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PDBsum entry 1jig
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Metal transport
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PDB id
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1jig
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Metal transport
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Title:
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Dlp-2 from bacillus anthracis
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Structure:
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Dlp-2. Chain: a, b, c, d. Engineered: yes
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Source:
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Bacillus anthracis. Organism_taxid: 1392. Gene: dlp-2. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dodecamer (from PDB file)
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Resolution:
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1.46Å
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R-factor:
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0.186
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R-free:
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0.206
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Authors:
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E.Papinutto,W.G.Dundon,N.Pitulis,R.Battistutta,C.Montecucco,G.Zanotti
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Key ref:
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E.Papinutto
et al.
(2002).
Structure of two iron-binding proteins from Bacillus anthracis.
J Biol Chem,
277,
15093-15098.
PubMed id:
DOI:
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Date:
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02-Jul-01
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Release date:
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19-Jun-02
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PROCHECK
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Headers
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References
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Q8RPQ1
(DPS1_BACAN) -
DNA protection during starvation protein 1 from Bacillus anthracis
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Seq:
Struc:
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147 a.a.
146 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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J Biol Chem
277:15093-15098
(2002)
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PubMed id:
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Structure of two iron-binding proteins from Bacillus anthracis.
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E.Papinutto,
W.G.Dundon,
N.Pitulis,
R.Battistutta,
C.Montecucco,
G.Zanotti.
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ABSTRACT
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Bacillus anthracis is currently under intense investigation due to its primary
importance as a human pathogen. Particularly important is the development of
novel anti-anthrax vaccines, devoid of the current side effects. A novel class
of immunogenic bacterial proteins consists of dodecamers homologous to the
DNA-binding protein of Escherichia coli (Dps). Two Dps homologous genes are
present in the B. anthracis genome. The crystal structures of these two proteins
(Dlp-1 and Dlp-2) have been determined and are presented here. They are
sphere-like proteins with an internal cavity. We also show that they act as
ferritins and are thus involved in iron uptake and regulation, a fundamental
function during bacterial growth.
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Selected figure(s)
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Figure 2.
Fig. 2. A, stereo view of two monomers of Dlp-2 related
by a molecular 2-fold axis. Hydrophobic residues at the
interface of the dimer (Leu-77 and Met-73) are drawn in ball and
sticks. Red spheres represent metal ions. B, stereo view of the
superposition of a C  chain trace
of Dlp-1 (green), Dlp-2 (light blue), Dps (red), and Flp
(violet). Dps is 22 amino acids longer than Dlp-2 at the
N-terminal, while Flp extends 5 amino acids at the C-terminal.
The most significant conformational difference is located in the
region from 85 to 100.
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Figure 3.
Fig. 3. Ribbon view of Dlp-2 dodecameric assembly, as
seen down a 3-fold axis. Monomers are in different colors; red
spheres indicate the cations bound to each monomer.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2002,
277,
15093-15098)
copyright 2002.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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L.N.Calhoun,
and
Y.M.Kwon
(2011).
Structure, function and regulation of the DNA-binding protein Dps and its role in acid and oxidative stress resistance in Escherichia coli: a review.
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J Appl Microbiol,
110,
375-386.
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F.Alaleona,
S.Franceschini,
P.Ceci,
A.Ilari,
and
E.Chiancone
(2010).
Thermosynechococcus elongatus DpsA binds Zn(II) at a unique three histidine-containing ferroxidase center and utilizes O2 as iron oxidant with very high efficiency, unlike the typical Dps proteins.
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FEBS J,
277,
903-917.
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PDB code:
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R.Colangeli,
A.Haq,
V.L.Arcus,
E.Summers,
R.S.Magliozzo,
A.McBride,
A.K.Mitra,
M.Radjainia,
A.Khajo,
W.R.Jacobs,
P.Salgame,
and
D.Alland
(2009).
The multifunctional histone-like protein Lsr2 protects mycobacteria against reactive oxygen intermediates.
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Proc Natl Acad Sci U S A,
106,
4414-4418.
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Z.Ma,
F.E.Jacobsen,
and
D.P.Giedroc
(2009).
Coordination chemistry of bacterial metal transport and sensing.
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Chem Rev,
109,
4644-4681.
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L.Ping,
R.Büchler,
A.Mithöfer,
A.Svatos,
D.Spiteller,
K.Dettner,
S.Gmeiner,
J.Piel,
B.Schlott,
and
W.Boland
(2007).
A novel Dps-type protein from insect gut bacteria catalyses hydrolysis and synthesis of N-acyl amino acids.
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Environ Microbiol,
9,
1572-1583.
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P.Ceci,
L.Mangiarotti,
C.Rivetti,
and
E.Chiancone
(2007).
The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA.
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Nucleic Acids Res,
35,
2247-2256.
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A.Hindupur,
D.Liu,
Y.Zhao,
H.D.Bellamy,
M.A.White,
and
R.O.Fox
(2006).
The crystal structure of the E. coli stress protein YciF.
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Protein Sci,
15,
2605-2611.
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PDB code:
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A.Thumiger,
A.Polenghi,
E.Papinutto,
R.Battistutta,
C.Montecucco,
and
G.Zanotti
(2006).
Crystal structure of antigen TpF1 from Treponema pallidum.
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Proteins,
62,
827-830.
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PDB code:
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A.W.Maresso,
T.J.Chapa,
and
O.Schneewind
(2006).
Surface protein IsdC and Sortase B are required for heme-iron scavenging of Bacillus anthracis.
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J Bacteriol,
188,
8145-8152.
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C.V.Romão,
E.P.Mitchell,
and
S.McSweeney
(2006).
The crystal structure of Deinococcus radiodurans Dps protein (DR2263) reveals the presence of a novel metal centre in the N terminus.
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J Biol Inorg Chem,
11,
891-902.
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PDB codes:
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M.Castruita,
M.Saito,
P.C.Schottel,
L.A.Elmegreen,
S.Myneni,
E.I.Stiefel,
and
F.M.Morel
(2006).
Overexpression and characterization of an iron storage and DNA-binding Dps protein from Trichodesmium erythraeum.
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Appl Environ Microbiol,
72,
2918-2924.
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S.Franceschini,
P.Ceci,
F.Alaleona,
E.Chiancone,
and
A.Ilari
(2006).
Antioxidant Dps protein from the thermophilic cyanobacterium Thermosynechococcus elongatus.
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FEBS J,
273,
4913-4928.
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PDB code:
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S.Reindel,
C.L.Schmidt,
S.Anemüller,
and
B.F.Matzanke
(2006).
Expression and regulation pattern of ferritin-like DpsA in the archaeon Halobacterium salinarum.
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Biometals,
19,
19-29.
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A.Lewin,
G.R.Moore,
and
N.E.Le Brun
(2005).
Formation of protein-coated iron minerals.
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Dalton Trans,
(),
3597-3610.
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A.T.Pulliainen,
A.Kauko,
S.Haataja,
A.C.Papageorgiou,
and
J.Finne
(2005).
Dps/Dpr ferritin-like protein: insights into the mechanism of iron incorporation and evidence for a central role in cellular iron homeostasis in Streptococcus suis.
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Mol Microbiol,
57,
1086-1100.
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S.Reindel,
C.L.Schmidt,
S.Anemüller,
and
B.F.Matzanke
(2005).
Expression and regulation pattern of ferritin-like DpsA in the archaeon Halobacterium Salinarum.
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Biometals,
18,
387-397.
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T.J.Stillman,
M.Upadhyay,
V.A.Norte,
S.E.Sedelnikova,
M.Carradus,
S.Tzokov,
P.A.Bullough,
C.A.Shearman,
M.J.Gasson,
C.H.Williams,
P.J.Artymiuk,
and
J.Green
(2005).
The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an N-terminal helix that is required for DNA binding.
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Mol Microbiol,
57,
1101-1112.
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PDB codes:
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K.Zeth,
S.Offermann,
L.O.Essen,
and
D.Oesterhelt
(2004).
Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.
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Proc Natl Acad Sci U S A,
101,
13780-13785.
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PDB codes:
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P.Ceci,
S.Cellai,
E.Falvo,
C.Rivetti,
G.L.Rossi,
and
E.Chiancone
(2004).
DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus.
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Nucleic Acids Res,
32,
5935-5944.
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M.A.Carrondo
(2003).
Ferritins, iron uptake and storage from the bacterioferritin viewpoint.
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EMBO J,
22,
1959-1968.
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S.Roy,
S.Gupta,
S.Das,
K.Sekar,
D.Chatterji,
and
M.Vijayan
(2003).
Crystallization and preliminary X-ray diffraction analysis of Mycobacterium smegmatis Dps.
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Acta Crystallogr D Biol Crystallogr,
59,
2254-2256.
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T.Ishikawa,
Y.Mizunoe,
S.Kawabata,
A.Takade,
M.Harada,
S.N.Wai,
and
S.Yoshida
(2003).
The iron-binding protein Dps confers hydrogen peroxide stress resistance to Campylobacter jejuni.
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J Bacteriol,
185,
1010-1017.
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S.Haataja,
A.Penttinen,
A.T.Pulliainen,
K.Tikkanen,
J.Finne,
and
A.C.Papageorgiou
(2002).
Expression, purification and crystallization of Dpr, a ferritin-like protein from the Gram-positive meningitis-associated bacterium Streptococcus suis.
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Acta Crystallogr D Biol Crystallogr,
58,
1851-1853.
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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
code is
shown on the right.
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Links
