3WDP

Structural analysis of a beta-glucosidase mutant derived from a hyperthermophilic tetrameric structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of beta-glucosidase mutants derived from a hyperthermophilic tetrameric structure.

Nakabayashi, M.Kataoka, M.Mishima, Y.Maeno, Y.Ishikawa, K.

(2014) Acta Crystallogr D Biol Crystallogr 70: 877-888

  • DOI: https://doi.org/10.1107/S1399004713032276
  • Primary Citation of Related Structures:  
    3WDP

  • PubMed Abstract: 

    β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed.


  • Organizational Affiliation

    Biomass Refinery Research Center, National Institute of Advanced Industrial Science, 3-11-32, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidaseA [auth P],
B [auth Q],
C [auth R],
D [auth S]
473Pyrococcus furiosusMutation(s): 3 
Gene Names: celB
EC: 3.2.1.21
UniProt
Find proteins for Q51723 (Pyrococcus furiosus)
Explore Q51723 
Go to UniProtKB:  Q51723
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51723
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth S]
I [auth P]
J [auth P]
K [auth P]
L [auth P]
AA [auth S],
I [auth P],
J [auth P],
K [auth P],
L [auth P],
P [auth Q],
Q,
R [auth Q],
S [auth Q],
W [auth R],
X [auth R],
Y [auth R]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth P]
F [auth P]
G [auth P]
H [auth P]
M [auth Q]
E [auth P],
F [auth P],
G [auth P],
H [auth P],
M [auth Q],
N [auth Q],
O [auth Q],
T [auth R],
U [auth R],
V [auth R],
Z [auth S]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.15α = 90
b = 161.145β = 108.38
c = 183.824γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description