6ZIV

Crystal structure of a Beta-glucosidase from Alicyclobacillus acidiphilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Producing natural vanilla extract from green vanilla beans using a beta-glucosidase from Alicyclobacillus acidiphilus.

Delgado, L.Heckmann, C.M.De Benedetti, S.Nardini, M.Gourlay, L.J.Paradisi, F.

(2021) J Biotechnol 329: 21-28

  • DOI: https://doi.org/10.1016/j.jbiotec.2021.01.017
  • Primary Citation of Related Structures:  
    6ZIV

  • PubMed Abstract: 

    Current methods for the production of natural vanilla extract are long and tedious, and the efficiency of the vanillin extraction is usually conditioned by different factors during the traditional curing process (temperatures and weather conditions). As an important fraction of vanillin is present in the form of glucovanillin in green beans, endogenous β-glucosidases contribute to its hydrolysis; however, these enzymes lose efficiency during the curing process. The use of extremophilic organisms as a source of an appropriate exogenous enzyme can offer a valid alternative when producing natural vanillin. Here, a β-glucosidase from the thermo-acidophilic organism Alicyclobacillus acidiphilus (AacGH1) was cloned, expressed in E. coli BL21, and fully characterized in respect to both function and crystal structure. Notably, AacGH1 was stable at a temperature up to 50 °C and exhibited good tolerance to glucose, fructose and organic solvents, in particular it maintained full activity in the presence of up to 20 % (v/v) ethanol. The enzyme was then successfully applied to an ethanol-water (20 % (v/v)) extract of green vanilla beans and the complete hydrolysis of glucovanillin (1.7 mM) to vanillin, and other flavour compounds commonly found in vanilla, was achieved using 0.5 mg/mL of enzyme in just 15 min at 30 °C.


  • Organizational Affiliation

    University of Nottingham, School of Chemistry, University Park, Nottingham, NG7 2RD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase477Alicyclobacillus tengchongensisMutation(s): 0 
Gene Names: SD51_06195
EC: 3.2.1.21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download Ideal Coordinates CCD File 
AA [auth GGG]
FA [auth HHH]
I [auth AAA]
L [auth BBB]
P [auth CCC]
AA [auth GGG],
FA [auth HHH],
I [auth AAA],
L [auth BBB],
P [auth CCC],
T [auth DDD],
U [auth EEE],
W [auth FFF]
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
S [auth CCC]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth GGG]
CA [auth GGG]
J [auth AAA]
M [auth BBB]
N [auth BBB]
BA [auth GGG],
CA [auth GGG],
J [auth AAA],
M [auth BBB],
N [auth BBB],
O [auth BBB],
X [auth FFF]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth GGG]
EA [auth GGG]
K [auth AAA]
Q [auth CCC]
R [auth CCC]
DA [auth GGG],
EA [auth GGG],
K [auth AAA],
Q [auth CCC],
R [auth CCC],
V [auth EEE],
Y [auth FFF],
Z [auth FFF]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.262 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.654α = 91.616
b = 91.644β = 90.422
c = 159.342γ = 89.988
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2021-02-17
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Derived calculations