9U77

Crystal structure of Glycogen branching enzyme (VvGBE) from Vibrio vulnificus MO6-24/O

Summary for 9U77

• Entry DOI: 10.2210/pdb9u77/pdb
• Descriptor: 1,4-alpha-glucan branching enzyme GlgB (2 entities in total)
• Functional Keywords: glycogen branching enzyme, gh13_9, transferase
• Biological source: Vibrio vulnificus MO6-24/O
• Total number of polymer chains: 2
• Total formula weight: 170279.42

Authors

An, Y.,Lee, S.J.,Park, J.T.,Woo, E.J. (deposition date: 2025-03-24, release date: 2026-02-04, Last modification date: 2026-08-26)

Primary citation

An, Y.,Tran, P.L.,Lee, S.J.,Ahn, W.C.,Park, K.H.,Woo, E.J.,Park, J.T.
Structural and functional analysis of transglycosylation mechanism of glycogen branching enzyme from Vibrio vulnificus.
Int.J.Biol.Macromol., 343:150415-150415, 2026

PubMed Abstract: Glycogen branching enzymes (GBEs) catalyze the formation of α-1,6-glucosidic branches during glycogen biosynthesis. In this study, we characterized the GBE from Vibrio vulnificus (VvGBE), highlighting its distinct transglycosylation activity and capacity to generate short-chain branches from defined maltooligosaccharides. The VvGBE crystal structure revealed a typical (β/α)-barrel fold comprising four domains (N1, N2, A, and C), characteristic of type I GBEs. Key residues, including Y229, F312, N389, D423, and E476, formed a negatively charged substrate-binding pocket, with N389 influencing branch length by favoring shorter chains. Biochemical assays showed that VvGBE preferentially transfers glucan chains with a peak degree of polymerization (DP) of 5. Structural superposition with the cceBE1 ligand model indicated that its binding pocket accommodates six glucose residues, with Y229 playing a role in determining the branching pattern. Substrate analysis revealed that a minimum DP of 11 is required for branch activity. Shorter substrates (< 11 glucose units) bound at the A1 site (M490, F489) for α-1,4-chain elongation, whereas longer substrates (≥11 units) adopt a U-shaped conformation at the A2 site (W644, V530) to form α-1,6-branches, with Y433 essential for proper acceptor positioning. These results refine our understanding of GBE substrate specificity and provide a structural framework for enzyme engineering.

PubMed: 41577281
DOI: 10.1016/j.ijbiomac.2026.150415

Experimental method

X-RAY DIFFRACTION (2.5 Å)