4C1O

Geobacillus thermoglucosidasius GH family 52 xylosidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A Novel Beta-Xylosidase Structure from Geobacillus Thermoglucosidasius: The First Crystal Structure of a Glycoside Hydrolase Family Gh52 Enzyme Reveals Unpredicted Similarity to Other Glycoside Hydrolase Folds

Espina, G.Eley, K.Pompidor, G.Schneider, T.R.Crennell, S.J.Danson, M.J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1366

  • DOI: https://doi.org/10.1107/S1399004714002788
  • Primary Citation of Related Structures:  
    4C1O, 4C1P

  • PubMed Abstract: 

    Geobacillus thermoglucosidasius is a thermophilic bacterium that is able to ferment both C6 and C5 sugars to produce ethanol. During growth on hemicellulose biomass, an intracellular β-xylosidase catalyses the hydrolysis of xylo-oligosaccharides to the monosaccharide xylose, which can then enter the pathways of central metabolism. The gene encoding a G. thermoglucosidasius β-xylosidase belonging to CAZy glycoside hydrolase family GH52 has been cloned and expressed in Escherichia coli. The recombinant enzyme has been characterized and a high-resolution (1.7 Å) crystal structure has been determined, resulting in the first reported structure of a GH52 family member. A lower resolution (2.6 Å) structure of the enzyme-substrate complex shows the positioning of the xylobiose substrate to be consistent with the proposed retaining mechanism of the family; additionally, the deep cleft of the active-site pocket, plus the proximity of the neighbouring subunit, afford an explanation for the lack of catalytic activity towards the polymer xylan. Whilst the fold of the G. thermoglucosidasius β-xylosidase is completely different from xylosidases in other CAZy families, the enzyme surprisingly shares structural similarities with other glycoside hydrolases, despite having no more than 13% sequence identity.


  • Organizational Affiliation

    Centre for Extremophile Research, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-XYLOSIDASE727Parageobacillus thermoglucosidasiusMutation(s): 0 
EC: 3.2.1.37
UniProt
Find proteins for A0A067XG64 (Parageobacillus thermoglucosidasius)
Explore A0A067XG64 
Go to UniProtKB:  A0A067XG64
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067XG64
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
HA [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
L [auth A]
M [auth A]
N [auth A]
AA [auth A],
BA [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.557α = 90
b = 105.143β = 90
c = 195.565γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 1.2: 2014-12-17
    Changes: Data collection
  • Version 1.3: 2018-03-07
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 2.0: 2024-05-08
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other