4FNU

Crystal structure of GH36 alpha-galactosidase AgaA A355E D478A from Geobacillus stearothermophilus in complex with stachyose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The molecular mechanism of the thermostable alpha-galactosidases AgaA and AgaB explained by X-ray crystallography and mutational studies

Merceron, R.Foucault, M.Haser, R.Mattes, R.Watzlawick, H.Gouet, P.

(2012) J.Biol.Chem. 287: 39642-39652

  • DOI: 10.1074/jbc.M112.394114
  • Primary Citation of Related Structures:  4FNP, 4FNQ, 4FNR, 4FNS, 4FNT

  • PubMed Abstract: 
  • The α-galactosidase AgaA from the thermophilic microorganism Geobacillus stearothermophilus has great industrial potential because it is fully active at 338 K against raffinose and can increase the yield of manufactured sucrose. AgaB has lower affini ...

    The α-galactosidase AgaA from the thermophilic microorganism Geobacillus stearothermophilus has great industrial potential because it is fully active at 338 K against raffinose and can increase the yield of manufactured sucrose. AgaB has lower affinity for its natural substrates but is a powerful tool for the enzymatic synthesis of disaccharides by transglycosylation. These two enzymes have 97% identity and belong to the glycoside hydrolase (GH) family GH36 for which few structures are available. To understand the structural basis underlying the differences between these two enzymes, we determined the crystal structures of AgaA and AgaB by molecular replacement at 3.2- and 1.8 Å-resolution, respectively. We also solved a 2.8-Å structure of the AgaA(A355E) mutant, which has enzymatic properties similar to those of AgaB. We observe that residue 355 is located 20 Å away from the active site and that the A355E substitution causes structural rearrangements resulting in a significant displacement of the invariant Trp(336) at catalytic subsite -1. Hence, the active cleft of AgaA is narrowed in comparison with AgaB, and AgaA is more efficient than AgaB against its natural substrates. The structure of AgaA(A355E) complexed with 1-deoxygalactonojirimycin reveals an induced fit movement; there is a rupture of the electrostatic interaction between Glu(355) and Asn(335) and a return of Trp(336) to an optimal position for ligand stacking. The structures of two catalytic mutants of AgaA(A355E) complexed with raffinose and stachyose show that the binding interactions are stronger at subsite -1 to enable the binding of various α-galactosides.


    Organizational Affiliation

    Biocrystallography and Structural Biology of Therapeutic Targets, Bases Moléculaires et Structurales des Systèmes Infectieux-Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69367 Lyon Cedex 07, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-galactosidase AgaA
A, B, C, D
729Geobacillus stearothermophilusGene Names: agaA
Find proteins for Q9ALJ4 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9ALJ4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRU
Query on FRU

Download SDF File 
Download CCD File 
A, B, C, D
FRUCTOSE
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.070α = 90.00
b = 154.070β = 90.00
c = 238.020γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
PHENIXrefinement
ADSCdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references