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Structural description of the active sites of mouse L-chain ferritin at 1.2 A resolution.

Granier T, Langlois d'Estaintot B, Gallois B, Chevalier JM, Précigoux G, Santambrogio P, Arosio P
J Biol Inorg Chem 8 105-11 (2003)
Cited: 35 times
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Abstract

The first ferritin structure refined at the atomic level has been achieved on recombinant mouse L-chain apoferritin (rMoLF) crystals. These latter diffract to 1.2 A resolution under cryogenic conditions. When cryo-cooling the sample, the thermal disorder usually observed at room temperature is reduced and the low-temperature structure reveals several details concerning the protein putative active sites and their properties. Within the pores built up by the molecular three-fold symmetry axes, the iron entry route to the ferritin cavity, residues H118, D131 and E134, exhibit alternate conformations associated with the binding of partially hydrated cadmium ions, a metal used as a crystallization agent. At the mineral ferrihydrite nucleation center, the electron density maps evidence the orientation of E57, E60, E61 and E64 glutamate side chains (whereas they were observed highly disordered in previous ferritin structures determined at room temperature) and allow a description of the site taking into account the binding geometry of four Cd(2+) ions. Moreover, the side chain of residue K140, lying in the vicinity of the ferrihydrite nucleation center, is shown to interact with residue E61. As previously highlighted, this observation confirms the importance of K140 in the rMoLF sequence, as being responsible for the low level of iron incorporation by mousel L-chain ferritin compared to human L-chain ferritin. Finally, the diffusion of small molecules within the ferritin cavity is illustrated here by the presence of ordered molecules of glycerol used as a cryo-protectant, which bind the inner cavity surface of the protein.

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  2. De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. Structure 27 679-691.e14 (2019)
  3. Compact Representation of Continuous Energy Surfaces for More Efficient Protein Design. Hallen MA, Gainza P, Donald BR. J Chem Theory Comput 11 2292-2306 (2015)
  4. Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. Tan CW, Jones DT. BMC Bioinformatics 9 94 (2008)
  5. Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. Li R, Yu L, Zhou B, Zeng X, Wang Z, Yang X, Zhang J, Gao X, Jiang R, Xu M. PLoS Comput Biol 16 e1008227 (2020)
  6. Folding of an Intrinsically Disordered Iron-Binding Peptide in Response to Sedimentation Revealed by Cryo-EM. Davidov G, Abelya G, Zalk R, Izbicki B, Shaibi S, Spektor L, Shagidov D, Meyron-Holtz EG, Zarivach R, Frank GA. J Am Chem Soc 142 19551-19557 (2020)
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Reviews citing this publication (7)

  1. Ferritins, iron uptake and storage from the bacterioferritin viewpoint. Carrondo MA. EMBO J 22 1959-1968 (2003)
  2. Self-assembling protein nanoparticles in the design of vaccines. López-Sagaseta J, Malito E, Rappuoli R, Bottomley MJ. Comput Struct Biotechnol J 14 58-68 (2016)
  3. Biological inorganic chemistry at the beginning of the 21st century. Gray HB. Proc Natl Acad Sci U S A 100 3563-3568 (2003)
  4. Formation of protein-coated iron minerals. Lewin A, Moore GR, Le Brun NE. Dalton Trans 3597-3610 (2005)
  5. Neurodegeneration caused by proteins with an aberrant carboxyl-terminus. Vidal R, Delisle MB, Ghetti B. J Neuropathol Exp Neurol 63 787-800 (2004)
  6. Iron chaperones for mitochondrial Fe-S cluster biosynthesis and ferritin iron storage. Subramanian P, Rodrigues AV, Ghimire-Rijal S, Stemmler TL. Curr Opin Chem Biol 15 312-318 (2011)
  7. Cyclen-based Gd3+ complexes as MRI contrast agents: Relaxivity enhancement and ligand design. Rashid HU, Martines MAU, Jorge J, de Moraes PM, Umar MN, Khan K, Rehman HU. Bioorg Med Chem 24 5663-5684 (2016)

Articles citing this publication (21)

  1. Crystal structure and biochemical properties of the human mitochondrial ferritin and its mutant Ser144Ala. Langlois d'Estaintot B, Santambrogio P, Granier T, Gallois B, Chevalier JM, Précigoux G, Levi S, Arosio P. J Mol Biol 340 277-293 (2004)
  2. Crystal structure of plant ferritin reveals a novel metal binding site that functions as a transit site for metal transfer in ferritin. Masuda T, Goto F, Yoshihara T, Mikami B. J Biol Chem 285 4049-4059 (2010)
  3. Moving metal ions through ferritin-protein nanocages from three-fold pores to catalytic sites. Tosha T, Ng HL, Bhattasali O, Alber T, Theil EC. J Am Chem Soc 132 14562-14569 (2010)
  4. High-resolution X-ray structures of human apoferritin H-chain mutants correlated with their activity and metal-binding sites. Toussaint L, Bertrand L, Hue L, Crichton RR, Declercq JP. J Mol Biol 365 440-452 (2007)
  5. Ferritin reactions: direct identification of the site for the diferric peroxide reaction intermediate. Liu X, Theil EC. Proc Natl Acad Sci U S A 101 8557-8562 (2004)
  6. Crystal structure of a secreted insect ferritin reveals a symmetrical arrangement of heavy and light chains. Hamburger AE, West AP, Hamburger ZA, Hamburger P, Bjorkman PJ. J Mol Biol 349 558-569 (2005)
  7. Ferritin structure from Mycobacterium tuberculosis: comparative study with homologues identifies extended C-terminus involved in ferroxidase activity. Khare G, Gupta V, Nangpal P, Gupta RK, Sauter NK, Tyagi AK. PLoS One 6 e18570 (2011)
  8. A new approach to the ferritin iron core growth: influence of the H/L ratio on the core shape. López-Castro JD, Delgado JJ, Perez-Omil JA, Gálvez N, Cuesta R, Watt RK, Domínguez-Vera JM. Dalton Trans 41 1320-1324 (2012)
  9. Chemistry at the protein-mineral interface in L-ferritin assists the assembly of a functional (μ3-oxo)Tris[(μ2-peroxo)] triiron(III) cluster. Pozzi C, Ciambellotti S, Bernacchioni C, Di Pisa F, Mangani S, Turano P. Proc Natl Acad Sci U S A 114 2580-2585 (2017)
  10. Structural analysis of haemin demetallation by L-chain apoferritins. de Val N, Declercq JP, Lim CK, Crichton RR. J Inorg Biochem 112 77-84 (2012)
  11. Fe(2+) substrate transport through ferritin protein cage ion channels influences enzyme activity and biomineralization. Behera RK, Torres R, Tosha T, Bradley JM, Goulding CW, Theil EC. J Biol Inorg Chem 20 957-969 (2015)
  12. Oxidative modification of ferritin induced by hydrogen peroxide. Yoon JH, An SH, Kyeong IG, Lee MS, Kwon SC, Kang JH. BMB Rep 44 165-169 (2011)
  13. Orally delivered sour cherry seed extract (SCSE) affects cardiovascular and hematological parameters in humans. Csiki Z, Papp-Bata A, Czompa A, Nagy A, Bak I, Lekli I, Javor A, Haines DD, Balla G, Tosaki A. Phytother Res 29 444-449 (2015)
  14. Oxidative modification of ferritin induced by methylglyoxal. An SH, Lee MS, Kang JH. BMB Rep 45 147-152 (2012)
  15. Ferritin enhances salsolinol-mediated DNA strand breakage: protection by carnosine and related compounds. Kang JH. Toxicol Lett 188 20-25 (2009)
  16. The C-terminal regions have an important role in the activity of the ferroxidase center and the stability of Chlorobium tepidum ferritin. Brito C, Matias C, González-Nilo FD, Watt RK, Yévenes A. Protein J 33 211-220 (2014)
  17. Hematoma Resolution In Vivo Is Directed by Activating Transcription Factor 1. Seneviratne A, Han Y, Wong E, Walter ERH, Jiang L, Cave L, Long NJ, Carling D, Mason JC, Haskard DO, Boyle JJ. Circ Res 127 928-944 (2020)
  18. Cloning, purification and preliminary X-ray crystallographic analysis of a hypothetical protein, MJ0754, from Methanococcus jannaschii DSM 2661. Lee EH, Nam KH, Hwang KY. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 1065-1067 (2009)
  19. Defining the mobility range of a hinge-type connection using molecular dynamics and metadynamics. Horx P, Geyer A. PLoS One 15 e0230962 (2020)
  20. Bacterioferritin nanocage structures uncover the biomineralization process in ferritins. Jobichen C, Ying Chong T, Rattinam R, Basak S, Srinivasan M, Choong YK, Pandey KP, Ngoc TB, Shi J, Angayarkanni J, Sivaraman J. PNAS Nexus 2 pgad235 (2023)
  21. Capturing and Stabilizing Folded Proteins in Lattices Formed with Branched Oligonucleotide Hybrids. Schwenger A, Jurkowski TP, Richert C. Chembiochem 19 1523-1530 (2018)


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