3BSH

Barley alpha-amylase isozyme 1 (AMY1) double mutant Y105A/Y380A in complex with inhibitor acarbose

• PDB DOI: https://doi.org/10.2210/pdb3BSH/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2007-12-24 Released: 2008-08-26 
• Deposition Author(s): Aghajari, N., Robert, X., Haser, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Multi-site substrate binding and interplay in barley alpha-amylase 1

Nielsen, M.M., Seo, E.S., Bozonnet, S., Aghajari, N., Robert, X., Haser, R., Svensson, B.

(2008) FEBS Lett 582: 2567-2571

• PubMed: 18588886 
• DOI: https://doi.org/10.1016/j.febslet.2008.06.027
• Primary Citation of Related Structures:  
  3BSG, 3BSH


• PubMed Abstract: 
  

  Certain starch hydrolases possess secondary carbohydrate binding sites outside of the active site, suggesting that multi-site substrate interactions are functionally significant. In barley alpha-amylase both Tyr380, situated on a remote non-catalytic domain, and Tyr105 in subsite -6 of the active site cleft are principal carbohydrate binding residues. The dual active site/secondary site mutants Y105A/Y380A and Y105A/Y380M show that each of Tyr380 and Tyr105 is important, albeit not essential for binding, degradation, and multiple attack on polysaccharides, while Tyr105 predominates in oligosaccharide hydrolysis. Additional delicate structure/function relationships of the secondary site are uncovered using Y380A/H395A, Y380A, and H395A AMY1 mutants.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 45.61 kDa 
• Atom Count: 3,253 
• Modelled Residue Count: 404 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase type A isozyme	A	414	Hordeum vulgare	Mutation(s): 2  EC: 3.2.1.1
UniProt
Find proteins for P00693 (Hordeum vulgare) Explore P00693  Go to UniProtKB:  P00693

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CA	C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.5	α = 90
b = 72.1	β = 90
c = 60.8	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Aghajari, N., Robert, X., Haser, R.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2021-11-10
  Changes: Database references, Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description