4XGS

Crystal structure analysis of novel iron uptake mechanism of Gram-negative bacterial ferritin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    4XGS, 4ZTT, 5C6F

  • 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 uptake and the structural identification of intermediates still remain incomplete ...

    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

    Department of Biotechnology & Bioinformatics, Korea University, Sejong 339-700, Korea. Electronic address: khkim@korea.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FerritinA, B, C, D, E, F165Escherichia coli K-12Mutation(s): 1 
Gene Names: ftnAftngen-165rsgAb1905JW1893
EC: 1.16.3.2
UniProt
Find proteins for P0A998 (Escherichia coli (strain K12))
Explore P0A998 
Go to UniProtKB:  P0A998
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OFO
Query on OFO

Download Ideal Coordinates CCD File 
BA [auth E], G [auth A], GA [auth F], M [auth B], P [auth C], V [auth D]HYDROXY DIIRON-OXO MOIETY
Fe2 H O2
HLBQEWFJZLSCMX-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth E], H [auth A], Q [auth C], W [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D] , DA [auth E] , EA [auth E] , FA [auth E] , HA [auth F] , I [auth A] , IA [auth F] , J [auth A] , 
AA [auth D], DA [auth E], EA [auth E], FA [auth E], HA [auth F], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D], Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.025α = 90
b = 129.025β = 90
c = 172.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2015-01-02 
  • Released Date: 2016-07-06 
  • Deposition Author(s): Kim, S.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2016-12-21
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection