5D0F

Crystal Structure of the Candida Glabrata Glycogen Debranching Enzyme (E564Q) in complex with maltopentaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2016) Nat Commun 7: 11229-11229

  • DOI: 10.1038/ncomms11229
  • Primary Citation of Related Structures:  

  • PubMed 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‚ÄČkDa glycogen debranching enzyme (GDE) catalyses this reaction. GDE deficiencies in h ...

    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‚ÄČkDa 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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A, B
1528Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65)Mutations: Q564E
Gene Names: GDB1
Find proteins for Q6FSK0 (Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65))
Go to UniProtKB:  Q6FSK0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLR
Query on MLR

Download SDF File 
Download CCD File 
A, B
MALTOTRIOSE
AMYLOTRIOSE
C18 H32 O16
FYGDTMLNYKFZSV-PXXRMHSHSA-N
 Ligand Interaction
CEX
Query on CEX

Download SDF File 
Download CCD File 
A, B
alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranosyl-(1->4)-alpha-D-glucopyranose
maltopentaose
C30 H52 O26
FTNIPWXXIGNQQF-DWTFCAFKSA-N
 Ligand Interaction
MTT
Query on MTT

Download SDF File 
Download CCD File 
A, B
MALTOTETRAOSE
C24 H42 O21
LUEWUZLMQUOBSB-ZLBHSGTGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 158.070α = 90.00
b = 202.010β = 101.32
c = 135.240γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
HKL-2000data collection
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-03 
  • Released Date: 2016-05-18 
  • Deposition Author(s): Zhai, L., Xiang, S.

Funding OrganizationCountryGrant Number
Ministry of Science and TechnologyChina2011CB910500

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Structure summary