6ZIV | pdb_00006ziv

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 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.262 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6ZIV

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 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.

Macromolecule Content 

  • Total Structure Weight: 439.79 kDa 
  • Atom Count: 30,782 
  • Modeled Residue Count: 3,492 
  • Deposited Residue Count: 3,816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure

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 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.262 (Depositor) 
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

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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