4AIO

Crystal structure of the starch debranching enzyme barley limit dextrinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Starch-Debranching Enzyme Barley Limit Dextrinase Reveals Homology of the N-Terminal Domain to Cbm21.

Moeller, M.S.Abou Hachem, M.Svensson, B.Henriksen, A.

(2012) Acta Crystallogr.,Sect.F 68: 1008

  • DOI: 10.1107/S1744309112031004

  • PubMed Abstract: 
  • Barley limit dextrinase (HvLD) is a debranching enzyme from glycoside hydrolase family 13 subfamily 13 (GH13_13) that hydrolyses α-1,6-glucosidic linkages in limit dextrins derived from amylopectin. The structure of HvLD was solved and refined to 1.9 ...

    Barley limit dextrinase (HvLD) is a debranching enzyme from glycoside hydrolase family 13 subfamily 13 (GH13_13) that hydrolyses α-1,6-glucosidic linkages in limit dextrins derived from amylopectin. The structure of HvLD was solved and refined to 1.9 Å resolution. The structure has a glycerol molecule in the active site and is virtually identical to the structures of HvLD in complex with the competitive inhibitors α-cyclodextrin and β-cyclodextrin solved to 2.5 and 2.1 Å resolution, respectively. However, three loops in the N-terminal domain that are shown here to resemble carbohydrate-binding module family 21 were traceable and were included in the present HvLD structure but were too flexible to be traced and included in the structures of the two HvLD-inhibitor complexes.


    Related Citations: 
    • Crystal Structure of an Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins.
      Vester-Christensen, M.B.,Abou Hachem, M.,Svensson, B.,Henriksen, A.
      (2010) J.Mol.Biol. 403: 739


    Organizational Affiliation

    Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Søltofts Plads, Building 224, 2800 Kgs. Lyngby, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LIMIT DEXTRINASE
A
884Hordeum vulgareMutation(s): 1 
Gene Names: HvLD99
Find proteins for O48541 (Hordeum vulgare)
Go to UniProtKB:  O48541
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 176.058α = 90.00
b = 82.072β = 96.20
c = 59.378γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references
  • Version 1.2: 2012-09-19
    Type: Database references, Structure summary
  • Version 1.3: 2012-11-14
    Type: Database references