4CVW

Structure of the barley limit dextrinase-limit dextrinase inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Barley Limit Dextrinase:Limit Dextrinase Inhibitor (Ld:Ldi) Complex Reveals Insights Into Mechanism and Diversity of Cereal-Type Inhibitors.

Moller, M.S.Vester-Christensen, M.B.Jensen, J.M.Abou Hachem, M.Henriksen, A.Svensson, B.

(2015) J Biol Chem 290: 12614

  • DOI: 10.1074/jbc.M115.642777
  • Primary Citation of Related Structures:  
    4CVW

  • PubMed Abstract: 
  • Molecular details underlying regulation of starch mobilization in cereal seed endosperm remain unknown despite the paramount role of this process in plant growth. The structure of the complex between the starch debranching enzyme barley limit dextrinase (LD), hydrolyzing α-1,6-glucosidic linkages, and its endogenous inhibitor (LDI) was solved at 2 ...

    Molecular details underlying regulation of starch mobilization in cereal seed endosperm remain unknown despite the paramount role of this process in plant growth. The structure of the complex between the starch debranching enzyme barley limit dextrinase (LD), hydrolyzing α-1,6-glucosidic linkages, and its endogenous inhibitor (LDI) was solved at 2.7 Å. The structure reveals an entirely new and unexpected binding mode of LDI as compared with previously solved complex structures of related cereal type family inhibitors (CTIs) bound to glycoside hydrolases but is structurally analogous to binding of dual specificity CTIs to proteases. Site-directed mutagenesis establishes that a hydrophobic cluster flanked by ionic interactions in the protein-protein interface is vital for the picomolar affinity of LDI to LD as assessed by analysis of binding by using surface plasmon resonance and also supported by LDI inhibition of the enzyme activity. A phylogenetic analysis identified four LDI-like proteins in cereals among the 45 sequences from monocot databases that could be classified as unique CTI sequences. The unprecedented binding mechanism shown here for LDI has likely evolved in cereals from a need for effective inhibition of debranching enzymes having characteristic open active site architecture. The findings give a mechanistic rationale for the potency of LD activity regulation and provide a molecular understanding of the debranching events associated with optimal starch mobilization and utilization during germination. This study unveils a hitherto not recognized structural basis for the features endowing diversity to CTIs.


    Organizational Affiliation

    From Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark and bis@bio.dtu.dk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIMIT DEXTRINASEA, B884Hordeum vulgareMutation(s): 3 
EC: 3.2.1.41
UniProt
Find proteins for O48541 (Hordeum vulgare subsp. vulgare)
Explore O48541 
Go to UniProtKB:  O48541
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LIMIT DEXTRINASE INHIBITORC, D120Hordeum vulgareMutation(s): 0 
UniProt
Find proteins for Q2V8X0 (Hordeum vulgare)
Explore Q2V8X0 
Go to UniProtKB:  Q2V8X0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.979α = 90
b = 168.606β = 90
c = 157.708γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-06-03
    Changes: Database references