title: Structural rationale for the short branched substrate specificity of the glycogen debranching enzyme GlgX.
abstract: Glycogen serves as major energy storage in most living organisms. GlgX, with its gene in the glycogen degradation operon, functions in glycogen catabolism by selectively catalyzing the debranching of polysaccharide outer chains in bacterial glycosynthesis. GlgX hydrolyzes alpha-1,6-glycosidic linkages of phosphorylase-limit dextrin containing only three or four glucose subunits produced by glycogen phosphorylase. To understand its mechanism and unique substrate specificity toward short branched alpha-polyglucans, we determined the structure of GlgX from Escherichia Coli K12 at 2.25 A resolution. The structure reveals a monomer consisting of three major domains with high structural similarity to the subunit of TreX, the oligomeric bifunctional glycogen debranching enzyme (GDE) from Sulfolobus. In the overlapping substrate binding groove, conserved residues Leu270, Asp271, and Pro208 block the cleft, yielding a shorter narrow GlgX cleft compared to that of TreX. Residues 207-213 form a unique helical conformation that is observed in both GlgX and TreX, possibly distinguishing GDEs from isoamylases and pullulanases. The structural feature observed at the substrate binding groove provides a molecular explanation for the unique substrate specificity of GlgX for G4 phosphorylase-limit dextrin and the discriminative activity of TreX and GlgX toward substrates of varying lengths.
authors.affiliation: Medical Proteomics Research Center, Korea Institute of Bioscience and Biotechnology, Daejeon, Korea.
authors.forename: Hyung-Nam
authors.initials: HN
authors.lastname: Song
authors.forename: Tae-Yang
authors.initials: TY
authors.lastname: Jung
authors.forename: Jong-Tae
authors.initials: JT
authors.lastname: Park
authors.forename: Byung-Chul
authors.initials: BC
authors.lastname: Park
authors.forename: Pyung Keun
authors.initials: PK
authors.lastname: Myung
authors.forename: Winfried
authors.initials: W
authors.lastname: Boos
authors.forename: Eui-Jeon
authors.initials: EJ
authors.lastname: Woo
authors.forename: Kwan-Hwa
authors.initials: KH
authors.lastname: Park
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D002855:Chromatography, Thin Layer; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D006004:Glycogen Debranching Enzyme System / Q000737:chemistry* / Q000378:metabolism*; D006868:Hydrolysis; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013499:Surface Properties
chemical_list: D029968:Escherichia coli Proteins; D006004:Glycogen Debranching Enzyme System