6YN7 | pdb_00006yn7

Crystal Structure of AHE enzyme from Alicyclobacillus herbarius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Release of Soybean Isoflavones by Using a beta-Glucosidase from Alicyclobacillus herbarius.

Delgado, L.Heckmann, C.M.Di Pisa, F.Gourlay, L.Paradisi, F.

(2021) Chembiochem 22: 1223-1231

  • DOI: https://doi.org/10.1002/cbic.202000688
  • Primary Citation Related Structures: 
    6YN7

  • PubMed Abstract: 

    β-Glucosidases are used in the food industry to hydrolyse glycosidic bonds in complex sugars, with enzymes sourced from extremophiles better able to tolerate the process conditions. In this work, a novel β-glycosidase from the acidophilic organism Alicyclobacillus herbarius was cloned and heterologously expressed in Escherichia coli BL21(DE3). AheGH1 was stable over a broad range of pH values (5-11) and temperatures (4-55 °C). The enzyme exhibited excellent tolerance to fructose and good tolerance to glucose, retaining 65 % activity in the presence of 10 % (w/v) glucose. It also tolerated organic solvents, some of which appeared to have a stimulating effect, in particular ethanol with a 1.7-fold increase in activity at 10 % (v/v). The enzyme was then applied for the cleavage of isoflavone from isoflavone glucosides in an ethanolic extract of soy flour, to produce soy isoflavones, which constitute a valuable food supplement, full conversion was achieved within 15 min at 30 °C.


  • Organizational Affiliation
    • University of Nottingham, School of Chemistry, Department of Chemical Biology, University Park, Nottingham, NG7 2RD, UK.

Macromolecule Content 

  • Total Structure Weight: 208.54 kDa 
  • Atom Count: 14,649 
  • Modeled Residue Count: 1,774 
  • Deposited Residue Count: 1,808 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AHE, beta-glucosidase enzyme
A, B, C, D
452Paenalicyclobacillus herbariusMutation(s): 0 
EC: 3.2.1.23 (PDB Primary Data), 3.2.1.21 (UniProt)
UniProt
Find proteins for A0A8I3B065 (Alicyclobacillus herbarius)
Explore A0A8I3B065 
Go to UniProtKB:  A0A8I3B065
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I3B065
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
(Subject of Investigation/LOI)

Query on PGE



Download:Ideal Coordinates CCD File
N [auth A],
S [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
(Subject of Investigation/LOI)

Query on PEG



Download:Ideal Coordinates CCD File
T [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
(Subject of Investigation/LOI)

Query on NI



Download:Ideal Coordinates CCD File
M [auth A],
R [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.298 (Depositor), 0.299 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.045α = 90
b = 93.35β = 98.692
c = 106.383γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description