1FI2

CRYSTAL STRUCTURE OF GERMIN (OXALATE OXIDASE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.

Woo, E.J.Dunwell, J.M.Goodenough, P.W.Marvier, A.C.Pickersgill, R.W.

(2000) Nat.Struct.Mol.Biol. 7: 1036-1040

  • DOI: 10.1038/80954

  • PubMed Abstract: 
  • Germin is a hydrogen peroxide generating oxalate oxidase with extreme thermal stability; it is involved in the defense against biotic and abiotic stress in plants. The structure, determined at 1.6 A resolution, comprises beta-jellyroll monomers locke ...

    Germin is a hydrogen peroxide generating oxalate oxidase with extreme thermal stability; it is involved in the defense against biotic and abiotic stress in plants. The structure, determined at 1.6 A resolution, comprises beta-jellyroll monomers locked into a homohexamer (a trimer of dimers), with extensive surface burial accounting for its remarkable stability. The germin dimer is structurally equivalent to the monomer of the 7S seed storage proteins (vicilins), indicating evolution from a common ancestral protein. A single manganese ion is bound per germin monomer by ligands similar to those of manganese superoxide dismutase (MnSOD). Germin is also shown to have SOD activity and we propose that the defense against extracellular superoxide radicals is an important additional role for germin and related proteins.


    Related Citations: 
    • Barley Oxalate Oxidase is a Hexameric Protein Related to Seed Storage Proteins: Evidence from X-ray Crystallography
      Woo, E.J.,Dunwell, J.M.,Goodenough, P.W.,Pickersgill, R.W.
      (1998) FEBS Lett. 437: 87


    Organizational Affiliation

    Institute of Food Research, Reading Laboratory, Earley Gate, Reading RG6 6BZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OXALATE OXIDASE
A
201Hordeum vulgareEC: 1.2.3.4
Find proteins for P45850 (Hordeum vulgare)
Go to UniProtKB:  P45850
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 95.593α = 90.00
b = 95.593β = 90.00
c = 107.109γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
MLPHAREphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance