2XG9

Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha-D- glucopyranosylmoranoline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

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Ligand Structure Quality Assessment 


This is version 1.5 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.M.Southard, A.M.Stanley, D.Denyer, K.Smith, A.M.Naldrett, M.J.Lawson, D.M.Field, R.A.

(2011) Mol Biosyst 7: 718

  • DOI: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-AMYLASEA535Hordeum vulgareMutation(s): 0 
Gene Names: BMY1AMYB
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
NOJ
Query on NOJ

Download Ideal Coordinates CCD File 
B [auth A]1-DEOXYNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.582α = 90
b = 71.237β = 90
c = 92.304γ = 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: 2012-10-03
    Changes: Data collection, Database references, Refinement description, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Data collection
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.4: 2019-05-22
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary