 |
PDBsum entry 2fl0
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Metal binding protein
|
PDB id
|
|
|
|
2fl0
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Metal binding protein
|
|
|
Title:
|
|
Oxidized (all ferric) form of the azotobacter vinelandii bacterioferritin
|
|
Structure:
|
|
Bacterioferritin. Chain: a, b, c, d, e, f, g, h. Synonym: bfr, cytochrome b-557.5
|
|
Source:
|
|
Azotobacter vinelandii. Organism_taxid: 354
|
|
Biol. unit:
|
|
24mer (from PDB file)
|
|
Resolution:
|
|
|
2.70Å
|
R-factor:
|
0.203
|
R-free:
|
0.256
|
|
|
Authors:
|
|
L.Swartz,K.Kunchinskas,H.Li,T.L.Poulos,W.N.Lanzilotta
|
Key ref:
|
|
L.Swartz
et al.
(2006).
Redox-dependent structural changes in the Azotobacter vinelandii bacterioferritin: new insights into the ferroxidase and iron transport mechanism.
Biochemistry,
45,
4421-4428.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
05-Jan-06
|
Release date:
|
04-Apr-06
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
P22759
(BFR_AZOVI) -
Bacterioferritin from Azotobacter vinelandii
|
|
|
|
Seq:
Struc:
|
|
|
|
156 a.a.
155 a.a.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
|
|
|
|
|
|
|
|
|
|
|
Enzyme class:
|
|
E.C.1.16.3.1
- ferroxidase.
|
|
|
|
|
|
|
Reaction:
|
|
4 Fe2+ + O2 + 4 H+ = 4 Fe3+ + 2 H2O
|
|
|
|
|
|
4
×
Fe(2+)
|
+
|
O2
|
+
|
4
×
H(+)
|
=
|
4
×
Fe(3+)
|
+
|
2
×
H2O
|
|
|
|
|
|
|
|
|
|
Cofactor:
|
|
Cu cation
|
|
|
|
|
|
|
|
|
Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
Biochemistry
45:4421-4428
(2006)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Redox-dependent structural changes in the Azotobacter vinelandii bacterioferritin: new insights into the ferroxidase and iron transport mechanism.
|
|
L.Swartz,
M.Kuchinskas,
H.Li,
T.L.Poulos,
W.N.Lanzilotta.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
In this work, we report the X-ray crystal structure of the aerobically isolated
(oxidized) and the anaerobic dithionite-reduced (at pH 8.0) forms of the native
Azotobacter vinelandii bacterioferritin to 2.7 and 2.0 A resolution,
respectively. Iron K-edge multiple anomalous dispersion (MAD) experiments
unequivocally identified the presence of three independent iron-containing sites
within the protein structure. Specifically, a dinuclear (ferroxidase) site, a
b-type heme site, and the binding of a single iron atom at the four-fold
molecular axis of the protein shell were observed. In addition to the novel
observation of iron at the four-fold pore, these data also reveal that the
oxidized form of the protein has a symmetrical ferroxidase site containing two
five-coordinate iron atoms. Each iron atom is ligated by four carboxylate oxygen
atoms and a single histidyl nitrogen atom. A single water molecule is found
within hydrogen bonding distance of the ferroxidase site that bridges the two
iron atoms on the side opposite the histidine ligands. Chemical reduction of the
protein under anaerobic conditions results in an increase in the average Fe-Fe
distance in the ferroxidase site from approximately 3.5 to approximately 4.0 A
and the loss of one of the ligands, H130. In addition, there is significant
movement of the bridging water molecule and several other amino acid side chains
in the vicinity of the ferroxidase site and along the D helix to the three-fold
symmetry axis. In contrast to previous work, the higher-resolution data for the
dithionite-reduced structure suggest that the heme may be bound in multiple
conformations. Taken together, these data allow a molecular movie of the
ferroxidase gating mechanism to be developed and provide further insight into
the iron uptake and/or release and mineralization mechanism of bacterioferritins
in general.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
S.K.Weeratunga,
S.Lovell,
H.Yao,
K.P.Battaile,
C.J.Fischer,
C.E.Gee,
and
M.Rivera
(2010).
Structural studies of bacterioferritin B from Pseudomonas aeruginosa suggest a gating mechanism for iron uptake via the ferroxidase center .
|
| |
Biochemistry,
49,
1160-1175.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.G.Wong,
S.A.Tom-Yew,
A.Lewin,
N.E.Le Brun,
G.R.Moore,
M.E.Murphy,
and
A.G.Mauk
(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.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.K.Weeratunga,
C.E.Gee,
S.Lovell,
Y.Zeng,
C.L.Woodin,
and
M.Rivera
(2009).
Binding of Pseudomonas aeruginosa apobacterioferritin-associated ferredoxin to bacterioferritin B promotes heme mediation of electron delivery and mobilization of core mineral iron.
|
| |
Biochemistry,
48,
7420-7431.
|
|
|
|
|
|
|
V.Gupta,
R.K.Gupta,
G.Khare,
D.M.Salunke,
and
A.K.Tyagi
(2009).
Crystal structure of Bfr A from Mycobacterium tuberculosis: incorporation of selenomethionine results in cleavage and demetallation of haem.
|
| |
PLoS One,
4,
e8028.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
R.Janowski,
T.Auerbach-Nevo,
and
M.S.Weiss
(2008).
Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site.
|
| |
Protein Sci,
17,
1138-1150.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
V.Gupta,
R.K.Gupta,
G.Khare,
D.M.Salunke,
and
A.K.Tyagi
(2008).
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of bacterioferritin A from Mycobacterium tuberculosis.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
398-401.
|
|
|
|
|
|
|
R.Aranda,
C.E.Worley,
M.Liu,
E.Bitto,
M.S.Cates,
J.S.Olson,
B.Lei,
and
G.N.Phillips
(2007).
Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp.
|
| |
J Mol Biol,
374,
374-383.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.van Eerde,
S.Wolterink-van Loo,
J.van der Oost,
and
B.W.Dijkstra
(2006).
Fortuitous structure determination of 'as-isolated' Escherichia coli bacterioferritin in a novel crystal form.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
1061-1066.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.H.Gauss,
P.Benas,
B.Wiedenheft,
M.Young,
T.Douglas,
and
C.M.Lawrence
(2006).
Structure of the DPS-like protein from Sulfolobus solfataricus reveals a bacterioferritin-like dimetal binding site within a DPS-like dodecameric assembly.
|
| |
Biochemistry,
45,
10815-10827.
|
|
|
PDB code:
|
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
|
Links
