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

Mikami B, Ban M, Suzuki S, Yoon HJ, Miyake O, Yamasaki M, Ogura K, Maruyama Y, Hashimoto W, Murata K
Acta Crystallogr D Biol Crystallogr 68 1207-16 (2012)
Related entries: 4e1y, 4f13

Cited: 30 times
EuropePMC logo PMID: 22948922

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.

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  2. Catalytic mechanism and mode of action of the periplasmic alginate epimerase AlgG. Wolfram F, Kitova EN, Robinson H, Walvoort MT, Codée JD, Klassen JS, Howell PL. J Biol Chem 289 6006-6019 (2014)
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  5. Structural and functional aspects of mannuronic acid-specific PL6 alginate lyase from the human gut microbe Bacteroides cellulosilyticus. Stender EGP, Dybdahl Andersen C, Fredslund F, Holck J, Solberg A, Teze D, Peters GHJ, Christensen BE, Christensen BE, Aachmann FL, Welner DH, Svensson B. J Biol Chem 294 17915-17930 (2019)
  6. Alginate Degradation: Insights Obtained through Characterization of a Thermophilic Exolytic Alginate Lyase. Arntzen MØ, Pedersen B, Klau LJ, Stokke R, Oftebro M, Antonsen SG, Fredriksen L, Sletta H, Aarstad OA, Aachmann FL, Horn SJ, Eijsink VGH. Appl Environ Microbiol 87 e02399-20 (2021)
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  11. Distinct Modes of Hidden Structural Dynamics in the Functioning of an Allosteric Polysaccharide Lyase. Dash P, Acharya R. ACS Cent Sci 8 933-947 (2022)
  12. Site-Directed Mutagenesis-Based Functional Analysis and Characterization of Endolytic Lyase Activity of N- and C-Terminal Domains of a Novel Oligoalginate Lyase from Sphingomonas sp. MJ-3 Possessing Exolytic Lyase Activity in the Intact Enzyme. Kim HS, Chu YJ, Park CH, Lee EY, Kim HS. Mar Biotechnol (NY) 17 782-792 (2015)
  13. A Surface Loop in the N-Terminal Domain of Pedobacter heparinus Heparin Lyase II is Important for Activity. Mori M, Ichikawa M, Kiguchi Y, Miyazaki T, Hattori M, Nishikawa A, Tonozuka T. J Appl Glycosci (1999) 63 7-11 (2016)


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