4E1Y

Alginate lyase A1-III H192A apo form

Replaces:  3EVH

Summary for 4E1Y

• Entry DOI: 10.2210/pdb4e1y/pdb
• Related: 4E23 4E25
• Descriptor: Alginate lyase (2 entities in total)
• Functional Keywords: alpha barrel, polysaccharide lyase, alginate, lyase
• Biological source: Sphingomonas
• Total number of polymer chains: 2
• Total formula weight: 79507.35

Authors

Mikami, B.,Ban, M.,Suzuki, S.,Yoon, H.-J.,Miyake, O.,Yamasaki, M.,Ogura, K.,Maruyama, Y.,Hashimoto, W.,Murata, K. (deposition date: 2012-03-07, release date: 2012-04-11, Last modification date: 2024-10-16)

Primary citation

Mikami, B.,Ban, M.,Suzuki, S.,Yoon, H.-J.,Miyake, O.,Yamasaki, M.,Ogura, K.,Maruyama, Y.,Hashimoto, W.,Murata, K.
Induced-fit motion of a lid loop involved in catalysis in alginate lyase A1-III
Acta Crystallogr.,Sect.D, 68:1207-1216, 2012

PubMed 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.

PubMed: 22948922
DOI: 10.1107/S090744491202495X

Experimental method

X-RAY DIFFRACTION (2.1 Å)