5GMT image
Deposition Date 2016-07-16
Release Date 2017-01-04
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5GMT
Keywords:
Title:
Crystal structure of the marine PL-14 alginate lyase from Aplysia kurodai
Biological Source:
Source Organism:
Aplysia kurodai (Taxon ID: 6501)
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.77 Å
R-Value Free:
0.19
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Alginate lyase
Gene (Uniprot):AkAly30
Chain IDs:A, B
Chain Length:279
Number of Molecules:2
Biological Source:Aplysia kurodai
Primary Citation
Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14.
J. Biol. Chem. 292 2182 2190 (2017)
PMID: 28011642 DOI: 10.1074/jbc.M116.749929

Abstact

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 Aplysia kurodai, 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.

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