2WSK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1002/prot.22697

  • 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 glycosynt ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOGEN DEBRANCHING ENZYME
A
657Escherichia coli (strain K12)Gene Names: glgX (glyX)
EC: 3.2.1.-
Find proteins for P15067 (Escherichia coli (strain K12))
Go to UniProtKB:  P15067
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.852α = 90.00
b = 91.937β = 90.00
c = 97.596γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance