a hydrogen bond to the side chain of a presumed catalytic residue, O(η) of Tyr246, which acts both as an acid and a base catalyst in a syn mechanism.

PMID:
22948922
DOI:
10.1107/S090744491202495X
[Indexed for MEDLINE]

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