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PDBsum entry 1mzb
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Gene regulation
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PDB id
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1mzb
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Contents |
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* Residue conservation analysis
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Mol Microbiol
47:903-915
(2003)
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PubMed id:
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Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator.
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E.Pohl,
J.C.Haller,
A.Mijovilovich,
W.Meyer-Klaucke,
E.Garman,
M.L.Vasil.
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ABSTRACT
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Iron is an essential element for almost all organisms, although an overload of
this element results in toxicity because of the formation of hydroxyl radicals.
Consequently, most living entities have developed sophisticated mechanisms to
control their intracellular iron concentration. In many bacteria, including the
opportunistic pathogen Pseudomonas aeruginosa, this task is performed by the
ferric uptake regulator (Fur). Fur controls a wide variety of basic
physiological processes including iron uptake systems and the expression of
exotoxin A. Here, we present the first crystal structure of Fur from P.
aeruginosa in complex with Zn2+ determined at a resolution of 1.8 A.
Furthermore, X-ray absorption spectroscopic measurements and microPIXE analysis
were performed in order to characterize the distinct zinc and iron binding sites
in solution. The combination of these complementary techniques enables us to
present a model for the activation and DNA binding of the Fur protein.
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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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A.S.Fleischhacker,
and
P.J.Kiley
(2011).
Iron-containing transcription factors and their roles as sensors.
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Curr Opin Chem Biol,
15,
335-341.
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C.Dian,
S.Vitale,
G.A.Leonard,
C.Bahlawane,
C.Fauquant,
D.Leduc,
C.Muller,
H.de Reuse,
I.Michaud-Soret,
and
L.Terradot
(2011).
The structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites.
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Mol Microbiol,
79,
1260-1275.
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PDB code:
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H.Ando,
T.Kitao,
T.Miyoshi-Akiyama,
S.Kato,
T.Mori,
and
T.Kirikae
(2011).
Downregulation of katG expression is associated with isoniazid resistance in Mycobacterium tuberculosis.
|
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Mol Microbiol,
79,
1615-1628.
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J.H.Shin,
H.J.Jung,
Y.J.An,
Y.B.Cho,
S.S.Cha,
and
J.H.Roe
(2011).
Graded expression of zinc-responsive genes through two regulatory zinc-binding sites in Zur.
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Proc Natl Acad Sci U S A,
108,
5045-5050.
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PDB code:
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L.F.Ferraz,
L.C.Verde,
R.Vicentini,
A.P.Felício,
M.L.Ribeiro,
F.Alexandrino,
M.T.Novo,
O.Garcia,
D.J.Rigden,
and
L.M.Ottoboni
(2011).
Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR.
|
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Antonie Van Leeuwenhoek,
99,
609-617.
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N.Vajrala,
L.A.Sayavedra-Soto,
P.J.Bottomley,
and
D.J.Arp
(2011).
Role of a Fur homolog in iron metabolism in Nitrosomonas europaea.
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BMC Microbiol,
11,
37.
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D.Osman,
and
J.S.Cavet
(2010).
Bacterial metal-sensing proteins exemplified by ArsR-SmtB family repressors.
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Nat Prod Rep,
27,
668-680.
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H.L.Pedersen,
R.Ahmad,
E.K.Riise,
H.K.Leiros,
S.Hauglid,
S.Espelid,
B.O.Brandsdal,
I.Leiros,
N.P.Willassen,
and
P.Haugen
(2010).
Experimental and computational characterization of the ferric uptake regulator from Aliivibrio salmonicida (Vibrio salmonicida).
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J Microbiol,
48,
174-183.
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R.Uebe,
B.Voigt,
T.Schweder,
D.Albrecht,
E.Katzmann,
C.Lang,
L.Böttger,
B.Matzanke,
and
D.Schüler
(2010).
Deletion of a fur-like gene affects iron homeostasis and magnetosome formation in Magnetospirillum gryphiswaldense.
|
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J Bacteriol,
192,
4192-4204.
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S.Miles,
B.M.Carpenter,
H.Gancz,
and
D.S.Merrell
(2010).
Helicobacter pylori apo-Fur regulation appears unconserved across species.
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J Microbiol,
48,
378-386.
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T.Jittawuttipoka,
R.Sallabhan,
P.Vattanaviboon,
M.Fuangthong,
and
S.Mongkolsuk
(2010).
Mutations of ferric uptake regulator (fur) impair iron homeostasis, growth, oxidative stress survival, and virulence of Xanthomonas campestris pv. campestris.
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Arch Microbiol,
192,
331-339.
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B.J.Gaffney
(2009).
EPR of Mononuclear Non-Heme Iron Proteins.
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Biol Magn Reson,
28,
233-268.
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B.M.Carpenter,
J.M.Whitmire,
and
D.S.Merrell
(2009).
This is not your mother's repressor: the complex role of fur in pathogenesis.
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Infect Immun,
77,
2590-2601.
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D.P.Giedroc
(2009).
Hydrogen peroxide sensing in Bacillus subtilis: it is all about the (metallo)regulator.
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Mol Microbiol,
73,
1-4.
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G.A.Somerville,
and
R.A.Proctor
(2009).
At the crossroads of bacterial metabolism and virulence factor synthesis in Staphylococci.
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Microbiol Mol Biol Rev,
73,
233-248.
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K.Sun,
S.Cheng,
F.Wang,
and
L.Sun
(2009).
Domain analysis of the Edwardsiella tarda ferric uptake regulator.
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J Gen Appl Microbiol,
55,
351-358.
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L.Jacquamet,
D.A.Traoré,
J.L.Ferrer,
O.Proux,
D.Testemale,
J.L.Hazemann,
E.Nazarenko,
A.El Ghazouani,
C.Caux-Thang,
V.Duarte,
and
J.M.Latour
(2009).
Structural characterization of the active form of PerR: insights into the metal-induced activation of PerR and Fur proteins for DNA binding.
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Mol Microbiol,
73,
20-31.
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PDB code:
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M.A.Sheikh,
and
G.L.Taylor
(2009).
Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals insights into metal co-ordination.
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Mol Microbiol,
72,
1208-1220.
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PDB code:
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M.Sandy,
and
A.Butler
(2009).
Microbial iron acquisition: marine and terrestrial siderophores.
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Chem Rev,
109,
4580-4595.
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N.Huang,
J.De Ingeniis,
L.Galeazzi,
C.Mancini,
Y.D.Korostelev,
A.B.Rakhmaninova,
M.S.Gelfand,
D.A.Rodionov,
N.Raffaelli,
and
H.Zhang
(2009).
Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.
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Structure,
17,
939-951.
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PDB codes:
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R.Ahmad,
B.O.Brandsdal,
I.Michaud-Soret,
and
N.P.Willassen
(2009).
Ferric uptake regulator protein: binding free energy calculations and per-residue free energy decomposition.
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Proteins,
75,
373-386.
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S.C.Wang,
A.V.Dias,
and
D.B.Zamble
(2009).
The "metallo-specific" response of proteins: a perspective based on the Escherichia coli transcriptional regulator NikR.
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Dalton Trans,
(),
2459-2466.
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S.Jabour,
and
M.Y.Hamed
(2009).
Binding of the Zn(2+) ion to ferric uptake regulation protein from E. coli and the competition with Fe(2+) binding: a molecular modeling study of the effect on DNA binding and conformational changes of Fur.
|
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J Comput Aided Mol Des,
23,
199-208.
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S.K.Small,
S.Puri,
and
M.R.O'Brian
(2009).
Heme-dependent metalloregulation by the iron response regulator (Irr) protein in Rhizobium and other Alpha-proteobacteria.
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Biometals,
22,
89-97.
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Y.J.An,
B.E.Ahn,
A.R.Han,
H.M.Kim,
K.M.Chung,
J.H.Shin,
Y.B.Cho,
J.H.Roe,
and
S.S.Cha
(2009).
Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition.
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Nucleic Acids Res,
37,
3442-3451.
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PDB code:
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Z.Ma,
F.E.Jacobsen,
and
D.P.Giedroc
(2009).
Coordination chemistry of bacterial metal transport and sensing.
|
| |
Chem Rev,
109,
4644-4681.
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|
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A.Mijovilovich
(2008).
XANES study of the carboxylate binding mode in two pterin hydroxylases.
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Chem Biodivers,
5,
2131-2139.
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D.Lucarelli,
M.L.Vasil,
W.Meyer-Klaucke,
and
E.Pohl
(2008).
The Metal-Dependent Regulators FurA and FurB from Mycobacterium Tuberculosis.
|
| |
Int J Mol Sci,
9,
1548-1560.
|
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H.L.Briggs,
N.Pul,
R.Seshadri,
M.J.Wilson,
C.Tersteeg,
K.E.Russell-Lodrigue,
M.Andoh,
A.J.Bäumler,
and
J.E.Samuel
(2008).
Limited role for iron regulation in Coxiella burnetii pathogenesis.
|
| |
Infect Immun,
76,
2189-2201.
|
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J.D.Awaya,
and
J.L.Dubois
(2008).
Identification, isolation, and analysis of a gene cluster involved in iron acquisition by Pseudomonas mendocina ymp.
|
| |
Biometals,
21,
353-366.
|
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|
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K.Sun,
S.Cheng,
M.Zhang,
F.Wang,
and
L.Sun
(2008).
Cys-92, Cys-95, and the C-terminal 12 residues of the Vibrio harveyi ferric uptake regulator (Fur) are functionally inessential.
|
| |
J Microbiol,
46,
670-680.
|
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L.van Oeffelen,
P.Cornelis,
W.Van Delm,
F.De Ridder,
B.De Moor,
and
Y.Moreau
(2008).
Detecting cis-regulatory binding sites for cooperatively binding proteins.
|
| |
Nucleic Acids Res,
36,
e46.
|
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Y.Feng,
M.Li,
H.Zhang,
B.Zheng,
H.Han,
C.Wang,
J.Yan,
J.Tang,
and
G.F.Gao
(2008).
Functional definition and global regulation of Zur, a zinc uptake regulator in a Streptococcus suis serotype 2 strain causing streptococcal toxic shock syndrome.
|
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J Bacteriol,
190,
7567-7578.
|
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Y.J.An,
B.E.Ahn,
J.H.Roe,
and
S.S.Cha
(2008).
Crystallization and preliminary X-ray crystallographic analyses of Nur, a nickel-responsive transcription regulator from Streptomyces coelicolor.
|
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
64,
130-132.
|
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Z.Liu,
J.T.Guo,
T.Li,
and
Y.Xu
(2008).
Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach.
|
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Proteins,
72,
1114-1124.
|
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D.Koch,
D.H.Nies,
and
G.Grass
(2007).
The RcnRA (YohLM) system of Escherichia coli: a connection between nickel, cobalt and iron homeostasis.
|
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Biometals,
20,
759-771.
|
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D.Lucarelli,
S.Russo,
E.Garman,
A.Milano,
W.Meyer-Klaucke,
and
E.Pohl
(2007).
Crystal structure and function of the zinc uptake regulator FurB from Mycobacterium tuberculosis.
|
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J Biol Chem,
282,
9914-9922.
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PDB code:
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D.P.Giedroc,
and
A.I.Arunkumar
(2007).
Metal sensor proteins: nature's metalloregulated allosteric switches.
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Dalton Trans,
(),
3107-3120.
|
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H.Yijun,
Z.Weijia,
J.Wei,
R.Chengbo,
and
L.Ying
(2007).
Disruption of a fur-like gene inhibits magnetosome formation in Magnetospirillum gryphiswaldense MSR-1.
|
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Biochemistry (Mosc),
72,
1247-1253.
|
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J.H.Shin,
S.Y.Oh,
S.J.Kim,
and
J.H.Roe
(2007).
The zinc-responsive regulator Zur controls a zinc uptake system and some ribosomal proteins in Streptomyces coelicolor A3(2).
|
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J Bacteriol,
189,
4070-4077.
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J.W.Lee,
and
J.D.Helmann
(2007).
Functional specialization within the Fur family of metalloregulators.
|
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Biometals,
20,
485-499.
|
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M.L.Vasil
(2007).
How we learnt about iron acquisition in Pseudomonas aeruginosa: a series of very fortunate events.
|
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Biometals,
20,
587-601.
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M.Miethke,
and
M.A.Marahiel
(2007).
Siderophore-based iron acquisition and pathogen control.
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Microbiol Mol Biol Rev,
71,
413-451.
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T.Kawamura,
L.U.Le,
H.Zhou,
and
F.W.Dahlquist
(2007).
Solution structure of Escherichia coli PapI, a key regulator of the pap pili phase variation.
|
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J Mol Biol,
365,
1130-1142.
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PDB code:
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Z.Chen,
K.A.Lewis,
R.K.Shultzaberger,
I.G.Lyakhov,
M.Zheng,
B.Doan,
G.Storz,
and
T.D.Schneider
(2007).
Discovery of Fur binding site clusters in Escherichia coli by information theory models.
|
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Nucleic Acids Res,
35,
6762-6777.
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B.E.Ahn,
J.Cha,
E.J.Lee,
A.R.Han,
C.J.Thompson,
and
J.H.Roe
(2006).
Nur, a nickel-responsive regulator of the Fur family, regulates superoxide dismutases and nickel transport in Streptomyces coelicolor.
|
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Mol Microbiol,
59,
1848-1858.
|
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D.A.Rodionov,
M.S.Gelfand,
J.D.Todd,
A.R.Curson,
and
A.W.Johnston
(2006).
Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.
|
| |
PLoS Comput Biol,
2,
e163.
|
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D.A.Traoré,
A.El Ghazouani,
S.Ilango,
J.Dupuy,
L.Jacquamet,
J.L.Ferrer,
C.Caux-Thang,
V.Duarte,
and
J.M.Latour
(2006).
Crystal structure of the apo-PerR-Zn protein from Bacillus subtilis.
|
| |
Mol Microbiol,
61,
1211-1219.
|
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PDB code:
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D.Zhou,
L.Qin,
Y.Han,
J.Qiu,
Z.Chen,
B.Li,
Y.Song,
J.Wang,
Z.Guo,
J.Zhai,
Z.Du,
X.Wang,
and
R.Yang
(2006).
Global analysis of iron assimilation and fur regulation in Yersinia pestis.
|
| |
FEMS Microbiol Lett,
258,
9.
|
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G.Rudolph,
H.Hennecke,
and
H.M.Fischer
(2006).
Beyond the Fur paradigm: iron-controlled gene expression in rhizobia.
|
| |
FEMS Microbiol Rev,
30,
631-648.
|
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H.Louvel,
S.Bommezzadri,
N.Zidane,
C.Boursaux-Eude,
S.Creno,
A.Magnier,
Z.Rouy,
C.Médigue,
I.Saint Girons,
C.Bouchier,
and
M.Picardeau
(2006).
Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp.
|
| |
J Bacteriol,
188,
7893-7904.
|
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J.A.Hernández,
S.López-Gomollón,
A.Muro-Pastor,
A.Valladares,
M.T.Bes,
M.L.Peleato,
and
M.F.Fillat
(2006).
Interaction of FurA from Anabaena sp. PCC 7120 with DNA: a reducing environment and the presence of Mn(2+) are positive effectors in the binding to isiB and furA promoters.
|
| |
Biometals,
19,
259-268.
|
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J.I.Kliegman,
S.L.Griner,
J.D.Helmann,
R.G.Brennan,
and
A.Glasfeld
(2006).
Structural basis for the metal-selective activation of the manganese transport regulator of Bacillus subtilis.
|
| |
Biochemistry,
45,
3493-3505.
|
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PDB codes:
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J.W.Lee,
and
J.D.Helmann
(2006).
The PerR transcription factor senses H2O2 by metal-catalysed histidine oxidation.
|
| |
Nature,
440,
363-367.
|
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J.W.Lee,
and
J.D.Helmann
(2006).
Biochemical characterization of the structural Zn2+ site in the Bacillus subtilis peroxide sensor PerR.
|
| |
J Biol Chem,
281,
23567-23578.
|
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K.Agnoli,
C.A.Lowe,
K.L.Farmer,
S.I.Husnain,
and
M.S.Thomas
(2006).
The ornibactin biosynthesis and transport genes of Burkholderia cenocepacia are regulated by an extracytoplasmic function sigma factor which is a part of the Fur regulon.
|
| |
J Bacteriol,
188,
3631-3644.
|
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|
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|
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L.Pecqueur,
B.D'Autréaux,
J.Dupuy,
Y.Nicolet,
L.Jacquamet,
B.Brutscher,
I.Michaud-Soret,
and
B.Bersch
(2006).
Structural changes of Escherichia coli ferric uptake regulator during metal-dependent dimerization and activation explored by NMR and X-ray crystallography.
|
| |
J Biol Chem,
281,
21286-21295.
|
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PDB code:
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|
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C.M.Moore,
and
J.D.Helmann
(2005).
Metal ion homeostasis in Bacillus subtilis.
|
| |
Curr Opin Microbiol,
8,
188-195.
|
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|
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|
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D.Parker,
R.M.Kennan,
G.S.Myers,
I.T.Paulsen,
and
J.I.Rood
(2005).
Identification of a Dichelobacter nodosus ferric uptake regulator and determination of its regulatory targets.
|
| |
J Bacteriol,
187,
366-375.
|
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|
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G.Grass,
M.Otto,
B.Fricke,
C.J.Haney,
C.Rensing,
D.H.Nies,
and
D.Munkelt
(2005).
FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress.
|
| |
Arch Microbiol,
183,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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Where a reference describes a PDB structure, the PDB
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}
}
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