Journal Article

Molecular architecture and catalytic mechanism of human glycogen debranching enzyme

Ma, Ruifang, Liu, Zhongmin, Yan, Kaige, Guan, Huiyi, Geng, He, Chen, Huan, Chen, Yifang, Wang, Yong

2025

Overview

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 ( hs GDE) 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 hs GDE’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. In this study, the authors utilize cryo-EM and Molecular Dynamic analysis to elucidate the selective and catalytic mechanisms of the glycogen debranching enzyme (GDE). Their findings also reveal how disease-causing mutations disrupt GDE function, thereby contributing to Glycogen Storage Disease Type III.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 101/28 / 101/58 / 631/45/221 / 631/535/1258/1259 / 631/92/173 / 631/92/56 / 82/16 / Catalysis / Chromatography / Cryoelectron Microscopy / Dextrin / Enzymatic activity / Enzymes / Glucose / Glycogen / Glycogen - metabolism / Glycogen Debranching Enzyme System - chemistry / Glycogen Debranching Enzyme System - genetics / Glycogen Debranching Enzyme System - metabolism / Glycogen Debranching Enzyme System - ultrastructure / Glycogen Storage Disease Type III - enzymology / Glycogen Storage Disease Type III - genetics / Glycogens / Humanities and Social Sciences / Humans / Interfaces / Kinases / Mammalian cells / Metabolism / Microscopy / Models, Molecular / Molecular dynamics / Molecular structure / multidisciplinary / Mutation / Pathogenesis / Polymers / Protein Conformation / Science / Science (multidisciplinary) / Selectivity / Storage diseases / Structural integrity / Substrate Specificity