5gmt | pdb_00005gmt

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

spinqualitylabelsall models 5gmt, resolution 1.77Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5gmt is a 2 chain structure with sequence from Aplku. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Gene: AkAly30 (APLKU) Activity: Poly(beta-D-mannuronate) lyase, with EC number 4.2.2.3 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Alginate is an abundant algal polysaccharide, composed of beta-d-mannuronate and its C5 epimer alpha-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 beta-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 A resolution and the putative substrate-binding model show that the enzyme adopts a beta-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 beta-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. Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14.,Qin HM, Miyakawa T, Inoue A, Nishiyama R, Nakamura A, Asano A, Sawano Y, Ojima T, Tanokura M J Biol Chem. 2017 Feb 10;292(6):2182-2190. doi: 10.1074/jbc.M116.749929. Epub, 2016 Dec 23. PMID:28011642 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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