PDBsum entry 3e2c

Oxidoreductase

PDB id: 3e2c

Contents

Protein chains

158 a.a. *

Ligands

SO4 ×2

HEM-HEM

EDO ×4

Metals

_ZN ×2

Waters ×228

* Residue conservation analysis

PDB id:

3e2c

Name:

Oxidoreductase

Title:

Escherichia coli bacterioferritin mutant e128r/e135r

Structure:

Bacterioferritin. Chain: a, b. Synonym: bfr, cytochrome b-1, cytochrome b-557. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: bfr, b3336, jw3298. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.203 R-free: 0.228

Authors:

S.G.Wong,S.A.L.Tom-Yew,A.Lewin,N.E.Le Brun,G.R.Moore,M.E.P.Murphy, A.G.Mauk

Key ref:

S.G.Wong et al. (2009). Structural and Mechanistic Studies of a Stabilized Subunit Dimer Variant of Escherichia coli Bacterioferritin Identify Residues Required for Core Formation. J Biol Chem, 284, 18873-18881. PubMed id: 19439409 DOI: 10.1074/jbc.M901747200

Date:

05-Aug-08 Release date: 12-May-09

Protein chains

P0ABD3  (BFR_ECOLI) -  Bacterioferritin from Escherichia coli (strain K12)

Seq: 158 a.a.

Struc: 158 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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: 10.1074/jbc.M901747200

J Biol Chem 284:18873-18881 (2009)

PubMed id: 19439409

Structural and Mechanistic Studies of a Stabilized Subunit Dimer Variant of Escherichia coli Bacterioferritin Identify Residues Required for Core Formation.

S.G.Wong, S.A.Tom-Yew, A.Lewin, N.E.Le Brun, G.R.Moore, M.E.Murphy, A.G.Mauk.

ABSTRACT

Bacterioferritin (BFR) is a bacterial member of the ferritin family that functions in iron metabolism and protects against oxidative stress. BFR differs from the mammalian protein in that it is comprised of 24 identical subunits and is able to bind 12 equivalents of heme at sites located between adjacent pairs of subunits. The mechanism by which iron enters the protein to form the dinuclear (ferroxidase) catalytic site present in every subunit and the mineralized iron core housed within the 24-mer is not well understood. To address this issue, the properties of a catalytically functional assembly variant (E128R/E135R) of Escherichia coli BFR are characterized by a combination of X-ray crystallography, site directed mutagenesis, and kinetics. The three-dimensional structure of the protein (1.8 A resolution) includes two ethylene glycol molecules located on either side of the dinuclear iron site. One of these ethylene glycol molecules is integrated into the surface of the protein that would normally be exposed to solvent (the outer surface) and the other is integrated into the surface of the protein that would normally face the iron core (the inner surface) where it is surrounded by the negatively charged residues E47, D50, and D126. We propose that the sites occupied by these ethylene glycol molecules define regions where iron interacts with the protein, and, in keeping with this proposal, a significant reduction in ferroxidase activity results on replacing them with the corresponding amides.

Selected figure(s)

Figure 2.
Images of the partially occupied dinuclear iron site.A, 2F[o] − F[c] representative electron density of the dinuclear iron site contoured at 1 σ (blue) and 5 σ (green). B, the metal ion (magenta) and ethylene glycol (yellow) are highlighted. His^130 is directed away from the vacant site where the iron is normally coordinated by His^130.

Figure 3.
Molecular surfaces showing the ferroxidase pore openings at the inner and outer surface.A, side view showing the relative positions of the ethylene glycol molecules and metal ion inside the protein. B, outer surface of BFR subunit dimer showing ethylene glycol molecule colored yellow in outer pore. C, inner surface of wild-type BFR showing previously observed conformations of His^46, Glu^47, and His^130 in the closed state. D, inner surface of BFR subunit dimer showing ethylene glycol molecule in inner pore and alternate conformations of His^46, Glu^47, and His^130 in the open state.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 18873-18881) copyright 2009.

Figures were selected by an automated process.