Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60767.08 
• Atom Count: 4281 
• Residue Count: 535 
• Unique protein chains: 1

2XFY

Crystal structure of Barley Beta-Amylase complexed with alpha- cyclodextrin

• DOI: 10.2210/pdb2XFY/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare


• Deposited: 2010-05-28 Released: 2010-12-01 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.207 Å
• R-Value Free: 0.153 
• R-Value Work: 0.122 

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

• PubMed: 21085740 
• DOI: 10.1039/c0mb00204f
• Primary Citation of Related Structures:  
  2XGI, 2XGB, 2XG9, 2XFR, 2XFF


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
BETA-AMYLASE	A	535	Hordeum vulgare	Mutation(s): 0  Gene Names: BMY1 (AMYB) EC: 3.2.1.2
Find proteins for P16098 (Hordeum vulgare) Go to UniProtKB:  P16098

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACX	A	ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE) C36 H60 O30 HFHDHCJBZVLPGP-RWMJIURBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.207 Å
• R-Value Free: 0.153 
• R-Value Work: 0.122 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 68.846	α = 90.00
b = 71.466	β = 90.00
c = 92.472	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
MOSFLM	data reduction
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-28 
• Released Date: 2010-12-01 
• Deposition Author(s): 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.

Revision History 

• Version 1.0: 2010-12-01
  Type: Initial release
• Version 1.1: 2012-01-11
  Type: Database references, Refinement description, Version format compliance