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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1016/j.febslet.2012.02.029

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoglucanase A
A
319Pyrococcus furiosusMutation(s): 0 
Gene Names: eglA
Find proteins for Q9V2T0 (Pyrococcus furiosus)
Go to UniProtKB:  Q9V2T0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

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Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.127 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.014α = 90.00
b = 118.665β = 90.00
c = 46.759γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-12
    Type: Initial release