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Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.

Zhai L, Feng L, Xia L, Yin H, Xiang S - Nat Commun (2016)

Bottom Line: These studies reveal that distinct domains in GDE catalyse sequential reactions in glycogen debranching, the mechanism of their catalysis and highly specific substrate recognition.The unique tertiary structure of GDE provides additional contacts to glycogen besides its active sites, and our biochemical experiments indicate that they mediate its recruitment to glycogen and regulate its activity.Combining the understanding of the GDE catalysis and functional characterizations of its disease-causing mutations provides molecular insights into GSDIII.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

ABSTRACT
Glycogen is a branched glucose polymer and serves as an important energy store. Its debranching is a critical step in its mobilization. In animals and fungi, the 170 kDa glycogen debranching enzyme (GDE) catalyses this reaction. GDE deficiencies in humans are associated with severe diseases collectively termed glycogen storage disease type III (GSDIII). We report crystal structures of GDE and its complex with oligosaccharides, and structure-guided mutagenesis and biochemical studies to assess the structural observations. These studies reveal that distinct domains in GDE catalyse sequential reactions in glycogen debranching, the mechanism of their catalysis and highly specific substrate recognition. The unique tertiary structure of GDE provides additional contacts to glycogen besides its active sites, and our biochemical experiments indicate that they mediate its recruitment to glycogen and regulate its activity. Combining the understanding of the GDE catalysis and functional characterizations of its disease-causing mutations provides molecular insights into GSDIII.

No MeSH data available.


Related in: MedlinePlus

Structure of CgGDE.(a) Domain arrangement of GDE. Domains M1, M2 and GC, and the GT subdomains A, B and C are colour-coded. This colouring scheme is used throughout the manuscript unless otherwise indicated. Domain boundaries for CgGDE are indicated. (b,c) Crystal structure of CgGDE. The views are related by an 180° rotation around the vertical axis. The red stars in b indicate the active sites. Bound oligosaccharides are shown in stick representation with their carbon atoms in black. Structural figures were prepared with pymol (http://www.pymol.org).
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f1: Structure of CgGDE.(a) Domain arrangement of GDE. Domains M1, M2 and GC, and the GT subdomains A, B and C are colour-coded. This colouring scheme is used throughout the manuscript unless otherwise indicated. Domain boundaries for CgGDE are indicated. (b,c) Crystal structure of CgGDE. The views are related by an 180° rotation around the vertical axis. The red stars in b indicate the active sites. Bound oligosaccharides are shown in stick representation with their carbon atoms in black. Structural figures were prepared with pymol (http://www.pymol.org).

Mentions: The structures revealed that CgGDE is composed of four domains, and adopts an elongated structure. Its GT and GC domains (see below) are located on opposite ends of the molecule, with two middle domains (M1 and M2) located in parallel between them (Fig. 1a–c and Supplementary Fig. 3b). Domains GT and GC have little contacts with each other. The middle domains form extensive interactions with them, playing important roles in stabilizing their structure and maintaining the GDE tertiary structure. The interface between them and domain GT buries 7,700 Å2 of surface area (6,800 Å2 for protomer B in the ligand-free crystal, due to the conformational change of residues 629–651), and that between them and domain GC buries 3,800 Å2.


Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.

Zhai L, Feng L, Xia L, Yin H, Xiang S - Nat Commun (2016)

Structure of CgGDE.(a) Domain arrangement of GDE. Domains M1, M2 and GC, and the GT subdomains A, B and C are colour-coded. This colouring scheme is used throughout the manuscript unless otherwise indicated. Domain boundaries for CgGDE are indicated. (b,c) Crystal structure of CgGDE. The views are related by an 180° rotation around the vertical axis. The red stars in b indicate the active sites. Bound oligosaccharides are shown in stick representation with their carbon atoms in black. Structural figures were prepared with pymol (http://www.pymol.org).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4837477&req=5

f1: Structure of CgGDE.(a) Domain arrangement of GDE. Domains M1, M2 and GC, and the GT subdomains A, B and C are colour-coded. This colouring scheme is used throughout the manuscript unless otherwise indicated. Domain boundaries for CgGDE are indicated. (b,c) Crystal structure of CgGDE. The views are related by an 180° rotation around the vertical axis. The red stars in b indicate the active sites. Bound oligosaccharides are shown in stick representation with their carbon atoms in black. Structural figures were prepared with pymol (http://www.pymol.org).
Mentions: The structures revealed that CgGDE is composed of four domains, and adopts an elongated structure. Its GT and GC domains (see below) are located on opposite ends of the molecule, with two middle domains (M1 and M2) located in parallel between them (Fig. 1a–c and Supplementary Fig. 3b). Domains GT and GC have little contacts with each other. The middle domains form extensive interactions with them, playing important roles in stabilizing their structure and maintaining the GDE tertiary structure. The interface between them and domain GT buries 7,700 Å2 of surface area (6,800 Å2 for protomer B in the ligand-free crystal, due to the conformational change of residues 629–651), and that between them and domain GC buries 3,800 Å2.

Bottom Line: These studies reveal that distinct domains in GDE catalyse sequential reactions in glycogen debranching, the mechanism of their catalysis and highly specific substrate recognition.The unique tertiary structure of GDE provides additional contacts to glycogen besides its active sites, and our biochemical experiments indicate that they mediate its recruitment to glycogen and regulate its activity.Combining the understanding of the GDE catalysis and functional characterizations of its disease-causing mutations provides molecular insights into GSDIII.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

ABSTRACT
Glycogen is a branched glucose polymer and serves as an important energy store. Its debranching is a critical step in its mobilization. In animals and fungi, the 170 kDa glycogen debranching enzyme (GDE) catalyses this reaction. GDE deficiencies in humans are associated with severe diseases collectively termed glycogen storage disease type III (GSDIII). We report crystal structures of GDE and its complex with oligosaccharides, and structure-guided mutagenesis and biochemical studies to assess the structural observations. These studies reveal that distinct domains in GDE catalyse sequential reactions in glycogen debranching, the mechanism of their catalysis and highly specific substrate recognition. The unique tertiary structure of GDE provides additional contacts to glycogen besides its active sites, and our biochemical experiments indicate that they mediate its recruitment to glycogen and regulate its activity. Combining the understanding of the GDE catalysis and functional characterizations of its disease-causing mutations provides molecular insights into GSDIII.

No MeSH data available.


Related in: MedlinePlus