4TOF

1.65A resolution structure of BfrB (C89S, K96C) crystal form 1 from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

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

(2015) Biochemistry 54: 1611-1627

  • DOI: 10.1021/bi501255r
  • Primary Citation of Related Structures:  
    4TOG, 4TOH, 4TOA, 4TOB, 4TOC, 4TOD, 4TOE, 4TOF, 4TO9

  • PubMed 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 ...

    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 Fe2+-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 Fe2+ 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.


    Organizational Affiliation

    Department of Chemistry, ‡Del Shankel Structural Biology Center, and §Department of Molecular Biosciences and Center for Bioinformatics, University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BacterioferritinA, B, C, D158Pseudomonas aeruginosa PAO1Mutation(s): 2 
Gene Names: bfrBPA3531
EC: 1.16.3.1
Find proteins for Q9HY79 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HY79 
Go to UniProtKB:  Q9HY79
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A], O [auth C], T [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , K [auth B] , L [auth B] , M [auth B] , P [auth C] , Q [auth C] , 
F [auth A],  G [auth A],  H [auth A],  K [auth B],  L [auth B],  M [auth B],  P [auth C],  Q [auth C],  R [auth C],  U [auth D],  V [auth D],  W [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
J [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], S [auth C], X [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.568α = 90
b = 158.568β = 90
c = 152.381γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1158469

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence, Derived calculations