1HT6 | pdb_00001ht6

CRYSTAL STRUCTURE AT 1.5A RESOLUTION OF THE BARLEY ALPHA-AMYLASE ISOZYME 1

• PDB DOI: https://doi.org/10.2210/pdb1HT6/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2000-12-29 Released: 2003-07-08 
• Deposition Author(s): Robert, X., Haser, R., Aghajari, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.163 (Depositor) 
• R-Value Work: 
  0.136 (Depositor), 0.155 (DCC) 

Starting Model: experimental

Literature

The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs

Robert, X., Haser, R., Gottschalk, T.E., Ratajczak, F., Driguez, H., Svensson, B., Aghajari, N.

(2003) Structure 11: 973-984

• PubMed: 12906828 
• DOI: https://doi.org/10.1016/s0969-2126(03)00151-5
• Primary Citation Related Structures: 
  1HT6, 1P6W


• PubMed Abstract: 
  

  Though the three-dimensional structures of barley alpha-amylase isozymes AMY1 and AMY2 are very similar, they differ remarkably from each other in their affinity for Ca(2+) and when interacting with substrate analogs. A surface site recognizing maltooligosaccharides, not earlier reported for other alpha-amylases and probably associated with the different activity of AMY1 and AMY2 toward starch granules, has been identified. It is located in the C-terminal part of the enzyme and, thus, highlights a potential role of domain C. In order to scrutinize the possible biological significance of this domain in alpha-amylases, a thorough comparison of their three-dimensional structures was conducted. An additional role for an earlier-identified starch granule binding surface site is proposed, and a new calcium ion is reported.

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Organizational Affiliation: 
• Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, UMR 5086-CNRS/UCBL1, 7 Passage du Vercors, F-69367 Lyon cedex 07, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.32 kDa 
• Atom Count: 4,123 
• Modeled Residue Count: 404 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-AMYLASE ISOZYME 1	A	405	Hordeum vulgare	Mutation(s): 0  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
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.163 (Depositor) 
• R-Value Work:  0.136 (Depositor), 0.155 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.36	α = 90
b = 72.82	β = 90
c = 61.74	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-08 
Deposition Author(s): Robert, X., Haser, R., Aghajari, N.

Revision History  

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description