2X2J

Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-glucan lyase with deoxynojirimycin

Summary for 2X2J

• Entry DOI: 10.2210/pdb2x2j/pdb
• Related: 2X2H 2X2I
• Descriptor: ALPHA-1,4-GLUCAN LYASE ISOZYME 1, 1-DEOXYNOJIRIMYCIN, GLYCEROL, ... (5 entities in total)
• Functional Keywords: starch binding domain, anhydrofructose pathway, lyase, glycoside hydrolase family 31
• Biological source: GRACILARIOPSIS LEMANEIFORMIS
• Total number of polymer chains: 4
• Total formula weight: 466056.16

Authors

Rozeboom, H.J.,Yu, S.,Madrid, S.,Kalk, K.H.,Dijkstra, B.W. (deposition date: 2010-01-13, release date: 2011-01-19, Last modification date: 2024-11-20)

Primary citation

Rozeboom, H.J.,Yu, S.,Madrid, S.,Kalk, K.H.,Zhang, R.,Dijkstra, B.W.
Crystal Structure of Alpha-1,4-Glucan Lyase, a Unique Glycoside Hydrolase Family Member with a Novel Catalytic Mechanism.
J.Biol.Chem., 288:26764-, 2013

PubMed Abstract: α-1,4-Glucan lyase (EC 4.2.2.13) from the red seaweed Gracilariopsis lemaneiformis cleaves α-1,4-glucosidic linkages in glycogen, starch, and malto-oligosaccharides, yielding the keto-monosaccharide 1,5-anhydro-D-fructose. The enzyme belongs to glycoside hydrolase family 31 (GH31) but degrades starch via an elimination reaction instead of hydrolysis. The crystal structure shows that the enzyme, like GH31 hydrolases, contains a (β/α)8-barrel catalytic domain with B and B' subdomains, an N-terminal domain N, and the C-terminal domains C and D. The N-terminal domain N of the lyase was found to bind a trisaccharide. Complexes of the enzyme with acarbose and 1-dexoynojirimycin and two different covalent glycosyl-enzyme intermediates obtained with fluorinated sugar analogues show that, like GH31 hydrolases, the aspartic acid residues Asp(553) and Asp(665) are the catalytic nucleophile and acid, respectively. However, as a unique feature, the catalytic nucleophile is in a position to act also as a base that abstracts a proton from the C2 carbon atom of the covalently bound subsite -1 glucosyl residue, thus explaining the unique lyase activity of the enzyme. One Glu to Val mutation in the active site of the homologous α-glucosidase from Sulfolobus solfataricus resulted in a shift from hydrolytic to lyase activity, demonstrating that a subtle amino acid difference can promote lyase activity in a GH31 hydrolase.

PubMed: 23902768
DOI: 10.1074/JBC.M113.485896

Experimental method

X-RAY DIFFRACTION (2.35 Å)