1KXH

Crystal structure of the complex between an inactive mutant of psychrophilic alpha-amylase (D174N) and acarbose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.138 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase.

Aghajari, N.Roth, M.Haser, R.

(null) Biochemistry 41: 4273-4280

  • DOI: 10.1021/bi0160516
  • Primary Citation of Related Structures:  
    1KXH, 1G94, 1G9H

  • PubMed Abstract: 
  • The psychrophilic Pseudoalteromonas haloplanctis alpha-amylase is shown to form ternary complexes with two alpha-amylase inhibitors present in the active site region, namely, a molecule of Tris and a trisaccharide inhibitor or heptasaccharide inhibitor, respectively ...

    The psychrophilic Pseudoalteromonas haloplanctis alpha-amylase is shown to form ternary complexes with two alpha-amylase inhibitors present in the active site region, namely, a molecule of Tris and a trisaccharide inhibitor or heptasaccharide inhibitor, respectively. The crystal structures of these complexes have been determined by X-ray crystallography to 1.80 and 1.74 A resolution, respectively. In both cases, the prebound inhibitor Tris is expelled from the active site by the incoming oligosaccharide inhibitor substrate analogue, but stays linked to it, forming well-defined ternary complexes with the enzyme. These results illustrate competition in the crystalline state between two inhibitors, an oligosaccharide substrate analogue and a Tris molecule, bound at the same time in the active site region. Taken together, these structures show that the enzyme performs transglycosylation in the complex with the pseudotetrasaccharide acarbose (confirmed by a mutant structure), leading to a well-defined heptasaccharide, considered as a more potent inhibitor. Furthermore, the substrate-induced ordering of water molecules within a channel highlights a possible pathway used for hydrolysis of starch and related poly- and oligosaccharides.


    Related Citations: 
    • Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level
      (1998) Structure 6: 1503
    • Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor
      (1998) Protein Sci 7: 564

    Organizational Affiliation

    Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS and Université Claude Bernard Lyon 1, Laboratoire de Bio-Cristallographie, 7 Passage du Vercors, 69367 Lyon Cedex 07, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
alpha-amylase A448Pseudoalteromonas haloplanktisMutation(s): 1 
Gene Names: amy
EC: 3.2.1.1
Find proteins for P29957 (Pseudoalteromonas haloplanktis)
Explore P29957 
Go to UniProtKB:  P29957
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
3 N/A N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900007
Query on PRD_900007
Balpha-acarboseOligosaccharide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.138 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.1α = 90
b = 139.9β = 90
c = 115.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary