7URH

Crystal structure of Ferritin 2 from Caenorhabditis elegans, FTN-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biochemical Characterization of Caenorhabditis elegans Ferritins.

Mubarak, S.S.M.Malcolm, T.R.Brown, H.G.Hanssen, E.Maher, M.J.McColl, G.Jameson, G.N.L.

(2023) Biochemistry 62: 1484-1496

  • DOI: https://doi.org/10.1021/acs.biochem.3c00005
  • Primary Citation of Related Structures:  
    7URH, 7USN

  • PubMed Abstract: 

    The nematode Caenorhabditis elegans contains genes for two types of ferritin ( ftn-1 and ftn-2 ) that express FTN-1 and FTN-2. We have expressed and purified both proteins and characterized them by X-ray crystallography, cryo-electron microscopy, transmission electron microscopy, dynamic light scattering, and kinetically by oxygen electrode and UV-vis spectroscopy. Both show ferroxidase activity, but although they have identical ferroxidase active sites, FTN-2 is shown to react approximately 10 times faster than FTN-1, with L-type ferritin character over longer time periods. We hypothesize that the large variation in rate may be due to differences in the three- and four-fold channels into the interior of the protein 24-mer. FTN-2 is shown to have a wider entrance into the three-fold channel than FTN-1. Additionally, the charge gradient through the channel of FTN-2 is more pronounced, with Asn and Gln residues in FTN-1 replaced by Asp and Glu residues in FTN-2. Both FTN-1 and FTN-2 have an Asn residue near the ferroxidase active site that is a Val in most other species, including human H ferritin. This Asn residue has been observed before in ferritin from the marine pennate diatom Pseudo-mitzchia multiseries. By replacing this Asn residue with a Val in FTN-2, we show that the reactivity decreases over long time scales. We therefore propose that Asn106 is involved in iron transport from the ferroxidase active site to the central cavity of the protein.


  • Organizational Affiliation

    School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferritin168Caenorhabditis elegansMutation(s): 0 
Gene Names: ftn-2CELE_D1037.3D1037.3
EC: 1.16.3.1
UniProt
Find proteins for Q9TYS3 (Caenorhabditis elegans)
Explore Q9TYS3 
Go to UniProtKB:  Q9TYS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9TYS3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.159 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.84α = 90
b = 154.84β = 90
c = 128.763γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description