5GMT

Crystal structure of the marine PL-14 alginate lyase from Aplysia kurodai

Summary for 5GMT

• Entry DOI: 10.2210/pdb5gmt/pdb
• Descriptor: Alginate lyase (2 entities in total)
• Functional Keywords: alginate lyase, polysaccharide lyase family 14, glycosidic bond, beta-d-mannuronic acid, alpha-l-guluronic acid, lyase
• Biological source: Aplysia kurodai (Kuroda's sea hare)
• Total number of polymer chains: 2
• Total formula weight: 62339.17

Authors

Qin, H.-M.,Miyakawa, T.,Nakamura, A.,Tanokura, M. (deposition date: 2016-07-16, release date: 2017-01-04, Last modification date: 2024-10-23)

Primary citation

Qin, H.M.,Miyakawa, T.,Inoue, A.,Nishiyama, R.,Nakamura, A.,Asano, A.,Sawano, Y.,Ojima, T.,Tanokura, M.
Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14.
J. Biol. Chem., 292:2182-2190, 2017

PubMed Abstract: Alginate is an abundant algal polysaccharide, composed of β-d-mannuronate and its C5 epimer α-l-guluronate, that is a useful biomaterial in cell biology and tissue engineering, with applications in cancer and aging research. The alginate lyase (EC 4.2.2.3) from , AkAly30, is a eukaryotic member of the polysaccharide lyase 14 (PL-14) family and degrades alginate by cleaving the glycosidic bond through a β-elimination reaction. Here, we present the structural basis for the substrate specificity, with a preference for polymannuronate, of AkAly30. The crystal structure of AkAly30 at a 1.77 Å resolution and the putative substrate-binding model show that the enzyme adopts a β-jelly roll fold at the core of the structure and that Lys-99, Tyr-140, and Tyr-142 form catalytic residues in the active site. Their arrangements allow the carboxyl group of mannuronate residues at subsite +1 to form ionic bonds with Lys-99. The coupled tyrosine forms a hydrogen bond network with the glycosidic bond, and the hydroxy group of Tyr-140 is located near the C5 atom of the mannuronate residue. These interactions could promote the β-elimination of the mannuronate residue at subsite +1. More interestingly, Gly-118 and the disulfide bond formed by Cys-115 and Cys-124 control the conformation of an active-site loop, which makes the space suitable for substrate entry into subsite -1. The cleavage efficiency of AkAly30 is enhanced relative to that of mutants lacking either Gly-118 or the Cys-115-Cys-124 disulfide bond. The putative binding model and mutagenesis studies provide a novel substrate recognition mode explaining the polymannuronate specificity of PL-14 alginate lyases.

PubMed: 28011642
DOI: 10.1074/jbc.M116.749929

Experimental method

X-RAY DIFFRACTION (1.77 Å)