High-resolution X-ray Structures of Human Apoferritin H-chain Mutants Correlated with Their Activity and Metal-binding Sites

Toussaint, Louise; Bertrand, Luc; Hue, Louis; Crichton, Robert R.; Declercq, Jean-Paul

doi:10.1016/j.jmb.2006.10.010

Cited by 113Iron Metabolism and DisordersEnzyme Structure and FunctionMetal-Catalyzed Oxygenation Mechanisms

High-resolution X-ray Structures of Human Apoferritin H-chain Mutants Correlated with Their Activity and Metal-binding Sites

Toussaint, Louise, Bertrand, Luc, Hue, Louis, Crichton, Robert R., Declercq, Jean-Paul·2007·Journal of Molecular Biology

DOI 10.1016/j.jmb.2006.10.010

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Abstract

Ferritins are a family of proteins distributed widely in nature. In bacterial, plant, and animal cells, ferritin appears to serve as a soluble, bioavailable, and non-toxic form of iron provider. Ferritins from animal sources are heteropolymers composed of two types of subunit, H and L, which differ mainly by the presence (H) or absence (L) of active ferroxidase centres. We report the crystallographic structures of four human H apoferritin variants at a resolution of up to 1.5 Angstrom. Crystal derivatives using Zn(II) as redox-stable alternative for Fe(II), allows us to characterize the different metal-binding sites. The ferroxidase centre, which is composed of sites A and B, binds metal with a preference for the A site. In addition, distinct Zn(II)-binding sites were found in the 3-fold axes, 4-fold axes and on the cavity surface near the ferroxidase centre. To study the importance of the distance of the two metal atoms in the ferroxidase centre, single and double replacement of glutamate 27 (site A) and glutamate 107 (site B), the two axial ligands, by aspartate residues have been carried out. The consequences for metal binding and the correlation with Fe(II) oxidation rates are discussed.

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This induction is regulated at the transcriptional level through an antioxidant-responsive element (ARE) in the 5′-region of ferritin genes.
“This is regulated at the transcriptional level through an antioxidant-responsive element (ARE) (265) (also termed electrophile responsive element) (95) in the 5′-region of ferritin genes (133, 301, 302).”
From Intracellular iron transport and storage: from molecular mechanisms to health implications (2008) · cites this paper as [301]
The human ferritin H ARE is a 55-bp bidirectional ARE composed of an AP-1-like and an AP-1/NF-E2 sequence located 4.5 kb upstream from the transcription start site.
“The human ferritin H ARE is a 55-bp bidirectional ARE composed of an AP-1-like and an AP-1/NF-E2 sequence located 4.5 kb upstream from the transcription start site (301).”
From Intracellular iron transport and storage: from molecular mechanisms to health implications (2008) · cites this paper as [301]
Nrf2 binds and activates the human ferritin H ARE.
“Nrf2 was shown to bind and activate the human ferritin H ARE (143, 301).”
From Intracellular iron transport and storage: from molecular mechanisms to health implications (2008) · cites this paper as [301]
Ferritin H is transcriptionally activated by JunD through an ARE in the ferritin H promoter in response to oxidative stressors including H2O2.
“Ferritin H was transcriptionally activated by JunD through an ARE in the ferritin H promoter in response to oxidative stressors, including H2O2 (301).”
From Intracellular iron transport and storage: from molecular mechanisms to health implications (2008) · cites this paper as [301]
Ferritin has a cytoprotective role against free-iron-catalyzed production of ROS.
“Many studies set a precedent of ferritin in cytoprotection against free-iron–catalyzed production of ROS (227, 243, 301).”
From Intracellular iron transport and storage: from molecular mechanisms to health implications (2008) · cites this paper as [301]

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Apoferritin Applications in Nanomedicine
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The ferritin Fe2 site at the diiron catalytic center controls the reaction with O 2 in the rapid mineralization pathway
Tosha, T., Hasan, M. R., & Theil, E. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805083105 · Cited by 64 · see citing works
“[The figure was created from PDB 1MFR, frog M-ferritin, for Asp140, His54, Arg 143 Mg(II) cocrystals (18) and PDB 2CEI, Ala140(144), Glu143(147), and Gln54(58), human H-ferritin Zn(II) cocrystals (35).”
Time-lapse anomalous X-ray diffraction shows how Fe2+substrate ions move through ferritin protein nanocages to oxidoreductase sites
Pozzi, C., Pisa, F. D., Lalli, D., Rosa, C., Theil, E. C., Turano, P., & Mangani, S. (2015) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004715002333 · Cited by 62 · see citing works
Ferritin Structure from Mycobacterium tuberculosis: Comparative Study with Homologues Identifies Extended C-Terminus Involved in Ferroxidase Activity
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Ferritin variants: inspirations for rationally designing protein nanocarriers
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Spectroscopic Definition of the Ferroxidase Site in M Ferritin: Comparison of Binuclear Substrate vs Cofactor Active Sites
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Detection of isolated protein-bound metal ions by single-particle cryo-STEM
Elad, N., Bellapadrona, G., Houben, L., Sagi, I., & Elbaum, M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1708609114 · Cited by 56 · see citing works
“Extensive biochemistry shows that each ferroxidase site contains two nearby Zn-binding moieties, one of relatively high and one of relatively low affinity (26, 27) (Fig.”
BackgroundMethodInfluential
Ferritin iron uptake and release in the presence of metals and metalloproteins: Chemical implications in the brain
Carmona, F., Palacios, Ò., Gálvez, N., Cuesta, R., Atrian, S., Capdevila, M., & Dominguez-Vera, J. M. (2013) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2013.03.034 · Cited by 55 · see citing works
Two novel secreted ferritins involved in immune defense of Chinese mitten crab Eriocheir sinensis
Kong, P., Wang, L., Zhang, H., Zhou, Z., Qiu, L., Gai, Y., & Song, L. (2010) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2009.12.018 · Cited by 52 · see citing works
Use of Ferritin Capped Mesoporous Silica Nanoparticles for Redox and pH Triggered Drug Release In Vitro and In Vivo
Cai, Y., Deng, T., Pan, Y., & Zink, J. I. (2020) · Advanced Functional Materials · doi:10.1002/adfm.202002043 · Cited by 48 · see citing works
Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes into the Protein Nanocage of apo-Ferritin
Abe, S., Hikage, T., Watanabe, Y., Kitagawa, S., & Ueno, T. (2010) · Inorganic Chemistry · doi:10.1021/ic1003758 · Cited by 43 · see citing works
Metal binding sites of human H‐chain ferritin and iron transport mechanism to the ferroxidase sites: A molecular dynamics simulation study
Laghaei, R., Evans, D. G., & Coalson, R. D. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24251 · Cited by 43 · see citing works
Ferritin nanocages: a versatile platform for nanozyme design
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“This finding implies that ferritins from phytoferritin, unnamed FTN 2, and M-chain (clades 7, 8, and 9) have the capacity to both catalyze iron oxidation and promote efficient mineralization of the metal (Toussaint et al. 2007).”
Background
Effective encapsulation of a new cationic gadolinium chelate into apoferritin and its evaluation as an MRI contrast agent
Makino, A., Harada, H., Okada, T., Kimura, H., Amano, H., Saji, H., Hiraoka, M., & Kimura, S. (2011) · Nanomedicine Nanotechnology Biology and Medicine · doi:10.1016/j.nano.2011.01.015 · Cited by 38 · see citing works
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Quantitative Cryo‐Scanning Transmission Electron Microscopy of Biological Materials
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Structural analysis of haemin demetallation by L-chain apoferritins
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Maxi- and Mini-Ferritins: Minerals and Protein Nanocages
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“…protein cage side chains have been observed in high-resolution structures of ferritin, dependent on metals present during crystallization (e.g., Trikha et al. 1995; Toussaint et al. 2007) indicate the flexibility of the ligands at and near the active sites needed to move iron through the cage.”
Background
Iron redox pathway revealed in ferritin via electron transfer analysis
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Solution and Solid State NMR Approaches To Draw Iron Pathways in the Ferritin Nanocage
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Toward Compositional Contrast by Cryo-STEM.
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Loop Electrostatics Modulates the Intersubunit Interactions in Ferritin
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First biochemical and crystallographic characterization of a fast-performing ferritin from a marine invertebrate
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“236 Å) with that of HuHF (PDB ID: 2CEI (60)).”
Metal-Assisted Assembly of Protein Containers Loaded with Inorganic Nanoparticles
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The Ferritin Superfamily
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Calculation of Iron Transport through Human H-chain Ferritin
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Coordinating subdomains of ferritin protein cages with catalysis and biomineralization viewed from the C 4 cage axes
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Advancements of the Molecular Directed Design and Structure–Activity Relationship of Ferritin Nanocage
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Preparation of peptide- and protein-based molecular assemblies and their utilizations as nanocarriers for tumor imaging
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Structural basis of the zinc‐ and terbium‐mediated inhibition of ferroxidase activity in Dps ferritin‐like proteins
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“Indeed, crystallographic studies in ferritins in the presence of zinc have provided evidence of the di-iron complex formation during the ferroxidase reaction (Stillman et al. 2001; Toussaint et al. 2007).”
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Unsaturated Long‐Chain Fatty Acids Are Preferred Ferritin Ligands That Enhance Iron Biomineralization
Zanzoni, S., Pagano, K., D’Onofrio, M., Assfalg, M., Ciambellotti, S., Bernacchioni, C., Turano, P., Aime, S., Ragona, L., & Molinari, H. (2017) · Chemistry - A European Journal · doi:10.1002/chem.201701164 · Cited by 15 · see citing works
Assembly of Differently Sized Supercharged Protein Nanocages into Superlattices for Construction of Binary Nanoparticle–Protein Materials
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Below 3 Å structure of apoferritin using a multipurpose TEM with a side entry cryoholder
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The crystal structure of ferritin from Chlorobium tepidum reveals a new conformation of the 4-fold channel for this protein family
Arenas‐Salinas, M., Townsend, P. D., Brito, C. H., Márquez‐Miranda, V., Marabolí, V., González-Nilo, F. D., Matias, C., Watt, R. K., López‐Castro, J. D. D., Dominguez-Vera, J. M., et al. (2014) · Biochimie · doi:10.1016/j.biochi.2014.07.019 · Cited by 14 · see citing works
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Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis
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Mechanistic insights into metal ions transit through threefold ferritin channel
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Modification of 4-Fold and B-Pores in Bacterioferritin from Mycobacterium tuberculosis Reveals Their Role in Fe2+ Entry and Oxidoreductase Activity
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The Chemistry of Nature's Iron Biominerals in Ferritin Protein Nanocages
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Vertasile ferritin nanocages: Applications in detection and bioimaging
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Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage
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Unique Residues at the 3-Fold and 4-Fold Axis of Mycobacterial Ferritin Are Involved in Oligomer Switching
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Structural Insights Into the Effects of Interactions With Iron and Copper Ions on Ferritin From the Blood Clam Tegillarca granosa
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“5, containing 150 mM NaCl, with molar ratios of Fe ions to ferritin of 1,000:1 at 25°C (Toussaint et al., 2007).”
Precision design of ferritin nanocages: tumor-targeted delivery, multi-mechanism synergistic therapy and clinical translational challenges
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“Nevertheless, structural data on H-chains in complex with different metals, like Zn(II) and Tb(III), have been determined, based on which detailed studies on the bimetal binding centre have been performed (Lawson et al., 1989; Toussaint et al., 2007).”
Background
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“After single-particle reconstruction, Zn is found in a pattern that matches precisely its location at the ferroxidase sites determined previously by X-ray crystallography [2].”
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Fe Transport and Storage Related to Humans and Pathogens and Oxygen
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Authors: Toussaint, L., Bertrand, L., Hue, L., Crichton, R. R., & Declercq, J.-P.
Affiliations: UCLouvain (BE)
de Duve Institute (BE)
Corresponding author: Crichton, Robert R.
ORCID: Bertrand, Luc
Crichton, Robert R.
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 2007-01
Volume: 365
Issue: 2
Pages: 440-452
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/j.jmb.2006.10.010
OpenAlex: W1995803883
Cited by: 113
References: 48
Citations by year: 2026: 2 · 2025: 2 · 2024: 5 · 2023: 6 · 2022: 5 · 2021: 5 · 2020: 6 · 2019: 3 · 2018: 5 · 2017: 7 · 2016: 3 · 2015: 4 · 2014: 11 · 2013: 11 · 2012: 4
FWCI: 3.05
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
DIAL (Catholic University of Leuven) (submittedVersion)
ORBi (University of Liège) (submittedVersion)
Funders: Université Catholique de Louvain
European Synchrotron Radiation Facility
Topics: Health Sciences › Medicine › Hematology › Iron Metabolism and Disorders
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Physical Sciences › Chemistry › Inorganic Chemistry › Metal-Catalyzed Oxygenation Mechanisms
Keywords: apoferritin, human ferritin, metal binding sites, crystal structure, aspartate substitution, iron oxidation, iron storage protein, protein mutants
MeSH terms: Apoferritins, Binding Sites, Catalysis, Ceruloplasmin, Crystallization, Ferritins, Glycerol, Humans, Iron, Models, Molecular, Mutation, Structure-Activity Relationship, Zinc, Protein Structure, Secondary, Crystallography, X-Ray, Amino Acid Substitution, Protein Subunits

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High-resolution X-ray Structures of Human Apoferritin H-chain Mutants Correlated with Their Activity and Metal-binding Sites

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