PDBsum entry 5n5e

Oxidoreductase

PDB id: 5n5e

Contents

Protein chains

(+ 24 more) 98 a.a.

Metals

_FE ×30

Waters ×2014

PDB id:

5n5e

Name:

Oxidoreductase

Title:

Crystal structure of encapsulated ferritin domain from pyrococcus furiosus pfc_05175

Structure:

Pfc_05175. Chain: e, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, t, u, v, w, x, y, z, a, b, c, d. Engineered: yes

Source:

Pyrococcus furiosus com1. Organism_taxid: 1185654. Gene: pfc_05175. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.03Å R-factor: 0.165 R-free: 0.202

Authors:

J.Marles-Wright,D.He

Key ref:

D.He et al. (2019). Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea. Biochem J, 476, 975-989. PubMed id: 30837306 DOI: 10.1042/BCJ20180922

Date:

13-Feb-17 Release date: 24-Jan-18

Protein chains

Q8U1L4  (Q8U1L4_PYRFU) -  Ferritin-like-encapsulin shell fusion protein from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 345 a.a.

Struc: 98 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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

DOI no: 10.1042/BCJ20180922

Biochem J 476:975-989 (2019)

PubMed id: 30837306

Conservation of the structural and functional architecture of encapsulated ferritins in bacteria and archaea.

D.He, C.Piergentili, J.Ross, E.Tarrant, L.R.Tuck, C.L.Mackay, Z.McIver, K.J.Waldron, D.J.Clarke, J.Marles-Wright.

ABSTRACT

Ferritins are a large family of intracellular proteins that protect the cell from oxidative stress by catalytically converting Fe(II) into less toxic Fe(III) and storing iron minerals within their core. Encapsulated ferritins (EncFtn) are a sub-family of ferritin-like proteins, which are widely distributed in all bacterial and archaeal phyla. The recently characterized Rhodospirillum rubrum EncFtn displays an unusual structure when compared with classical ferritins, with an open decameric structure that is enzymatically active, but unable to store iron. This EncFtn must be associated with an encapsulin nanocage in order to act as an iron store. Given the wide distribution of the EncFtn family in organisms with diverse environmental niches, a question arises as to whether this unusual structure is conserved across the family. Here, we characterize EncFtn proteins from the halophile Haliangium ochraceum and the thermophile Pyrococcus furiosus, which show the conserved annular pentamer of dimers topology. Key structural differences are apparent between the homologues, particularly in the centre of the ring and the secondary metal-binding site, which is not conserved across the homologues. Solution and native mass spectrometry analyses highlight that the stability of the protein quaternary structure differs between EncFtn proteins from different species. The ferroxidase activity of EncFtn proteins was confirmed, and we show that while the quaternary structure around the ferroxidase centre is distinct from classical ferritins, the ferroxidase activity is still inhibited by Zn(II). Our results highlight the common structural organization and activity of EncFtn proteins, despite diverse host environments and contexts within encapsulins.