Molecular architecture and catalytic mechanism of human glycogen debranching enzyme

Huiyi Guan, Huan Chen, He Geng, Ruifang Ma, Zhongmin Liu, Yong Wang, Yifang Chen () and Kaige Yan ()
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Huiyi Guan: Southern University of Science and Technology
Huan Chen: Southern University of Science and Technology
He Geng: Southern University of Science and Technology
Ruifang Ma: Southern University of Science and Technology
Zhongmin Liu: Southern University of Science and Technology
Yong Wang: Zhejiang University
Yifang Chen: Zhejiang University
Kaige Yan: Southern University of Science and Technology

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Glycogen, a key branched glucose polymer, acts as a vital energy reservoir in mammalian cells, particularly during intense activity or fasting. The glycogen debranching enzyme (GDE) plays a key role in glycogen degradation by removing branches, ensuring efficient glucose release. Dysfunction of GDE leads to the accumulation of limit dextrin and is implicated in the pathogenesis of Glycogen Storage Disease Type III (GSD III). We present the cryo-EM structure of human GDE (hsGDE) at 3.23 Å resolution, providing molecular insights into its substrate selectivity and catalytic mechanism. Our study further investigates the molecular consequences of disease-associated mutations by correlating structural data with enzymatic activities of representative GSD III-causing variants. We discover that these mutations induce GSD III through diverse mechanisms, including significant reductions in enzymatic activity, and disruptions to the glycogen-bound region and overall structural integrity. The elucidation of these pathways not only advances our understanding of hsGDE’s role in substrate recognition and catalysis but also illuminates the molecular pathology of GSD III. Our findings pave the way for the development of targeted therapeutic strategies for this disease.

Date: 2025
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DOI: 10.1038/s41467-025-61077-6

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