3VGI

The crystal structure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Atomic resolution of the crystal structure of the hyperthermophilic family 12 endocellulase and stabilizing role of the DxDxDG calcium-binding motif in Pyrococcus furiosus.

Kim, H.-W.Kataoka, M.Ishikawa, K.

(2012) FEBS Lett 586: 1009-1013

  • DOI: https://doi.org/10.1016/j.febslet.2012.02.029
  • Primary Citation of Related Structures:  
    3VGI

  • PubMed Abstract: 

    Hyperthermophilic glycoside hydrolase family 12 endocellulase (EGPf) from the archaeon Pyrococcus furiosus catalyzes the hydrolytic cleavage of β-1,4-glucosidic linkage in β-glucan cellulose. A truncated EGPf (EGPfΔN30) mutant lacking the proline and hydroxyl-residue rich region at the N terminus was constructed, and its crystal structure was resolved at an atomic resolution of 1.07 Å. Our results indicate that the structure of EGPf, which consists of a β-jelly roll, exhibits structural similarity with the endocellulase of Thermotoga maritima. Additionally, we further determined that the thermostability of EGPf is maintained in part by the binding of Ca²⁺ in a DxDxDG Ca²⁺-binding motif, atypical of most archaeal proteins.


  • Organizational Affiliation

    National Institute of Advanced Industrial Science and Technology, Biomass Technology Research Center, 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
Endoglucanase A319Pyrococcus furiosusMutation(s): 0 
Gene Names: eglA
UniProt
Find proteins for Q9V2T0 (Pyrococcus furiosus)
Explore Q9V2T0 
Go to UniProtKB:  Q9V2T0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2T0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHE
Query on NHE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.014α = 90
b = 118.665β = 90
c = 46.759γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-12
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations