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FEBS Open Bio
2022 Mar 01;123:664-674. doi: 10.1002/2211-5463.13375.
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Crystallographic characterization of a marine invertebrate ferritin from the sea cucumber Apostichopus japonicus.
Wu Y
,
Ming T
,
Huo C
,
Qiu X
,
Su C
,
Lu C
,
Zhou J
,
Li Y
,
Su X
.
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Ferritin is considered to be an ubiquitous and conserved iron-binding protein that plays a crucial role in iron storage, detoxification, and immune response. Although ferritin is of critical importance for almost all kingdoms of life, there is a lack of knowledge about its role in the marine invertebrate sea cucumber (Apostichopus japonicus). In this study, we characterized the first crystal structure of A. japonicus ferritin (AjFER) at 2.75 Å resolution. The structure of AjFER shows a 4-3-2 symmetry cage-like hollow shell composed of 24 subunits, mostly similar to the structural characteristics of other known ferritin species, including the conserved ferroxidase center and 3-fold channel. The 3-fold channel consisting of three 3-fold negative amino acid rings suggests a potential pathway in which metal ions can be first captured by Asp120 from the outside environment, attracted by His116 and Cys128 when entering the channel, and then transferred by Glu138 from the 3-fold channel to the ferroxidase site. Overall, the presented crystal structure of AjFER may provide insights into the potential mechanism of the metal transport pathway for related marine invertebrate ferritins.
Fig. 1. Homology analysis and characterization of AjFER. (A) Phylogenetic tree diagram. (B) Multiple sequence alignment of Apostichopus japonicus ferritin and nine other ferritin polypeptides. AjFER, Apostichopus japonicus ferritin; FrogMF, Rana catesbeiana M ferritin; HuHF, Homo sapiens H chain; HuLF, Homo sapiens L chain; ChF, Chaetopterus sp. ferritin; MjFer, Marsupenaeus japonicus ferritin; Fer147, novel Phascolosoma esculenta ferritin; PeFer, Phascolosoma esculenta ferritin; ScFer, Sinonovacula constricta ferritin; DzFer, Dendrorhynchus zhejiangensis ferritin. (C) Superdex 200 gel filtration chromatography profile of AjFER. The absorbance at 280 nm is shown in the blue curve. (D) SDS/PAGE analysis of AjFER. Lane 1: protein marker; lane 2: recombinant protein. (E) DLS analysis of AjFER. The red curve is the volume distribution of particles. (F) CD spectrum and the secondary structure of AjFER.
Fig. 2. Overall structure of AjFER. (A) The building blocks of the subunit. (B) Structure superimposition for the monomeric ferritin subunit of AjFER and nine ferritins. (C) Cross‐sectional image of the cage‐like cavity of AjFER. Cartoon views of the overall structure viewed from the (D) 2‐fold channel, (E) 3‐fold channel, and (F) 4‐fold channel.
Fig. 3. The surface electrostatic potential of AjFER. The electrostatic potential of the 3‐fold channel from the (A) outside, (B) inside, and (C) cross‐section. The electrostatic potential of the 4‐fold channel from the (D) outside, (E) inside, and (F) cross‐section. Surface electrostatic potentials ranging from −10 kT·e−1 (red) to +10 kT·e−1 (blue) were calculated by APBS.
Fig. 4. Ion binding sites and transfer path of AjFER. (A) The electrostatic potential of the ferroxidase center. (B) The combination of Mg2+ ions is shown in the ferroxidase center. (C) The combination of Mg2+ ions was observed in the 3‐fold channel. (D) The key residues of the 4‐fold channel. (E) Transfer path of Mg2+ ions from the 3‐fold channel to the ferroxidase center into the cavity. Key residues are highlighted as sticks, Mg2+ ions are shown as green spheres, and water molecules are displayed as red spheres.
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