1COJ

FE-SOD FROM AQUIFEX PYROPHILUS, A HYPERTHERMOPHILIC BACTERIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of an Fe-superoxide dismutase from the hyperthermophile Aquifex pyrophilus at 1.9 A resolution: structural basis for thermostability.

Lim, J.H.Yu, Y.G.Han, Y.S.Cho, S.Ahn, B.Y.Kim, S.H.Cho, Y.

(1997) J.Mol.Biol. 270: 259-274


  • PubMed Abstract: 
  • Superoxide dismutase (SOD) from Aquifex pyrophilus, a hyperthermophilic bacterium, is an extremely heat-stable enzyme that maintains about 70% of its activity after heat treatment for 60 minutes at 100 degrees C. To understand the molecular basis of ...

    Superoxide dismutase (SOD) from Aquifex pyrophilus, a hyperthermophilic bacterium, is an extremely heat-stable enzyme that maintains about 70% of its activity after heat treatment for 60 minutes at 100 degrees C. To understand the molecular basis of thermostability of this enzyme, we have determined the crystal structure of A. pyrophilus superoxide dismutase (Ap SOD), an Fe containing homotetrameric enzyme, at 1.9 A resolution, and compared it with SOD structures from a mesophile and a thermophile, and other enzyme structures from other hyperthermophiles. The structure has been refined to a crystallographic R-factor (I > 2sigma) of 17.0% and R-free (I > 2sigma) of 19.9%. While the overall structure of the Ap SOD monomer is similar to the other SODs, significant conformational differences are observed in a highly variable loop region and the C-terminal helix. The conformational differences in these regions alter the subunit arrangement of this enzyme and generate a very compact tetramer. Structural comparisons of three SODs have revealed that Ap SOD has some stabilizing features at both the tertiary and the quaternary structural level: The Ap SOD monomer contains a large number of ion-pairs and the Ap SOD tetramer has a dramatically increased buried surface area per monomer. Comparisons of the Ap SOD structure with that of other known enzymes from hyperthermophiles reveal that the increased number of intrasubunit ion-pairs is a common feature.


    Organizational Affiliation

    Structural Biology Center, Korea Institute of Science and Technology, Seoul, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SUPEROXIDE DISMUTASE)
A
212Aquifex pyrophilusGene Names: sodB (sod)
EC: 1.15.1.1
Find proteins for Q9X6W9 (Aquifex pyrophilus)
Go to UniProtKB:  Q9X6W9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.700α = 90.00
b = 75.630β = 90.00
c = 87.300γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-14
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance