PDBsum entry 4das

Oxidoreductase

PDB id: 4das

Contents

Protein chains

(+ 18 more) 172 a.a.

Ligands

PGE ×22

EDO ×12

Waters ×1525

PDB id:

4das

Name:

Oxidoreductase

Title:

Crystal structure of bullfrog m ferritin

Structure:

Ferritin, middle subunit. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, x, w. Synonym: ferritin m, ferritin h', ferritin x. Engineered: yes

Source:

Rana catesbeiana. Bullfrogs. Organism_taxid: 8400. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

2.56Å R-factor: 0.189 R-free: 0.239

Authors:

I.Bertini,D.Lalli,S.Mangani,C.Pozzi,C.Rosa,P.Turano

Key ref:

I.Bertini et al. (2012). Structural insights into the ferroxidase site of ferritins from higher eukaryotes. J Am Chem Soc, 134, 6169-6176. PubMed id: 22424302

Date:

13-Jan-12 Release date: 16-Jan-13

Protein chains

P07798  (FRI2_LITCT) -  Ferritin, middle subunit from Lithobates catesbeianus

Seq: 176 a.a.

Struc: 172 a.a.

Enzyme reactions

• Enzyme class: E.C.1.16.3.1 - ferroxidase.
• Reaction: 4 Fe²⁺ + O2 + 4 H⁺ = 4 Fe³⁺ + 2 H2O
• Cofactor: Cu cation

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

J Am Chem Soc 134:6169-6176 (2012)

PubMed id: 22424302

Structural insights into the ferroxidase site of ferritins from higher eukaryotes.

I.Bertini, D.Lalli, S.Mangani, C.Pozzi, C.Rosa, E.C.Theil, P.Turano.

ABSTRACT

The first step of iron biomineralization mediated by ferritin is the oxidation at the ferroxidase active site of two ferrous ions to a diferric oxo/hydroxo species. Metal-loaded ferritin crystals obtained by soaking crystals of frog ferritin in FeSO(4) and CuSO(4) solutions followed by flash freezing provided X-ray crystal structures of the tripositive iron and bipositive copper adducts at 2.7 and 2.8 Å resolution, respectively. At variance with the already available structures, the crystal form used in this study contains 24 independent subunits in the asymmetric unit permitting comparison between them. For the first time, the diferric species at the ferroxidase site is identified in ferritins from higher eukaryotes. Anomalous difference Fourier maps for crystals (iron crystal 1) obtained after long soaking times in FeSO(4) solution invariantly showed diferric species with a Fe-Fe average distance of 3.1 ± 0.1 Å, strongly indicative of the presence of a μ-oxo/hydroxo bridge between the irons; protein ligands for each iron ion (Fe1 and Fe2) were also unequivocally identified and found to be the same in all subunits. For copper bound ferritin, dicopper(II) centers are also observed. While copper at site 1 is essentially in the same position and has the same coordination environment as Fe1, copper at site 2 is displaced toward His54, now acting as a ligand; this results in an increased intermetal distance (4.3 ± 0.4 Å). His54 coordination and longer metal-metal distances might represent peculiar features of divalent cations at the ferroxidase site. This oxidation-dependent structural information may provide key features for the mechanistic pathway in ferritins from higher eukaryotes that drive uptake of bivalent cation and release of ferric products at the catalytic site. This mechanism is supported by the X-ray picture obtained after only 1 min of soaking in FeSO(4) solutions (iron crystal 2) which reasonably contain the metal at different oxidation states. Here two different di-iron species are trapped in the active site, with intermetal distances corresponding to those of the ferric dimer in crystal 1 and of the dicopper centers and corresponding rearrangement of the His54 side chain.