3GHQ

Crystal Structure of E. coli W35F BFR mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Monitoring the iron status of the ferroxidase center of Escherichia coli bacterioferritin using fluorescence spectroscopy.

Lawson, T.L.Crow, A.Lewin, A.Yasmin, S.Moore, G.R.Le Brun, N.E.

(2009) Biochemistry 48: 9031-9039

  • DOI: https://doi.org/10.1021/bi900869x
  • Primary Citation of Related Structures:  
    3E1Q, 3GHQ

  • PubMed Abstract: 

    Ferritins solubilize and detoxify the essential metal iron through formation of a ferric mineral within the protein's central cavity. Key to this activity is an intrasubunit catalytic dinuclear iron center called the ferroxidase center. Here we show that the fluorescence intensity of Escherichia coli bacterioferritin (BFR), due to the presence of two tryptophan residues (Trp35 and Trp133) in each of the 24 subunits, is highly sensitive to the iron status of the ferroxidase center and is quenched to different extents by Fe2+ and Fe3+. Recovery of the quench following oxidation of Fe2+ to Fe3+ at the ferroxidase center was not observed, indicating that the di-Fe3+ form of the center is stable. Studies of the single-tryptophan variants W35F and W133F showed that Trp133, which lies approximately 10 A from the ferroxidase center, is primarily responsible for the observed fluorescence sensitivity to iron, while studies of a stable E. coli BFR subunit dimer demonstrated that the observed quench properties are principally derived from the interaction of iron with tryptophan residues within the subunit dimer. A double-tryptophan variant (W35F/W133F) was found to exhibit fluorescence from the seven tyrosine residues present in each subunit, which was also sensitive to the iron status of the ferroxidase center. Finally, we demonstrate using Zn2+, a potent competitive inhibitor of Fe2+ binding and oxidation, that the fluorescence response can be used to monitor the loss of iron from the ferroxidase center.


  • Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterioferritin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Escherichia coli K-12Mutation(s): 1 
Gene Names: b3336bfrJW3298
UniProt
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Explore P0ABD3 
Go to UniProtKB:  P0ABD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABD3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
CA [auth F]
JA [auth G]
O [auth A]
QA [auth I]
WA [auth L]
CA [auth F],
JA [auth G],
O [auth A],
QA [auth I],
WA [auth L],
X [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
FA [auth F]
GA [auth F]
HA [auth G]
AA [auth E],
DA [auth F],
FA [auth F],
GA [auth F],
HA [auth G],
KA [auth G],
LA [auth G],
M [auth A],
MA [auth H],
OA [auth I],
P [auth A],
Q [auth A],
R [auth B],
RA [auth J],
T [auth B],
TA [auth K],
U [auth C],
VA [auth K],
W [auth C],
XA [auth L],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
IA [auth G]
N [auth A]
NA [auth H]
BA [auth E],
EA [auth F],
IA [auth G],
N [auth A],
NA [auth H],
PA [auth I],
S [auth B],
SA [auth J],
UA [auth K],
V [auth C],
YA [auth L],
Z [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.641α = 90
b = 207.641β = 90
c = 142.43γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description