Structural comparison of two ferritins from the marine invertebrate Phascolosoma esculenta

Abstract

For marine invertebrates with no adaptive immune system, ferritin is a major intracellular iron‐storage protein with a critical role in innate immunity. Here, we present the crystal structures of two novel ferritins [Fer147 and Phascolosoma esculenta ferritin (PeFer)] from the marine invertebrate P. esculenta, which resides in muddy‐bottom coastal regions. Fer147 and PeFer exhibit the 4‐3‐2 symmetry of cage‐like hollow shells containing 24 subunits, similar to other known ferritins. Fer147 and PeFer contain both the conserved ferroxidase center and threefold channels. Subtle structural differences in the putative nucleation sites suggest possible routes of metal ion movement in the protein shells. However, the marked variation in the electrostatic potential of the threefold channels in Fer147 and the fourfold channels in PeFer suggests significant diversity between Fer147 and PeFer in terms of metal ion aggregation and cation exclusion. In summary, the presented crystal structures may serve as references for studies of the iron‐storage mechanism of additional ferritins from marine invertebrates.

Structural Insights Into the Effects of Interactions With Iron and Copper Ions on Ferritin From the Blood Clam Tegillarca granosa

“…Here, we established precise, three-dimensional, structural models using comparative analyses of X-ray crystal structures to reveal structural differences. The results showed that the overall structures of TgFer, TgFer + Cu, TgFer + Fe, and TgFer + CuFe were highly conserved (Figure 4), similar to previously identified ferritin structures (Su et al, 2020;Ming et al, 2021). In the crystal structures of TgFer and TgFer + Fe, only site A of the ferroxidase center was occupied by Fe-1, but no clear electron density indicative of a metal ligand was visible around site B (Figure 4I), similar to the structural features of Marsupenaeus japonicus ferritin (MjFer) (Masuda et al, 2018).…”

Crystallographic characterization of a marine invertebrate ferritin from the sea cucumber Apostichopus japonicus

“…The putative nucleation site of AjFER is composed of four glutamate residues (Glu58, Glu59, Glu62, and Glu65) (Fig. 4E), which is fully consistent with that of PeFer [38], with corresponding glutamate residues Glu53, Glu56, Glu57, and Glu60 of the HuLF [43] and horse spleen L ferritin (HoLF) [51]. Therefore, the highly conserved residues of AjFER at the nucleation site suggest equivalent capabilities to those of L ferritins.…”

“…Of note, the main chain Ca RMSD values between AjFER and DzFer (PDB ID: 7EMK) [34] is 0.73 A over 167 residues (67.5% identity over 169 amino acids). Moreover, multiple sequence alignment analysis indicated that AjFER shared the highest sequence identity (69.9% over 173 amino acids) with PeFer (PDB ID: 6LPE) [38] compared to the other ferritins (Fig. 1B), and their main Ca RMSD value was 0.57 A for 168 amino acid residues.…”

“…Furthermore, the RMSD values of the main chain Ca are 0.48 A between AjFER and ChF (PDB ID: 5WPN) [14] for 168 residues (64.5% identity over 169 amino acids) and 0.67 A between AjFER and MjFer (PDB ID: 6A4U) [15] for 167 residues (60.6% identity over 170 amino acids). The main chain Ca RMSD values between AjFER and ScFer (PDB ID: 6LP5) [36] with 66.1% identity over 171 amino acids are 0.57 A over 168 residues, while between AjFER and Fer147 (PDB ID: 6LPD) [38] with 64.7% identity over 173 amino acids are 0.55 A over 167 residues. Of note, the main chain Ca RMSD values between AjFER and DzFer (PDB ID: 7EMK) [34] is 0.73 A over 167 residues (67.5% identity over 169 amino acids).…”

“…1B). The AjFER protein sequence has the following levels of identity with other ferritins: 52.6% (H. sapiens L-chain ferritin: HuLF) [35], 62.8% (HuHF), 60.5% (Rana catesbeiana M ferritin: FrogMF) [12], 64.5% (ChF), 60.6% (MjFer), 66.1% (Sinonovacula constricta ferritin: ScFer) [36], 67.5% (DzFer), 64.7% [Phascolosoma esculenta ferritin (new): Fer147] [37], and 69.9% (P. esculenta ferritin: PeFer) [38]. Sequence alignment and prediction of functional domains revealed that AjFER had a highly conserved ferroxidase center with nine ferritins other than HuLF.…”