High resolution structure of the fully reduced form of rubrerythrin from P. furiosus

Experimental Data Snapshot

  • Resolution: 1.64 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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A cryo-crystallographic time course for peroxide reduction by rubrerythrin from Pyrococcus furiosus.

Dillard, B.D.Demick, J.M.Adams, M.W.Lanzilotta, W.N.

(2011) J Biol Inorg Chem 16: 949-959

  • DOI: https://doi.org/10.1007/s00775-011-0795-6
  • Primary Citation of Related Structures:  
    3MPS, 3PWF, 3PZA, 3QVD

  • PubMed Abstract: 

    High-resolution crystal structures of Pyrococcus furiosus rubrerythrin (PfRbr) in the resting (all-ferrous) state and at time points following exposure of the crystals to hydrogen peroxide are reported. This approach was possible because of the relativity slow turnover of PfRbr at room temperature. To this end, we were able to perform time-dependent peroxide treatment of the fully reduced enzyme, under strictly anaerobic conditions, in the crystalline state. In this work we demonstrate, for the first time, that turnover of a thermophilic rubrerythrin results in approximately 2-Å movement of one iron atom in the diiron site from a histidine to a carboxylate ligand. These results confirm that, despite the domain-swapped architecture, the hyperthermophilic rubrerythrins also utilize the classic combination of iron sites together with redox-dependent iron toggling to selectively reduce hydrogen peroxide over dioxygen. In addition, we have identified previously unobserved intermediates in the reaction cycle and observed structural changes that may explain the enzyme precipitation observed for the all-iron form of PfRbr upon oxidation to the all-ferric state.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
170Pyrococcus furiosusMutation(s): 0 
Find proteins for Q9UWP7 (Pyrococcus furiosus)
Explore Q9UWP7 
Go to UniProtKB:  Q9UWP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UWP7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.64 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.87α = 90
b = 104.87β = 90
c = 79.84γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations