5C6F

Crystal structures of ferritin mutants reveal side-on binding to diiron and end-on cleavage of oxygen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Novel Iron-Uptake Route and Reaction Intermediates in Ferritins from Gram-Negative Bacteria.

Kim, S.Lee, J.H.Seok, J.H.Park, Y.H.Jung, S.W.Cho, A.E.Lee, C.Chung, M.S.Kim, K.H.

(2016) J. Mol. Biol. 428: 5007-5018

  • DOI: 10.1016/j.jmb.2016.10.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Iron and oxygen chemistry is mediated by iron proteins for many biological functions. Carboxylate-bridged diiron enzymes including ferritin have the common mechanism of oxygen activation via peroxodiferric intermediates. However, the route for iron u ...

    Iron and oxygen chemistry is mediated by iron proteins for many biological functions. Carboxylate-bridged diiron enzymes including ferritin have the common mechanism of oxygen activation via peroxodiferric intermediates. However, the route for iron uptake and the structural identification of intermediates still remain incomplete. The 4-fold symmetry channel of Helicobacter pylori ferritin was previously proposed as the iron-uptake route in eubacteria, but the amino acid residues at the 4-fold channel are not highly conserved. Here, we show evidence for a short path for iron uptake from His93 on the surface to the ferroxidase center in H. pylori ferritin and Escherichia coli ferritin. The amino acid residues along this path are highly conserved in Gram-negative bacteria and some archaea, and the mutants containing S20A and H93L showed significantly decreased iron oxidation. Surprisingly, the E. coli ferritin S20A crystal structure showed oxygen binding and side-on, symmetric μ-η 2 2 peroxodiferric and oxodiferric intermediates. The results provide the structural basis for understanding the chemical nature of intermediates in iron oxidation in bacteria and some of archaea.


    Organizational Affiliation

    Functional Proteomics Center, Korea Institute of Science and Technology, Seoul 136-791, Korea.,Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea.,Department of Food and Nutrition, Duksung Women's University, Seoul 132-714, Korea.,Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea. Electronic address: khkim@korea.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacterial non-heme ferritin
A, B, C, D, E, F, G, H, I, J, K, L
173Helicobacter pylori (strain J99 / ATCC 700824)Mutation(s): 1 
Gene Names: ftnA (pfr)
EC: 1.16.3.2
Find proteins for Q9ZLI1 (Helicobacter pylori (strain J99 / ATCC 700824))
Go to UniProtKB:  Q9ZLI1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, F, G, I, J, K
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B, C, D, E, G, H, I, J, K, L
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.149 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 128.051α = 90.00
b = 128.051β = 90.00
c = 165.103γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2017-04-05
    Type: Database references