Crystal structure of Glycogen Debranching Enzyme GlgX from Escherichia coli K-12

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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Structural Rationale for the Short Branched Substrate Specificity of the Glycogen Debranching Enzyme Glgx.

Song, H.-N.Jung, T.-Y.Park, J.-T.Park, B.Myung, P.K.Boos, W.Woo, E.-J.Park, K.-H.

(2010) Proteins 78: 1847

  • DOI: https://doi.org/10.1002/prot.22697
  • Primary Citation of Related Structures:  

  • PubMed 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.

  • Organizational Affiliation

    Medical Proteomics Research Center, Korea Institute of Bioscience and Biotechnology, Daejeon, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLYCOGEN DEBRANCHING ENZYME657Escherichia coli K-12Mutation(s): 0 
Find proteins for P15067 (Escherichia coli (strain K12))
Explore P15067 
Go to UniProtKB:  P15067
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15067
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.852α = 90
b = 91.937β = 90
c = 97.596γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description