2XGI

Crystal structure of Barley Beta-Amylase complexed with 3,4- epoxybutyl alpha-D-glucopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Chemical genetics and cereal starch metabolism: structural basis of the non-covalent and covalent inhibition of barley beta-amylase.

Rejzek, M.Stevenson, C.E.Southard, A.M.Stanley, D.Denyer, K.Smith, A.M.Naldrett, M.J.Lawson, D.M.Field, R.A.

(2011) Mol Biosyst 7: 718-730

  • DOI: https://doi.org/10.1039/c0mb00204f
  • Primary Citation of Related Structures:  
    2XFF, 2XFR, 2XFY, 2XG9, 2XGB, 2XGI

  • PubMed Abstract: 

    There are major issues regarding the proposed pathway for starch degradation in germinating cereal grain. Given the commercial importance but genetic intractability of the problem, we have embarked on a program of chemical genetics studies to identify and dissect the pathway and regulation of starch degradation in germinating barley grains. As a precursor to in vivo studies, here we report systematic analysis of the reversible and irreversible inhibition of the major β-amylase of the grain endosperm (BMY1). The molecular basis of inhibitor action was defined through high resolution X-ray crystallography studies of unliganded barley β-amylase, as well as its complexes with glycone site binder disaccharide iminosugar G1M, irreversible inhibitors α-epoxypropyl and α-epoxybutyl glucosides, which target the enzyme's catalytic residues, and the aglycone site binders acarbose and α-cyclodextrin.


  • Organizational Affiliation

    Department of Biological Chemistry, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-AMYLASE535Hordeum vulgareMutation(s): 0 
EC: 3.2.1.2
UniProt
Find proteins for P16098 (Hordeum vulgare)
Explore P16098 
Go to UniProtKB:  P16098
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16098
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.631α = 90
b = 71.158β = 90
c = 92.273γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    Type: Initial release
  • Version 1.1: 2011-08-17
    Changes: Database references, Refinement description, Version format compliance
  • Version 1.2: 2012-01-11
    Changes: Other
  • Version 2.0: 2019-02-06
    Changes: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Structure summary
  • Version 2.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary