PDBsum entry 4toc

Oxidoreductase

PDB id: 4toc

Contents

Protein chains

(+ 18 more) 153 a.a.

Ligands

HEM ×12

SO4 ×8

Metals

FE2 ×120

Waters ×2110

PDB id:

4toc

Name:

Oxidoreductase

Title:

2.25a resolution structure of iron bound bfrb (q151l) from pseudomonas aeruginosa

Structure:

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

Source:

Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: atcc 15692 / pao1 / 1c / prs 101 / lmg 12228. Gene: bfrb, pa3531. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.25Å R-factor: 0.156 R-free: 0.192

Authors:

S.Lovell,K.P.Battaile,H.Yao,R.Kumar,K.Eshelman,M.Rivera

Key ref:

H.Yao et al. (2015). Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic. Biochemistry, 54, 1611-1627. PubMed id: 25640193 DOI: 10.1021/bi501255r

Date:

05-Jun-14 Release date: 11-Feb-15

Protein chains

Q9HY79  (Q9HY79_PSEAE) -  Bacterioferritin from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 158 a.a.

Struc: 153 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: 10.1021/bi501255r

Biochemistry 54:1611-1627 (2015)

PubMed id: 25640193

Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.

H.Yao, H.Rui, R.Kumar, K.Eshelman, S.Lovell, K.P.Battaile, W.Im, M.Rivera.

ABSTRACT

X-ray crystallography, molecular dynamics (MD) simulations, and biochemistry were utilized to investigate the effect of introducing hydrophobic interactions in the 4-fold (N148L and Q151L) and B-pores (D34F) of Pseudomonas aeruginosa bacterioferritin B (BfrB) on BfrB function. The structures show only local structural perturbations and confirm the anticipated hydrophobic interactions. Surprisingly, structures obtained after soaking crystals in Fe(2+)-containing crystallization solution revealed that although iron loads into the ferroxidase centers of the mutants, the side chains of ferroxidase ligands E51 and H130 do not reorganize to bind the iron ions, as is seen in the wt BfrB structures. Similar experiments with a double mutant (C89S/K96C) prepared to introduce changes outside the pores show competent ferroxidase centers that function akin to those in wt BfrB. MD simulations comparing wt BfrB with the D34F and N148L mutants show that the mutants exhibit significantly reduced flexibility and reveal a network of concerted motions linking ferroxidase centers and 4-fold and B-pores, which are important for imparting ferroxidase centers in BfrB with the required flexibility to function efficiently. In agreement, the efficiency of Fe(2+) oxidation and uptake of the 4-fold and B-pore mutants in solution is significantly compromised relative to wt or C89S/K96C BfrB. Finally, our structures show a large number of previously unknown iron binding sites in the interior cavity and B-pores of BfrB, which reveal in unprecedented detail conduits followed by iron and phosphate ions across the BfrB shell, as well as paths in the interior cavity that may facilitate nucleation of the iron phosphate mineral.